Starting phenix.real_space_refine on Fri Jan 24 00:49:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xi2_38362/01_2025/8xi2_38362_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xi2_38362/01_2025/8xi2_38362.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xi2_38362/01_2025/8xi2_38362.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xi2_38362/01_2025/8xi2_38362.map" model { file = "/net/cci-nas-00/data/ceres_data/8xi2_38362/01_2025/8xi2_38362_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xi2_38362/01_2025/8xi2_38362_neut.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 3 6.06 5 P 266 5.49 5 Mg 7 5.21 5 S 267 5.16 5 C 44930 2.51 5 N 13405 2.21 5 O 14448 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 666 residue(s): 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 73326 Number of models: 1 Model: "" Number of chains: 38 Chain: "A" Number of atoms: 15194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1931, 15194 Classifications: {'peptide': 1931} Incomplete info: {'truncation_to_alanine': 231} Link IDs: {'PCIS': 1, 'PTRANS': 106, 'TRANS': 1823} Chain breaks: 3 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 852 Unresolved non-hydrogen angles: 1096 Unresolved non-hydrogen dihedrals: 713 Unresolved non-hydrogen chiralities: 85 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 5, 'TYR:plan': 6, 'ASN:plan1': 11, 'TRP:plan': 6, 'ASP:plan': 12, 'PHE:plan': 11, 'GLU:plan': 18, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 439 Chain: "B" Number of atoms: 1817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1817 Classifications: {'RNA': 86} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 16, 'rna3p_pur': 32, 'rna3p_pyr': 32} Link IDs: {'rna2p': 21, 'rna3p': 64} Chain breaks: 2 Chain: "C" Number of atoms: 6973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 897, 6973 Classifications: {'peptide': 897} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 57, 'TRANS': 838} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 2441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2441 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 12, 'TRANS': 305} Chain: "F" Number of atoms: 1985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1985 Unusual residues: {'G5J': 1} Classifications: {'RNA': 91, 'undetermined': 1} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 11, 'rna3p_pur': 40, 'rna3p_pyr': 25} Link IDs: {'rna2p': 25, 'rna3p': 65, None: 1} Not linked: pdbres="G5J F 1 " pdbres=" U F 2 " Chain: "q" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 831 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain breaks: 1 Chain: "r" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1021 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 123} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "s" Number of atoms: 570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 570 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 68} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "t" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 504 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 2, 'TRANS': 59} Chain: "a" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 705 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain: "g" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 512 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain: "e" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 660 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "f" Number of atoms: 559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 559 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 68} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "d" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 810 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "c" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 684 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 3, 'TRANS': 84} Chain: "b" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 780 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 8, 'TRANS': 90} Chain breaks: 1 Chain: "I" Number of atoms: 4629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 4629 Classifications: {'peptide': 661} Incomplete info: {'truncation_to_alanine': 211} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 634} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 871 Unresolved non-hydrogen angles: 1122 Unresolved non-hydrogen dihedrals: 743 Unresolved non-hydrogen chiralities: 71 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 8, 'TYR:plan': 14, 'ASN:plan1': 4, 'TRP:plan': 6, 'ASP:plan': 15, 'PHE:plan': 8, 'GLU:plan': 19, 'ARG:plan': 26} Unresolved non-hydrogen planarities: 523 Chain: "J" Number of atoms: 4033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4033 Classifications: {'peptide': 595} Incomplete info: {'truncation_to_alanine': 251} Link IDs: {'PTRANS': 17, 'TRANS': 577} Chain breaks: 3 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1064 Unresolved non-hydrogen angles: 1364 Unresolved non-hydrogen dihedrals: 916 Unresolved non-hydrogen chiralities: 73 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 14, 'ASN:plan1': 4, 'TRP:plan': 10, 'ASP:plan': 18, 'PHE:plan': 13, 'GLU:plan': 31, 'ARG:plan': 36} Unresolved non-hydrogen planarities: 670 Chain: "P" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 867 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain breaks: 2 Chain: "M" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 644 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain breaks: 2 Chain: "T" Number of atoms: 2700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2700 Classifications: {'peptide': 344} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 327} Chain: "O" Number of atoms: 2136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2136 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 17, 'TRANS': 255} Chain breaks: 1 Chain: "N" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1412 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain breaks: 1 Chain: "R" Number of atoms: 1994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1994 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 27, 'TRANS': 232} Chain breaks: 1 Chain: "H" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 838 Classifications: {'RNA': 40} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 15, 'rna3p_pur': 9, 'rna3p_pyr': 10} Link IDs: {'rna2p': 21, 'rna3p': 18} Chain: "S" Number of atoms: 1198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1198 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "W" Number of atoms: 2826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 2826 Classifications: {'peptide': 487} Incomplete info: {'truncation_to_alanine': 293} Link IDs: {'PTRANS': 25, 'TRANS': 461} Chain breaks: 5 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 1119 Unresolved non-hydrogen angles: 1436 Unresolved non-hydrogen dihedrals: 993 Unresolved non-hydrogen chiralities: 72 Planarities with less than four sites: {'GLN:plan1': 12, 'ARG:plan': 14, 'TYR:plan': 14, 'ASN:plan1': 13, 'TRP:plan': 11, 'ASP:plan': 26, 'PHE:plan': 18, 'GLU:plan': 11, 'HIS:plan': 11} Unresolved non-hydrogen planarities: 639 Chain: "L" Number of atoms: 3795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3795 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 18, 'TRANS': 449} Chain breaks: 6 Chain: "K" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1688 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 196} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 4 Chain: "U" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 191 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 1, 'TRANS': 24} Chain: "V" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1020 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 141} Link IDs: {'PTRANS': 5, 'TRANS': 180} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 531 Unresolved non-hydrogen angles: 677 Unresolved non-hydrogen dihedrals: 451 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 4, 'PHE:plan': 14, 'GLU:plan': 12, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 315 Chain: "Q" Number of atoms: 6423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1299, 6423 Classifications: {'peptide': 1299} Incomplete info: {'truncation_to_alanine': 1095} Link IDs: {'PCIS': 1, 'PTRANS': 69, 'TRANS': 1228} Chain breaks: 11 Unresolved chain link angles: 70 Unresolved non-hydrogen bonds: 4212 Unresolved non-hydrogen angles: 5398 Unresolved non-hydrogen dihedrals: 3526 Unresolved non-hydrogen chiralities: 357 Planarities with less than four sites: {'GLN:plan1': 59, 'HIS:plan': 30, 'TYR:plan': 46, 'ASN:plan1': 34, 'TRP:plan': 14, 'ASP:plan': 65, 'PHE:plan': 67, 'GLU:plan': 99, 'ARG:plan': 100} Unresolved non-hydrogen planarities: 2429 Chain: "5" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 150 Classifications: {'RNA': 7} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 3, 'rna3p_pyr': 1} Link IDs: {'rna2p': 3, 'rna3p': 3} Chain: "3" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 694 Classifications: {'RNA': 34} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 4, 'rna3p_pur': 13, 'rna3p_pyr': 15} Link IDs: {'rna2p': 6, 'rna3p': 27} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {' G%rna3p_pur:plan2': 1, ' G%rna3p_pur:plan': 1, ' A%rna3p_pur:plan2': 1, ' A%rna3p_pur:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' MG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "O" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 50000 SG CYS O 166 156.103 109.645 154.187 1.00 19.38 S ATOM 50061 SG CYS O 174 157.215 109.943 157.473 1.00 23.17 S ATOM 50103 SG CYS O 180 154.503 107.466 156.459 1.00 20.66 S ATOM 48985 SG CYS O 26 145.518 96.279 139.390 1.00 18.95 S ATOM 49419 SG CYS O 80 141.895 96.504 136.656 1.00 20.92 S ATOM 49441 SG CYS O 83 145.152 97.151 136.064 1.00 18.84 S ATOM 51915 SG CYS N 102 142.457 99.506 172.036 1.00 3.84 S ATOM 52049 SG CYS N 120 143.131 97.488 168.661 1.00 6.72 S ATOM 52215 SG CYS N 141 145.939 98.600 171.135 1.00 3.49 S ATOM 52235 SG CYS N 144 143.344 96.240 172.081 1.00 6.42 S Time building chain proxies: 30.40, per 1000 atoms: 0.41 Number of scatterers: 73326 At special positions: 0 Unit cell: (257.6, 211.6, 253.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 3 29.99 S 267 16.00 P 266 15.00 Mg 7 11.99 O 14448 8.00 N 13405 7.00 C 44930 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 156 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.97 Conformation dependent library (CDL) restraints added in 7.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN N 301 " pdb="ZN ZN N 301 " - pdb=" SG CYS N 144 " pdb="ZN ZN N 301 " - pdb=" SG CYS N 141 " pdb="ZN ZN N 301 " - pdb=" SG CYS N 120 " pdb="ZN ZN N 301 " - pdb=" SG CYS N 102 " pdb=" ZN O 500 " pdb="ZN ZN O 500 " - pdb=" SG CYS O 166 " pdb="ZN ZN O 500 " - pdb=" SG CYS O 174 " pdb="ZN ZN O 500 " - pdb=" SG CYS O 180 " pdb="ZN ZN O 500 " - pdb=" NE2 HIS O 184 " pdb=" ZN O 501 " pdb="ZN ZN O 501 " - pdb=" SG CYS O 80 " pdb="ZN ZN O 501 " - pdb=" SG CYS O 83 " pdb="ZN ZN O 501 " - pdb=" SG CYS O 26 " Number of angles added : 9 18574 Ramachandran restraints generated. 9287 Oldfield, 0 Emsley, 9287 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17786 Finding SS restraints... Secondary structure from input PDB file: 347 helices and 64 sheets defined 50.0% alpha, 12.9% beta 47 base pairs and 128 stacking pairs defined. Time for finding SS restraints: 20.82 Creating SS restraints... Processing helix chain 'A' and resid 88 through 104 Processing helix chain 'A' and resid 121 through 132 removed outlier: 4.259A pdb=" N VAL A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 142 No H-bonds generated for 'chain 'A' and resid 140 through 142' Processing helix chain 'A' and resid 143 through 150 Processing helix chain 'A' and resid 153 through 163 Processing helix chain 'A' and resid 195 through 217 Processing helix chain 'A' and resid 236 through 241 Processing helix chain 'A' and resid 289 through 305 removed outlier: 4.106A pdb=" N GLN A 302 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N LEU A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 327 removed outlier: 3.651A pdb=" N PHE A 321 " --> pdb=" O GLU A 317 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 327 " --> pdb=" O THR A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 374 Processing helix chain 'A' and resid 459 through 470 removed outlier: 4.034A pdb=" N ALA A 463 " --> pdb=" O THR A 459 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER A 464 " --> pdb=" O ASP A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 477 removed outlier: 3.523A pdb=" N ASN A 476 " --> pdb=" O PRO A 472 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ARG A 477 " --> pdb=" O PRO A 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 472 through 477' Processing helix chain 'A' and resid 492 through 497 Processing helix chain 'A' and resid 504 through 524 Processing helix chain 'A' and resid 535 through 542 Processing helix chain 'A' and resid 553 through 573 Processing helix chain 'A' and resid 595 through 602 Processing helix chain 'A' and resid 605 through 630 Processing helix chain 'A' and resid 634 through 648 Processing helix chain 'A' and resid 648 through 653 Processing helix chain 'A' and resid 654 through 658 Processing helix chain 'A' and resid 659 through 661 No H-bonds generated for 'chain 'A' and resid 659 through 661' Processing helix chain 'A' and resid 662 through 681 Processing helix chain 'A' and resid 694 through 725 Proline residue: A 710 - end of helix Processing helix chain 'A' and resid 737 through 739 No H-bonds generated for 'chain 'A' and resid 737 through 739' Processing helix chain 'A' and resid 740 through 761 Processing helix chain 'A' and resid 769 through 786 Processing helix chain 'A' and resid 796 through 828 Processing helix chain 'A' and resid 832 through 862 removed outlier: 3.722A pdb=" N CYS A 836 " --> pdb=" O ASP A 832 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG A 837 " --> pdb=" O LYS A 833 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 859 " --> pdb=" O GLN A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.946A pdb=" N ALA A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 913 removed outlier: 3.982A pdb=" N GLN A 913 " --> pdb=" O ARG A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 937 Processing helix chain 'A' and resid 937 through 952 Processing helix chain 'A' and resid 976 through 998 removed outlier: 3.875A pdb=" N THR A 982 " --> pdb=" O LEU A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 1011 through 1025 Processing helix chain 'A' and resid 1053 through 1065 removed outlier: 3.756A pdb=" N LEU A1063 " --> pdb=" O ARG A1059 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE A1064 " --> pdb=" O LEU A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1078 removed outlier: 3.645A pdb=" N ASN A1077 " --> pdb=" O ILE A1073 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN A1078 " --> pdb=" O THR A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1127 removed outlier: 6.944A pdb=" N LEU A1119 " --> pdb=" O LEU A1115 " (cutoff:3.500A) removed outlier: 8.867A pdb=" N THR A1120 " --> pdb=" O LEU A1116 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG A1121 " --> pdb=" O LEU A1117 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR A1123 " --> pdb=" O LEU A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'A' and resid 1166 through 1181 Processing helix chain 'A' and resid 1207 through 1223 Processing helix chain 'A' and resid 1233 through 1235 No H-bonds generated for 'chain 'A' and resid 1233 through 1235' Processing helix chain 'A' and resid 1297 through 1313 Processing helix chain 'A' and resid 1319 through 1339 Processing helix chain 'A' and resid 1340 through 1342 No H-bonds generated for 'chain 'A' and resid 1340 through 1342' Processing helix chain 'A' and resid 1345 through 1366 Processing helix chain 'A' and resid 1376 through 1382 removed outlier: 4.086A pdb=" N PHE A1380 " --> pdb=" O PRO A1376 " (cutoff:3.500A) Processing helix chain 'A' and resid 1383 through 1387 Processing helix chain 'A' and resid 1403 through 1411 removed outlier: 4.515A pdb=" N GLN A1408 " --> pdb=" O LEU A1404 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N GLN A1409 " --> pdb=" O ARG A1405 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR A1410 " --> pdb=" O TYR A1406 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASP A1411 " --> pdb=" O SER A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1432 through 1436 Processing helix chain 'A' and resid 1438 through 1464 removed outlier: 5.735A pdb=" N ALA A1462 " --> pdb=" O GLU A1458 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN A1463 " --> pdb=" O GLU A1459 " (cutoff:3.500A) Processing helix chain 'A' and resid 1499 through 1507 Processing helix chain 'A' and resid 1508 through 1510 No H-bonds generated for 'chain 'A' and resid 1508 through 1510' Processing helix chain 'A' and resid 1521 through 1526 Processing helix chain 'A' and resid 1531 through 1542 Processing helix chain 'A' and resid 1543 through 1550 Processing helix chain 'A' and resid 1583 through 1586 Processing helix chain 'A' and resid 1587 through 1592 Processing helix chain 'A' and resid 1592 through 1607 Proline residue: A1604 - end of helix Processing helix chain 'A' and resid 1630 through 1639 Processing helix chain 'A' and resid 1644 through 1664 Processing helix chain 'A' and resid 1739 through 1752 Processing helix chain 'A' and resid 1786 through 1801 removed outlier: 3.539A pdb=" N GLN A1792 " --> pdb=" O PRO A1788 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LYS A1799 " --> pdb=" O ALA A1795 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER A1800 " --> pdb=" O LYS A1796 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN A1801 " --> pdb=" O ILE A1797 " (cutoff:3.500A) Processing helix chain 'A' and resid 1801 through 1816 Processing helix chain 'A' and resid 1828 through 1832 Processing helix chain 'A' and resid 1833 through 1837 removed outlier: 3.644A pdb=" N SER A1837 " --> pdb=" O GLU A1834 " (cutoff:3.500A) Processing helix chain 'A' and resid 1887 through 1892 Processing helix chain 'A' and resid 1896 through 1916 Processing helix chain 'A' and resid 1929 through 1931 No H-bonds generated for 'chain 'A' and resid 1929 through 1931' Processing helix chain 'A' and resid 1932 through 1940 removed outlier: 3.715A pdb=" N LEU A1936 " --> pdb=" O MET A1932 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU A1937 " --> pdb=" O LEU A1933 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A1938 " --> pdb=" O ASP A1934 " (cutoff:3.500A) Processing helix chain 'A' and resid 1956 through 1961 removed outlier: 3.587A pdb=" N ILE A1961 " --> pdb=" O PHE A1957 " (cutoff:3.500A) Processing helix chain 'A' and resid 1963 through 1973 removed outlier: 4.070A pdb=" N ILE A1970 " --> pdb=" O PHE A1966 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU A1971 " --> pdb=" O GLY A1967 " (cutoff:3.500A) Processing helix chain 'A' and resid 1986 through 1990 removed outlier: 4.134A pdb=" N LYS A1989 " --> pdb=" O ASP A1986 " (cutoff:3.500A) Processing helix chain 'A' and resid 1992 through 2009 removed outlier: 4.059A pdb=" N LEU A2002 " --> pdb=" O SER A1998 " (cutoff:3.500A) Processing helix chain 'A' and resid 2013 through 2018 removed outlier: 3.622A pdb=" N ILE A2017 " --> pdb=" O LYS A2013 " (cutoff:3.500A) Processing helix chain 'A' and resid 2036 through 2057 removed outlier: 3.533A pdb=" N ILE A2051 " --> pdb=" O LEU A2047 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP A2054 " --> pdb=" O LEU A2050 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS A2057 " --> pdb=" O ALA A2053 " (cutoff:3.500A) Processing helix chain 'A' and resid 2067 through 2077 removed outlier: 4.497A pdb=" N ILE A2074 " --> pdb=" O GLU A2070 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY A2077 " --> pdb=" O ASP A2073 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 82 Processing helix chain 'C' and resid 124 through 132 removed outlier: 3.565A pdb=" N ALA C 132 " --> pdb=" O ALA C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 135 No H-bonds generated for 'chain 'C' and resid 133 through 135' Processing helix chain 'C' and resid 149 through 162 Processing helix chain 'C' and resid 164 through 175 Processing helix chain 'C' and resid 184 through 189 removed outlier: 3.672A pdb=" N ALA C 189 " --> pdb=" O LEU C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 223 No H-bonds generated for 'chain 'C' and resid 221 through 223' Processing helix chain 'C' and resid 224 through 235 removed outlier: 3.649A pdb=" N VAL C 228 " --> pdb=" O PHE C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 262 removed outlier: 3.513A pdb=" N GLU C 253 " --> pdb=" O MET C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 278 removed outlier: 3.758A pdb=" N ILE C 277 " --> pdb=" O VAL C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 307 removed outlier: 4.227A pdb=" N CYS C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 321 Processing helix chain 'C' and resid 335 through 347 Processing helix chain 'C' and resid 352 through 361 removed outlier: 3.636A pdb=" N ARG C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TRP C 361 " --> pdb=" O ALA C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 390 Processing helix chain 'C' and resid 390 through 400 Processing helix chain 'C' and resid 405 through 416 removed outlier: 3.858A pdb=" N LEU C 416 " --> pdb=" O LEU C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 442 Processing helix chain 'C' and resid 444 through 455 removed outlier: 4.342A pdb=" N VAL C 448 " --> pdb=" O CYS C 444 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ALA C 453 " --> pdb=" O ASP C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 470 removed outlier: 3.502A pdb=" N SER C 462 " --> pdb=" O SER C 458 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ALA C 463 " --> pdb=" O ARG C 459 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASP C 464 " --> pdb=" O LYS C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 484 removed outlier: 3.750A pdb=" N SER C 480 " --> pdb=" O ALA C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 576 removed outlier: 3.640A pdb=" N THR C 575 " --> pdb=" O VAL C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 615 No H-bonds generated for 'chain 'C' and resid 613 through 615' Processing helix chain 'C' and resid 616 through 631 Processing helix chain 'C' and resid 650 through 664 Processing helix chain 'C' and resid 712 through 719 Processing helix chain 'C' and resid 727 through 739 Processing helix chain 'C' and resid 742 through 748 removed outlier: 3.689A pdb=" N GLY C 748 " --> pdb=" O LEU C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 772 through 793 removed outlier: 4.820A pdb=" N ASP C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N SER C 782 " --> pdb=" O ALA C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 820 Processing helix chain 'C' and resid 821 through 839 removed outlier: 3.821A pdb=" N ILE C 825 " --> pdb=" O GLY C 821 " (cutoff:3.500A) Proline residue: C 827 - end of helix Processing helix chain 'C' and resid 859 through 870 Processing helix chain 'C' and resid 895 through 898 Processing helix chain 'C' and resid 899 through 907 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 959 Processing helix chain 'q' and resid 25 through 36 Processing helix chain 'q' and resid 68 through 116 removed outlier: 3.535A pdb=" N LEU q 101 " --> pdb=" O THR q 97 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASP q 109 " --> pdb=" O LEU q 105 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N ALA q 110 " --> pdb=" O TYR q 106 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA q 111 " --> pdb=" O GLN q 107 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N THR q 112 " --> pdb=" O HIS q 108 " (cutoff:3.500A) Processing helix chain 'r' and resid 24 through 36 Processing helix chain 'r' and resid 64 through 67 removed outlier: 3.588A pdb=" N THR r 67 " --> pdb=" O ALA r 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 64 through 67' Processing helix chain 'r' and resid 68 through 130 removed outlier: 4.266A pdb=" N ASN r 89 " --> pdb=" O LEU r 85 " (cutoff:3.500A) Processing helix chain 's' and resid 68 through 136 removed outlier: 4.271A pdb=" N TYR s 106 " --> pdb=" O SER s 102 " (cutoff:3.500A) Processing helix chain 't' and resid 67 through 124 Processing helix chain 'a' and resid 9 through 18 removed outlier: 3.928A pdb=" N LYS a 13 " --> pdb=" O GLY a 9 " (cutoff:3.500A) Processing helix chain 'a' and resid 79 through 84 Processing helix chain 'a' and resid 85 through 92 Processing helix chain 'g' and resid 7 through 13 removed outlier: 3.519A pdb=" N MET g 13 " --> pdb=" O LYS g 10 " (cutoff:3.500A) Processing helix chain 'e' and resid 11 through 23 Processing helix chain 'f' and resid 8 through 16 Processing helix chain 'd' and resid 12 through 22 Processing helix chain 'd' and resid 25 through 35 Processing helix chain 'c' and resid 2 through 9 removed outlier: 3.847A pdb=" N ARG c 6 " --> pdb=" O VAL c 2 " (cutoff:3.500A) Processing helix chain 'c' and resid 76 through 82 removed outlier: 3.544A pdb=" N LEU c 80 " --> pdb=" O ASN c 76 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL c 82 " --> pdb=" O ASP c 78 " (cutoff:3.500A) Processing helix chain 'b' and resid 7 through 13 removed outlier: 3.539A pdb=" N LEU b 10 " --> pdb=" O SER b 7 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE b 13 " --> pdb=" O LEU b 10 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 83 Processing helix chain 'I' and resid 90 through 107 removed outlier: 4.105A pdb=" N GLU I 94 " --> pdb=" O ASP I 90 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER I 106 " --> pdb=" O ARG I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 110 through 125 Processing helix chain 'I' and resid 126 through 141 removed outlier: 3.736A pdb=" N GLY I 139 " --> pdb=" O ASP I 135 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 145 Processing helix chain 'I' and resid 146 through 158 removed outlier: 4.281A pdb=" N LEU I 152 " --> pdb=" O ARG I 148 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS I 155 " --> pdb=" O ALA I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 163 through 175 Processing helix chain 'I' and resid 178 through 180 No H-bonds generated for 'chain 'I' and resid 178 through 180' Processing helix chain 'I' and resid 181 through 191 removed outlier: 3.504A pdb=" N TYR I 185 " --> pdb=" O HIS I 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 194 through 206 removed outlier: 3.999A pdb=" N ARG I 200 " --> pdb=" O GLY I 196 " (cutoff:3.500A) Processing helix chain 'I' and resid 218 through 232 Processing helix chain 'I' and resid 241 through 251 Processing helix chain 'I' and resid 256 through 270 Processing helix chain 'I' and resid 273 through 286 Processing helix chain 'I' and resid 290 through 308 Processing helix chain 'I' and resid 342 through 372 Proline residue: I 361 - end of helix Processing helix chain 'I' and resid 375 through 386 removed outlier: 3.625A pdb=" N PHE I 386 " --> pdb=" O ARG I 382 " (cutoff:3.500A) Processing helix chain 'I' and resid 389 through 404 Processing helix chain 'I' and resid 412 through 427 removed outlier: 4.096A pdb=" N LEU I 416 " --> pdb=" O LYS I 412 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TRP I 417 " --> pdb=" O PRO I 413 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N HIS I 427 " --> pdb=" O PHE I 423 " (cutoff:3.500A) Processing helix chain 'I' and resid 429 through 443 Processing helix chain 'I' and resid 447 through 465 removed outlier: 3.940A pdb=" N LEU I 451 " --> pdb=" O TYR I 447 " (cutoff:3.500A) Processing helix chain 'I' and resid 467 through 479 Processing helix chain 'I' and resid 489 through 494 Processing helix chain 'I' and resid 497 through 502 Processing helix chain 'I' and resid 505 through 520 Processing helix chain 'I' and resid 521 through 536 Processing helix chain 'I' and resid 539 through 553 Processing helix chain 'I' and resid 555 through 570 removed outlier: 3.803A pdb=" N ALA I 568 " --> pdb=" O GLU I 564 " (cutoff:3.500A) Processing helix chain 'I' and resid 574 through 591 removed outlier: 4.597A pdb=" N ILE I 578 " --> pdb=" O HIS I 574 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG I 589 " --> pdb=" O ALA I 585 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY I 591 " --> pdb=" O VAL I 587 " (cutoff:3.500A) Processing helix chain 'I' and resid 594 through 609 Processing helix chain 'I' and resid 613 through 628 removed outlier: 4.123A pdb=" N LEU I 617 " --> pdb=" O GLU I 613 " (cutoff:3.500A) Processing helix chain 'I' and resid 630 through 645 Processing helix chain 'I' and resid 646 through 665 removed outlier: 3.835A pdb=" N LYS I 651 " --> pdb=" O LYS I 647 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N SER I 652 " --> pdb=" O ALA I 648 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU I 656 " --> pdb=" O SER I 652 " (cutoff:3.500A) Processing helix chain 'I' and resid 666 through 677 Processing helix chain 'I' and resid 687 through 706 removed outlier: 3.533A pdb=" N LYS I 704 " --> pdb=" O ALA I 700 " (cutoff:3.500A) Processing helix chain 'I' and resid 707 through 722 removed outlier: 3.656A pdb=" N ALA I 711 " --> pdb=" O GLU I 707 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA I 720 " --> pdb=" O VAL I 716 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL I 721 " --> pdb=" O HIS I 717 " (cutoff:3.500A) Processing helix chain 'I' and resid 727 through 742 removed outlier: 3.805A pdb=" N TRP I 731 " --> pdb=" O ALA I 727 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG I 740 " --> pdb=" O ALA I 736 " (cutoff:3.500A) Processing helix chain 'I' and resid 743 through 761 removed outlier: 3.812A pdb=" N ARG I 755 " --> pdb=" O MET I 751 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 36 removed outlier: 4.064A pdb=" N LEU J 29 " --> pdb=" O THR J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 74 Processing helix chain 'J' and resid 79 through 91 removed outlier: 3.530A pdb=" N LYS J 83 " --> pdb=" O GLY J 79 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 108 Processing helix chain 'J' and resid 111 through 124 Processing helix chain 'J' and resid 127 through 142 Processing helix chain 'J' and resid 145 through 159 removed outlier: 3.788A pdb=" N TRP J 149 " --> pdb=" O ILE J 145 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 175 Processing helix chain 'J' and resid 178 through 192 removed outlier: 3.587A pdb=" N TYR J 192 " --> pdb=" O PHE J 188 " (cutoff:3.500A) Processing helix chain 'J' and resid 194 through 209 Processing helix chain 'J' and resid 211 through 226 Processing helix chain 'J' and resid 228 through 242 Processing helix chain 'J' and resid 248 through 262 removed outlier: 3.616A pdb=" N PHE J 252 " --> pdb=" O THR J 248 " (cutoff:3.500A) Processing helix chain 'J' and resid 264 through 279 Processing helix chain 'J' and resid 283 through 299 removed outlier: 4.322A pdb=" N LEU J 287 " --> pdb=" O SER J 283 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLN J 297 " --> pdb=" O ALA J 293 " (cutoff:3.500A) Processing helix chain 'J' and resid 300 through 321 removed outlier: 3.623A pdb=" N ALA J 321 " --> pdb=" O GLU J 317 " (cutoff:3.500A) Processing helix chain 'J' and resid 327 through 340 Processing helix chain 'J' and resid 342 through 355 Processing helix chain 'J' and resid 363 through 384 Processing helix chain 'J' and resid 387 through 402 Processing helix chain 'J' and resid 409 through 423 removed outlier: 3.779A pdb=" N TRP J 413 " --> pdb=" O PHE J 409 " (cutoff:3.500A) Processing helix chain 'J' and resid 425 through 440 Processing helix chain 'J' and resid 442 through 457 Processing helix chain 'J' and resid 458 through 472 Processing helix chain 'J' and resid 477 through 490 Processing helix chain 'J' and resid 492 through 506 removed outlier: 3.501A pdb=" N GLN J 506 " --> pdb=" O LEU J 502 " (cutoff:3.500A) Processing helix chain 'J' and resid 512 through 526 removed outlier: 3.652A pdb=" N TRP J 516 " --> pdb=" O PRO J 512 " (cutoff:3.500A) Processing helix chain 'J' and resid 528 through 543 Processing helix chain 'J' and resid 545 through 558 Processing helix chain 'J' and resid 582 through 604 Processing helix chain 'J' and resid 607 through 625 removed outlier: 3.883A pdb=" N ALA J 611 " --> pdb=" O SER J 607 " (cutoff:3.500A) Processing helix chain 'J' and resid 629 through 643 removed outlier: 3.710A pdb=" N LYS J 643 " --> pdb=" O GLU J 639 " (cutoff:3.500A) Processing helix chain 'P' and resid 50 through 55 Processing helix chain 'P' and resid 58 through 73 Processing helix chain 'P' and resid 223 through 234 Processing helix chain 'M' and resid 443 through 461 removed outlier: 3.530A pdb=" N TYR M 461 " --> pdb=" O VAL M 457 " (cutoff:3.500A) Processing helix chain 'M' and resid 462 through 473 Processing helix chain 'M' and resid 493 through 510 removed outlier: 4.374A pdb=" N GLU M 497 " --> pdb=" O ALA M 493 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS M 509 " --> pdb=" O GLU M 505 " (cutoff:3.500A) Processing helix chain 'M' and resid 530 through 543 removed outlier: 3.551A pdb=" N HIS M 534 " --> pdb=" O ASP M 530 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG M 541 " --> pdb=" O LYS M 537 " (cutoff:3.500A) Processing helix chain 'T' and resid 176 through 188 Processing helix chain 'O' and resid 70 through 77 removed outlier: 4.250A pdb=" N LYS O 77 " --> pdb=" O VAL O 73 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 101 Processing helix chain 'O' and resid 110 through 124 removed outlier: 3.801A pdb=" N ASP O 123 " --> pdb=" O GLN O 119 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA O 124 " --> pdb=" O MET O 120 " (cutoff:3.500A) Processing helix chain 'O' and resid 145 through 151 Processing helix chain 'O' and resid 157 through 161 Processing helix chain 'O' and resid 166 through 171 removed outlier: 3.674A pdb=" N LYS O 171 " --> pdb=" O SER O 167 " (cutoff:3.500A) Processing helix chain 'O' and resid 176 through 180 Processing helix chain 'O' and resid 197 through 204 Processing helix chain 'O' and resid 207 through 221 Processing helix chain 'O' and resid 244 through 253 Processing helix chain 'O' and resid 276 through 288 Processing helix chain 'N' and resid 4 through 8 removed outlier: 3.783A pdb=" N LYS N 8 " --> pdb=" O ARG N 5 " (cutoff:3.500A) Processing helix chain 'N' and resid 15 through 36 removed outlier: 3.520A pdb=" N ILE N 19 " --> pdb=" O GLY N 15 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N GLU N 21 " --> pdb=" O GLU N 17 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N VAL N 22 " --> pdb=" O LEU N 18 " (cutoff:3.500A) Processing helix chain 'N' and resid 47 through 67 Processing helix chain 'N' and resid 72 through 82 Processing helix chain 'N' and resid 86 through 95 removed outlier: 3.688A pdb=" N LYS N 95 " --> pdb=" O ALA N 91 " (cutoff:3.500A) Processing helix chain 'N' and resid 103 through 108 removed outlier: 3.546A pdb=" N ILE N 107 " --> pdb=" O MET N 104 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN N 108 " --> pdb=" O LEU N 105 " (cutoff:3.500A) Processing helix chain 'N' and resid 118 through 122 Processing helix chain 'N' and resid 123 through 127 removed outlier: 3.515A pdb=" N ARG N 127 " --> pdb=" O LEU N 124 " (cutoff:3.500A) Processing helix chain 'N' and resid 128 through 133 removed outlier: 3.700A pdb=" N ARG N 132 " --> pdb=" O LYS N 129 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE N 133 " --> pdb=" O GLN N 130 " (cutoff:3.500A) Processing helix chain 'N' and resid 168 through 172 Processing helix chain 'R' and resid 48 through 53 removed outlier: 3.623A pdb=" N GLY R 53 " --> pdb=" O GLU R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 70 Processing helix chain 'R' and resid 93 through 97 Processing helix chain 'R' and resid 99 through 104 Processing helix chain 'R' and resid 110 through 114 removed outlier: 3.531A pdb=" N ALA R 113 " --> pdb=" O ASP R 110 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 155 Processing helix chain 'R' and resid 232 through 237 Processing helix chain 'R' and resid 256 through 263 removed outlier: 3.562A pdb=" N LEU R 261 " --> pdb=" O LEU R 257 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA R 263 " --> pdb=" O LYS R 259 " (cutoff:3.500A) Processing helix chain 'R' and resid 275 through 302 removed outlier: 3.738A pdb=" N ALA R 279 " --> pdb=" O ASP R 275 " (cutoff:3.500A) Processing helix chain 'S' and resid 24 through 37 Processing helix chain 'S' and resid 111 through 115 Processing helix chain 'S' and resid 127 through 136 removed outlier: 3.561A pdb=" N ASN S 136 " --> pdb=" O LYS S 132 " (cutoff:3.500A) Processing helix chain 'W' and resid 78 through 83 Processing helix chain 'W' and resid 116 through 129 removed outlier: 4.061A pdb=" N PHE W 120 " --> pdb=" O HIS W 116 " (cutoff:3.500A) Processing helix chain 'W' and resid 168 through 184 Processing helix chain 'W' and resid 212 through 230 Processing helix chain 'L' and resid 11 through 26 removed outlier: 3.682A pdb=" N ASP L 15 " --> pdb=" O LYS L 11 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 37 removed outlier: 3.668A pdb=" N SER L 35 " --> pdb=" O ALA L 31 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU L 36 " --> pdb=" O ARG L 32 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU L 37 " --> pdb=" O ILE L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 52 Processing helix chain 'L' and resid 64 through 77 Processing helix chain 'L' and resid 80 through 89 Proline residue: L 86 - end of helix Processing helix chain 'L' and resid 91 through 108 removed outlier: 3.635A pdb=" N VAL L 107 " --> pdb=" O LEU L 103 " (cutoff:3.500A) Processing helix chain 'L' and resid 144 through 160 removed outlier: 4.354A pdb=" N LEU L 151 " --> pdb=" O GLU L 147 " (cutoff:3.500A) Processing helix chain 'L' and resid 164 through 188 removed outlier: 3.801A pdb=" N ARG L 168 " --> pdb=" O LYS L 164 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA L 170 " --> pdb=" O ALA L 166 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG L 171 " --> pdb=" O LYS L 167 " (cutoff:3.500A) Processing helix chain 'L' and resid 226 through 239 Processing helix chain 'L' and resid 244 through 250 Processing helix chain 'L' and resid 542 through 559 Processing helix chain 'L' and resid 592 through 617 removed outlier: 3.633A pdb=" N LEU L 596 " --> pdb=" O SER L 592 " (cutoff:3.500A) Processing helix chain 'L' and resid 648 through 670 removed outlier: 3.940A pdb=" N LEU L 652 " --> pdb=" O GLU L 648 " (cutoff:3.500A) Processing helix chain 'L' and resid 676 through 691 removed outlier: 3.728A pdb=" N ASP L 690 " --> pdb=" O SER L 686 " (cutoff:3.500A) Processing helix chain 'L' and resid 715 through 833 removed outlier: 4.902A pdb=" N GLY L 746 " --> pdb=" O LEU L 742 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LEU L 747 " --> pdb=" O LEU L 743 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN L 764 " --> pdb=" O GLU L 760 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ASP L 767 " --> pdb=" O ALA L 763 " (cutoff:3.500A) Proline residue: L 787 - end of helix removed outlier: 4.631A pdb=" N LEU L 796 " --> pdb=" O ALA L 792 " (cutoff:3.500A) Processing helix chain 'K' and resid 42 through 57 removed outlier: 3.832A pdb=" N HIS K 46 " --> pdb=" O GLU K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 68 Processing helix chain 'K' and resid 80 through 91 Processing helix chain 'K' and resid 100 through 105 Processing helix chain 'K' and resid 110 through 115 removed outlier: 4.665A pdb=" N GLY K 115 " --> pdb=" O GLN K 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 116 through 148 removed outlier: 3.728A pdb=" N TRP K 120 " --> pdb=" O ASP K 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 148 through 227 removed outlier: 3.532A pdb=" N SER K 193 " --> pdb=" O HIS K 189 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU K 194 " --> pdb=" O ALA K 190 " (cutoff:3.500A) Processing helix chain 'K' and resid 228 through 235 Processing helix chain 'V' and resid 651 through 665 Processing helix chain 'V' and resid 668 through 679 Processing helix chain 'V' and resid 685 through 700 removed outlier: 3.994A pdb=" N LEU V 689 " --> pdb=" O GLN V 685 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET V 692 " --> pdb=" O GLU V 688 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N CYS V 697 " --> pdb=" O ILE V 693 " (cutoff:3.500A) Processing helix chain 'V' and resid 705 through 716 removed outlier: 4.221A pdb=" N TYR V 716 " --> pdb=" O GLN V 712 " (cutoff:3.500A) Processing helix chain 'V' and resid 718 through 736 removed outlier: 3.724A pdb=" N ALA V 722 " --> pdb=" O ASN V 718 " (cutoff:3.500A) Processing helix chain 'V' and resid 737 through 739 No H-bonds generated for 'chain 'V' and resid 737 through 739' Processing helix chain 'V' and resid 740 through 756 Processing helix chain 'V' and resid 762 through 768 removed outlier: 3.625A pdb=" N ILE V 768 " --> pdb=" O LEU V 765 " (cutoff:3.500A) Processing helix chain 'V' and resid 776 through 794 Processing helix chain 'V' and resid 795 through 803 Processing helix chain 'V' and resid 805 through 813 Proline residue: V 810 - end of helix Processing helix chain 'V' and resid 820 through 833 Processing helix chain 'Q' and resid 119 through 130 Processing helix chain 'Q' and resid 131 through 136 Processing helix chain 'Q' and resid 144 through 153 removed outlier: 4.288A pdb=" N VAL Q 148 " --> pdb=" O LYS Q 144 " (cutoff:3.500A) Processing helix chain 'Q' and resid 165 through 174 Processing helix chain 'Q' and resid 176 through 181 removed outlier: 3.503A pdb=" N TYR Q 181 " --> pdb=" O TYR Q 177 " (cutoff:3.500A) Processing helix chain 'Q' and resid 187 through 191 Processing helix chain 'Q' and resid 192 through 210 removed outlier: 3.566A pdb=" N VAL Q 196 " --> pdb=" O THR Q 192 " (cutoff:3.500A) Processing helix chain 'Q' and resid 214 through 220 removed outlier: 3.626A pdb=" N ARG Q 220 " --> pdb=" O CYS Q 216 " (cutoff:3.500A) Processing helix chain 'Q' and resid 223 through 236 removed outlier: 3.608A pdb=" N PHE Q 227 " --> pdb=" O ALA Q 223 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER Q 233 " --> pdb=" O LYS Q 229 " (cutoff:3.500A) Processing helix chain 'Q' and resid 243 through 259 Processing helix chain 'Q' and resid 263 through 275 removed outlier: 3.668A pdb=" N GLN Q 269 " --> pdb=" O MET Q 265 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ARG Q 272 " --> pdb=" O ALA Q 268 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU Q 273 " --> pdb=" O GLN Q 269 " (cutoff:3.500A) Processing helix chain 'Q' and resid 276 through 282 Processing helix chain 'Q' and resid 283 through 294 Processing helix chain 'Q' and resid 294 through 310 removed outlier: 4.156A pdb=" N ALA Q 298 " --> pdb=" O HIS Q 294 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS Q 299 " --> pdb=" O GLU Q 295 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N HIS Q 300 " --> pdb=" O ALA Q 296 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS Q 310 " --> pdb=" O LYS Q 306 " (cutoff:3.500A) Processing helix chain 'Q' and resid 338 through 353 Processing helix chain 'Q' and resid 368 through 388 removed outlier: 3.766A pdb=" N LEU Q 372 " --> pdb=" O ASN Q 368 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN Q 388 " --> pdb=" O ASP Q 384 " (cutoff:3.500A) Processing helix chain 'Q' and resid 388 through 402 removed outlier: 4.887A pdb=" N PHE Q 394 " --> pdb=" O PRO Q 390 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL Q 395 " --> pdb=" O THR Q 391 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N THR Q 397 " --> pdb=" O ARG Q 393 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU Q 398 " --> pdb=" O PHE Q 394 " (cutoff:3.500A) Processing helix chain 'Q' and resid 403 through 410 Processing helix chain 'Q' and resid 411 through 416 removed outlier: 3.636A pdb=" N LYS Q 415 " --> pdb=" O SER Q 411 " (cutoff:3.500A) Processing helix chain 'Q' and resid 643 through 656 removed outlier: 3.725A pdb=" N SER Q 656 " --> pdb=" O SER Q 652 " (cutoff:3.500A) Processing helix chain 'Q' and resid 668 through 691 Processing helix chain 'Q' and resid 694 through 703 Processing helix chain 'Q' and resid 705 through 709 removed outlier: 3.693A pdb=" N GLU Q 709 " --> pdb=" O GLY Q 706 " (cutoff:3.500A) Processing helix chain 'Q' and resid 710 through 716 Processing helix chain 'Q' and resid 722 through 732 Processing helix chain 'Q' and resid 741 through 745 removed outlier: 4.124A pdb=" N ALA Q 745 " --> pdb=" O PRO Q 742 " (cutoff:3.500A) Processing helix chain 'Q' and resid 746 through 758 Processing helix chain 'Q' and resid 763 through 770 Processing helix chain 'Q' and resid 776 through 781 removed outlier: 3.506A pdb=" N LEU Q 780 " --> pdb=" O THR Q 776 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TRP Q 781 " --> pdb=" O GLU Q 777 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 776 through 781' Processing helix chain 'Q' and resid 810 through 841 removed outlier: 3.709A pdb=" N TYR Q 814 " --> pdb=" O THR Q 810 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TYR Q 828 " --> pdb=" O LEU Q 824 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU Q 829 " --> pdb=" O GLU Q 825 " (cutoff:3.500A) Processing helix chain 'Q' and resid 898 through 904 Processing helix chain 'Q' and resid 938 through 942 Processing helix chain 'Q' and resid 989 through 1004 Processing helix chain 'Q' and resid 1024 through 1038 Processing helix chain 'Q' and resid 1044 through 1052 removed outlier: 3.975A pdb=" N ASP Q1049 " --> pdb=" O PRO Q1045 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N VAL Q1050 " --> pdb=" O TRP Q1046 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1102 through 1110 removed outlier: 3.525A pdb=" N VAL Q1107 " --> pdb=" O ALA Q1103 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE Q1110 " --> pdb=" O VAL Q1106 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1190 through 1194 Processing helix chain 'Q' and resid 1203 through 1215 Processing helix chain 'Q' and resid 1228 through 1244 Processing helix chain 'Q' and resid 1255 through 1267 removed outlier: 3.787A pdb=" N LEU Q1259 " --> pdb=" O SER Q1255 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1293 through 1319 Processing helix chain 'Q' and resid 1323 through 1330 removed outlier: 3.624A pdb=" N VAL Q1327 " --> pdb=" O GLU Q1323 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR Q1330 " --> pdb=" O SER Q1326 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1330 through 1342 removed outlier: 3.780A pdb=" N GLY Q1335 " --> pdb=" O CYS Q1331 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1342 through 1360 removed outlier: 3.524A pdb=" N LYS Q1348 " --> pdb=" O ALA Q1344 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG Q1355 " --> pdb=" O ALA Q1351 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1364 through 1370 Processing helix chain 'Q' and resid 1374 through 1378 removed outlier: 3.980A pdb=" N ASP Q1378 " --> pdb=" O TYR Q1375 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1388 through 1419 removed outlier: 4.610A pdb=" N ALA Q1415 " --> pdb=" O GLU Q1411 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N PHE Q1416 " --> pdb=" O GLU Q1412 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU Q1417 " --> pdb=" O CYS Q1413 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1421 through 1432 Processing helix chain 'Q' and resid 1441 through 1454 removed outlier: 5.114A pdb=" N ARG Q1449 " --> pdb=" O ALA Q1445 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N GLU Q1450 " --> pdb=" O LEU Q1446 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1470 through 1476 Processing helix chain 'Q' and resid 1477 through 1479 No H-bonds generated for 'chain 'Q' and resid 1477 through 1479' Processing helix chain 'Q' and resid 1508 through 1516 removed outlier: 4.280A pdb=" N GLN Q1512 " --> pdb=" O ASN Q1508 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS Q1513 " --> pdb=" O GLN Q1509 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1520 through 1529 Processing helix chain 'Q' and resid 1542 through 1547 Processing helix chain 'Q' and resid 1548 through 1553 removed outlier: 5.567A pdb=" N TRP Q1551 " --> pdb=" O LEU Q1548 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1559 through 1565 Processing helix chain 'Q' and resid 1565 through 1570 removed outlier: 3.635A pdb=" N ARG Q1569 " --> pdb=" O LEU Q1565 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1602 through 1619 Processing helix chain 'Q' and resid 1622 through 1624 No H-bonds generated for 'chain 'Q' and resid 1622 through 1624' Processing helix chain 'Q' and resid 1632 through 1647 removed outlier: 3.610A pdb=" N LYS Q1636 " --> pdb=" O TYR Q1632 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N CYS Q1647 " --> pdb=" O ILE Q1643 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1663 through 1666 Processing helix chain 'Q' and resid 1683 through 1687 removed outlier: 4.300A pdb=" N LEU Q1686 " --> pdb=" O VAL Q1683 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1688 through 1697 Processing helix chain 'Q' and resid 1708 through 1714 Processing helix chain 'Q' and resid 1715 through 1726 removed outlier: 4.242A pdb=" N ASN Q1720 " --> pdb=" O TYR Q1716 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N THR Q1721 " --> pdb=" O GLU Q1717 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU Q1724 " --> pdb=" O ASN Q1720 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1759 through 1777 removed outlier: 3.694A pdb=" N ALA Q1777 " --> pdb=" O GLU Q1773 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 188 Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 194 Processing sheet with id=AA3, first strand: chain 'A' and resid 286 through 287 Processing sheet with id=AA4, first strand: chain 'A' and resid 580 through 582 Processing sheet with id=AA5, first strand: chain 'A' and resid 969 through 974 Processing sheet with id=AA6, first strand: chain 'A' and resid 1149 through 1155 removed outlier: 6.504A pdb=" N MET A1162 " --> pdb=" O ARG A1150 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N TYR A1152 " --> pdb=" O HIS A1160 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N HIS A1160 " --> pdb=" O TYR A1152 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ARG A1154 " --> pdb=" O LYS A1158 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LYS A1158 " --> pdb=" O ARG A1154 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1249 through 1252 removed outlier: 3.507A pdb=" N ALA A1290 " --> pdb=" O LEU A1280 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1399 through 1400 Processing sheet with id=AA9, first strand: chain 'A' and resid 1565 through 1567 removed outlier: 3.613A pdb=" N TYR A1818 " --> pdb=" O PHE A1566 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1617 through 1618 Processing sheet with id=AB2, first strand: chain 'A' and resid 1706 through 1708 removed outlier: 5.855A pdb=" N ASP A1727 " --> pdb=" O ILE A1767 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ILE A1769 " --> pdb=" O ASP A1727 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLN A1729 " --> pdb=" O ILE A1769 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1841 through 1842 removed outlier: 6.112A pdb=" N TRP A1842 " --> pdb=" O ILE A1926 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR A1949 " --> pdb=" O ILE A1925 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1880 through 1885 Processing sheet with id=AB5, first strand: chain 'C' and resid 86 through 89 removed outlier: 6.313A pdb=" N GLU C 86 " --> pdb=" O VAL T 202 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N SER T 204 " --> pdb=" O GLU C 86 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU C 88 " --> pdb=" O SER T 204 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N MET T 199 " --> pdb=" O LYS T 494 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LYS T 494 " --> pdb=" O MET T 199 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 197 through 204 removed outlier: 6.689A pdb=" N ARG C 138 " --> pdb=" O ASN C 214 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LEU C 216 " --> pdb=" O ARG C 138 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N VAL C 140 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N GLY C 237 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ASN C 139 " --> pdb=" O GLY C 237 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N MET C 239 " --> pdb=" O ASN C 139 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ALA C 141 " --> pdb=" O MET C 239 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL C 241 " --> pdb=" O ALA C 141 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL C 143 " --> pdb=" O VAL C 241 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N ASP C 243 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 9.252A pdb=" N THR C 324 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU C 268 " --> pdb=" O THR C 324 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N SER C 326 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ILE C 270 " --> pdb=" O SER C 326 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 365 through 367 removed outlier: 3.699A pdb=" N VAL C 372 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 539 through 543 removed outlier: 7.050A pdb=" N VAL C 493 " --> pdb=" O MET C 514 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N MET C 514 " --> pdb=" O VAL C 493 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N VAL C 495 " --> pdb=" O ARG C 512 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ARG C 512 " --> pdb=" O VAL C 495 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 548 through 550 Processing sheet with id=AC1, first strand: chain 'C' and resid 636 through 638 removed outlier: 3.857A pdb=" N HIS C 644 " --> pdb=" O ALA C 609 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 636 through 638 removed outlier: 3.857A pdb=" N HIS C 644 " --> pdb=" O ALA C 609 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 680 through 683 removed outlier: 7.525A pdb=" N ILE C 885 " --> pdb=" O PRO C 879 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ILE C 887 " --> pdb=" O ASP C 877 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ASP C 877 " --> pdb=" O ILE C 887 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LYS C 889 " --> pdb=" O THR C 875 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 680 through 683 removed outlier: 6.690A pdb=" N LEU C 844 " --> pdb=" O VAL C 923 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL C 923 " --> pdb=" O LEU C 844 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLU C 846 " --> pdb=" O TRP C 921 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N TRP C 921 " --> pdb=" O GLU C 846 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL C 848 " --> pdb=" O ASP C 919 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 691 through 694 removed outlier: 3.999A pdb=" N ASP C 810 " --> pdb=" O THR C 703 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ILE C 705 " --> pdb=" O ILE C 808 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE C 808 " --> pdb=" O ILE C 705 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N GLU C 707 " --> pdb=" O PHE C 806 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N PHE C 806 " --> pdb=" O GLU C 707 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL C 761 " --> pdb=" O PHE C 806 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ILE C 808 " --> pdb=" O VAL C 761 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LEU C 763 " --> pdb=" O ILE C 808 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N ASP C 810 " --> pdb=" O LEU C 763 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA C 751 " --> pdb=" O LEU C 762 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 334 through 339 removed outlier: 3.559A pdb=" N GLU E 336 " --> pdb=" O ALA E 349 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR E 354 " --> pdb=" O SER E 350 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG b 107 " --> pdb=" O GLN E 60 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 68 through 73 removed outlier: 3.569A pdb=" N SER E 70 " --> pdb=" O GLY E 83 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR E 88 " --> pdb=" O SER E 84 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN E 102 " --> pdb=" O LEU E 91 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ARG E 93 " --> pdb=" O ASN E 100 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ASN E 100 " --> pdb=" O ARG E 93 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 113 through 116 removed outlier: 6.638A pdb=" N ALA E 132 " --> pdb=" O LYS E 145 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LYS E 145 " --> pdb=" O ALA E 132 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N CYS E 134 " --> pdb=" O ILE E 143 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA E 141 " --> pdb=" O ASP E 136 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 155 through 158 Processing sheet with id=AD1, first strand: chain 'E' and resid 195 through 200 Processing sheet with id=AD2, first strand: chain 'E' and resid 242 through 247 removed outlier: 6.491A pdb=" N ASN E 257 " --> pdb=" O THR E 243 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU E 245 " --> pdb=" O LEU E 255 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU E 255 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N VAL E 247 " --> pdb=" O HIS E 253 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N HIS E 253 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU E 263 " --> pdb=" O VAL E 280 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL E 280 " --> pdb=" O LEU E 263 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N GLU E 265 " --> pdb=" O THR E 278 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 295 through 297 removed outlier: 5.896A pdb=" N VAL E 313 " --> pdb=" O LYS E 326 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS E 326 " --> pdb=" O VAL E 313 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE E 315 " --> pdb=" O LEU E 324 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'q' and resid 22 through 24 Processing sheet with id=AD5, first strand: chain 'r' and resid 22 through 23 Processing sheet with id=AD6, first strand: chain 'a' and resid 22 through 27 removed outlier: 6.515A pdb=" N MET a 32 " --> pdb=" O ALA a 53 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA a 53 " --> pdb=" O MET a 32 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ARG a 34 " --> pdb=" O VAL a 51 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL a 51 " --> pdb=" O ARG a 34 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLN a 47 " --> pdb=" O CYS a 38 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ALA a 64 " --> pdb=" O ASP a 50 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N THR a 52 " --> pdb=" O GLN a 62 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N GLN a 62 " --> pdb=" O THR a 52 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N THR a 54 " --> pdb=" O VAL a 60 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL a 60 " --> pdb=" O THR a 54 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N HIS a 65 " --> pdb=" O ALA g 69 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA g 69 " --> pdb=" O HIS a 65 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU g 17 " --> pdb=" O GLY g 29 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG g 25 " --> pdb=" O LEU g 21 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N HIS g 26 " --> pdb=" O ASP g 47 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ASP g 47 " --> pdb=" O HIS g 26 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N SER g 28 " --> pdb=" O THR g 45 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR g 45 " --> pdb=" O SER g 28 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL g 41 " --> pdb=" O ARG g 32 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL g 41 " --> pdb=" O VAL g 58 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL g 58 " --> pdb=" O VAL g 41 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ASP g 43 " --> pdb=" O MET g 56 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N MET g 56 " --> pdb=" O ASP g 43 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N THR g 45 " --> pdb=" O ILE g 54 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N MET g 56 " --> pdb=" O THR e 84 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N THR e 84 " --> pdb=" O MET g 56 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N TRP e 29 " --> pdb=" O THR e 80 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ILE e 82 " --> pdb=" O GLN e 27 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N GLN e 27 " --> pdb=" O ILE e 82 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N THR e 84 " --> pdb=" O LYS e 25 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N LYS e 25 " --> pdb=" O THR e 84 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU e 30 " --> pdb=" O LEU e 36 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N LEU e 36 " --> pdb=" O LEU e 30 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N ASP e 35 " --> pdb=" O SER e 60 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N SER e 60 " --> pdb=" O ASP e 35 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ARG e 37 " --> pdb=" O GLU e 58 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLU e 58 " --> pdb=" O ARG e 37 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLU e 39 " --> pdb=" O ALA e 56 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA e 56 " --> pdb=" O GLU e 39 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL e 52 " --> pdb=" O ILE e 43 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL e 52 " --> pdb=" O LEU e 73 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU e 73 " --> pdb=" O VAL e 52 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASP e 54 " --> pdb=" O ARG e 71 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ARG e 71 " --> pdb=" O ASP e 54 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ALA e 56 " --> pdb=" O LEU e 69 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ARG e 71 " --> pdb=" O GLY f 76 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY f 76 " --> pdb=" O ARG e 71 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLU f 30 " --> pdb=" O GLU f 51 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLU f 51 " --> pdb=" O GLU f 30 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LYS f 32 " --> pdb=" O THR f 49 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N THR f 49 " --> pdb=" O LYS f 32 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLN f 45 " --> pdb=" O VAL f 36 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N GLN f 45 " --> pdb=" O ILE f 66 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE f 66 " --> pdb=" O GLN f 45 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N ALA f 47 " --> pdb=" O VAL f 64 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL f 64 " --> pdb=" O ALA f 47 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY f 62 " --> pdb=" O THR f 49 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLU f 51 " --> pdb=" O GLN f 60 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N GLN f 60 " --> pdb=" O GLU f 51 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N ILE f 53 " --> pdb=" O THR f 58 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N THR f 58 " --> pdb=" O ILE f 53 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLU f 63 " --> pdb=" O ARG d 107 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ARG d 107 " --> pdb=" O GLU f 63 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU f 65 " --> pdb=" O VAL d 105 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL d 105 " --> pdb=" O LEU f 65 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ASN d 41 " --> pdb=" O ILE d 103 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N VAL d 105 " --> pdb=" O LEU d 39 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU d 39 " --> pdb=" O VAL d 105 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ARG d 107 " --> pdb=" O GLN d 37 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N GLN d 37 " --> pdb=" O ARG d 107 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LYS d 47 " --> pdb=" O GLU d 68 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU d 68 " --> pdb=" O LYS d 47 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU d 49 " --> pdb=" O VAL d 66 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL d 66 " --> pdb=" O LEU d 49 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE d 62 " --> pdb=" O LYS d 53 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N SER d 93 " --> pdb=" O ASN d 65 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LYS d 67 " --> pdb=" O PHE d 91 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N PHE d 91 " --> pdb=" O LYS d 67 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N MET d 69 " --> pdb=" O ASP d 89 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP d 89 " --> pdb=" O MET d 69 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N THR d 71 " --> pdb=" O ASN d 87 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ASN d 87 " --> pdb=" O THR d 71 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU c 14 " --> pdb=" O ILE c 30 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL c 25 " --> pdb=" O LEU c 46 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N LEU c 46 " --> pdb=" O VAL c 25 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLN c 27 " --> pdb=" O VAL c 44 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL c 44 " --> pdb=" O GLN c 27 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N HIS c 40 " --> pdb=" O ALA c 31 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N HIS c 40 " --> pdb=" O SER c 60 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N SER c 60 " --> pdb=" O HIS c 40 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LYS c 42 " --> pdb=" O HIS c 58 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N HIS c 58 " --> pdb=" O LYS c 42 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N HIS c 58 " --> pdb=" O ILE b 83 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ILE b 83 " --> pdb=" O HIS c 58 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER b 80 " --> pdb=" O THR b 20 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLN b 26 " --> pdb=" O GLU b 47 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLU b 47 " --> pdb=" O GLN b 26 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL b 28 " --> pdb=" O SER b 45 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N SER b 45 " --> pdb=" O VAL b 28 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL b 41 " --> pdb=" O MET b 32 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASP b 44 " --> pdb=" O GLY b 69 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N GLY b 69 " --> pdb=" O ASP b 44 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLU b 46 " --> pdb=" O VAL b 67 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL b 67 " --> pdb=" O GLU b 46 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N PHE b 48 " --> pdb=" O ARG b 65 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ARG b 65 " --> pdb=" O PHE b 48 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'b' and resid 111 through 112 Processing sheet with id=AD8, first strand: chain 'T' and resid 210 through 215 removed outlier: 4.231A pdb=" N THR T 230 " --> pdb=" O SER T 226 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ASP T 235 " --> pdb=" O LEU T 241 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU T 241 " --> pdb=" O ASP T 235 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'T' and resid 252 through 257 removed outlier: 3.579A pdb=" N GLY T 254 " --> pdb=" O CYS T 267 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL T 273 " --> pdb=" O SER T 286 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N SER T 286 " --> pdb=" O VAL T 273 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N CYS T 275 " --> pdb=" O ILE T 284 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'T' and resid 294 through 299 removed outlier: 6.334A pdb=" N ASP T 319 " --> pdb=" O GLN T 325 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLN T 325 " --> pdb=" O ASP T 319 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'T' and resid 336 through 341 removed outlier: 4.126A pdb=" N VAL T 348 " --> pdb=" O TRP T 360 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE T 357 " --> pdb=" O VAL T 370 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL T 370 " --> pdb=" O ILE T 357 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU T 359 " --> pdb=" O SER T 368 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'T' and resid 380 through 383 removed outlier: 3.789A pdb=" N ALA T 380 " --> pdb=" O ALA T 393 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE T 398 " --> pdb=" O ASN T 411 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ASN T 411 " --> pdb=" O ILE T 398 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LYS T 400 " --> pdb=" O LEU T 409 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'T' and resid 420 through 425 removed outlier: 4.064A pdb=" N SER T 439 " --> pdb=" O GLY T 435 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ASP T 444 " --> pdb=" O CYS T 450 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N CYS T 450 " --> pdb=" O ASP T 444 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'O' and resid 65 through 66 removed outlier: 5.845A pdb=" N TYR O 51 " --> pdb=" O PHE O 40 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL O 33 " --> pdb=" O LYS R 192 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N GLN R 194 " --> pdb=" O VAL O 33 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N MET O 35 " --> pdb=" O GLN R 194 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'O' and resid 258 through 264 removed outlier: 6.396A pdb=" N THR O 273 " --> pdb=" O ALA O 259 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL O 261 " --> pdb=" O PHE O 271 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N PHE O 271 " --> pdb=" O VAL O 261 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LYS O 263 " --> pdb=" O CYS O 269 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N CYS O 269 " --> pdb=" O LYS O 263 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'O' and resid 292 through 293 removed outlier: 3.598A pdb=" N ILE O 293 " --> pdb=" O ALA O 296 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 141 through 143 removed outlier: 6.397A pdb=" N VAL N 155 " --> pdb=" O ILE N 142 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'R' and resid 84 through 85 Processing sheet with id=AF1, first strand: chain 'S' and resid 47 through 49 removed outlier: 3.772A pdb=" N ARG S 47 " --> pdb=" O GLN S 55 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU S 90 " --> pdb=" O PHE S 121 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N VAL S 124 " --> pdb=" O GLU S 18 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLU S 18 " --> pdb=" O VAL S 124 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'W' and resid 133 through 134 Processing sheet with id=AF3, first strand: chain 'W' and resid 239 through 242 removed outlier: 6.212A pdb=" N CYS W 319 " --> pdb=" O ASP W 312 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASP W 312 " --> pdb=" O CYS W 319 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ARG W 321 " --> pdb=" O ILE W 310 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE W 310 " --> pdb=" O ARG W 321 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LYS W 307 " --> pdb=" O GLY W 303 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N LEU W 298 " --> pdb=" O PHE W 291 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N PHE W 291 " --> pdb=" O LEU W 298 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU W 300 " --> pdb=" O VAL W 289 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL W 289 " --> pdb=" O LEU W 300 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ALA W 302 " --> pdb=" O ASN W 287 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'W' and resid 274 through 278 removed outlier: 5.552A pdb=" N TRP W 275 " --> pdb=" O ASP W 576 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N ASP W 576 " --> pdb=" O TRP W 275 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS W 277 " --> pdb=" O TYR W 574 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'W' and resid 334 through 335 removed outlier: 3.736A pdb=" N CYS W 334 " --> pdb=" O LEU W 343 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU W 343 " --> pdb=" O CYS W 334 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ASP W 355 " --> pdb=" O CYS W 361 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N CYS W 361 " --> pdb=" O ASP W 355 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'W' and resid 371 through 376 removed outlier: 3.703A pdb=" N CYS W 373 " --> pdb=" O GLY W 389 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ASP W 399 " --> pdb=" O SER W 405 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N SER W 405 " --> pdb=" O ASP W 399 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'W' and resid 416 through 422 removed outlier: 3.550A pdb=" N SER W 418 " --> pdb=" O THR W 431 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'W' and resid 462 through 464 Processing sheet with id=AF9, first strand: chain 'W' and resid 462 through 464 Processing sheet with id=AG1, first strand: chain 'W' and resid 511 through 512 removed outlier: 6.879A pdb=" N GLU W 532 " --> pdb=" O ILE W 539 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N ILE W 539 " --> pdb=" O GLU W 532 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 692 through 694 Processing sheet with id=AG3, first strand: chain 'Q' and resid 843 through 845 Processing sheet with id=AG4, first strand: chain 'Q' and resid 863 through 871 removed outlier: 7.388A pdb=" N LEU Q 863 " --> pdb=" O ASP Q 891 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ASP Q 891 " --> pdb=" O LEU Q 863 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR Q 885 " --> pdb=" O THR Q 869 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL Q 884 " --> pdb=" O LEU Q 988 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N THR Q 983 " --> pdb=" O LEU Q 954 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N LEU Q 954 " --> pdb=" O THR Q 983 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N THR Q 985 " --> pdb=" O ILE Q 952 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU Q 954 " --> pdb=" O MET Q 962 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Q' and resid 863 through 871 removed outlier: 7.388A pdb=" N LEU Q 863 " --> pdb=" O ASP Q 891 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ASP Q 891 " --> pdb=" O LEU Q 863 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR Q 885 " --> pdb=" O THR Q 869 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL Q 884 " --> pdb=" O LEU Q 988 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N THR Q 983 " --> pdb=" O LEU Q 954 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N LEU Q 954 " --> pdb=" O THR Q 983 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N THR Q 985 " --> pdb=" O ILE Q 952 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP Q 910 " --> pdb=" O VAL Q 951 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Q' and resid 1093 through 1097 removed outlier: 5.617A pdb=" N PHE Q1130 " --> pdb=" O PHE Q1096 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N LYS Q1114 " --> pdb=" O LEU Q1177 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL Q1179 " --> pdb=" O LYS Q1114 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N SER Q1116 " --> pdb=" O VAL Q1179 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ALA Q1181 " --> pdb=" O SER Q1116 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL Q1118 " --> pdb=" O ALA Q1181 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Q' and resid 1276 through 1278 Processing sheet with id=AG8, first strand: chain 'Q' and resid 1537 through 1538 Processing sheet with id=AG9, first strand: chain 'Q' and resid 1579 through 1582 removed outlier: 3.738A pdb=" N GLN Q1580 " --> pdb=" O LEU Q1703 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL Q1705 " --> pdb=" O GLN Q1580 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ASP Q1671 " --> pdb=" O ARG Q1700 " (cutoff:3.500A) removed outlier: 9.263A pdb=" N ALA Q1660 " --> pdb=" O ILE Q1626 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE Q1628 " --> pdb=" O ALA Q1660 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Q' and resid 1732 through 1734 3807 hydrogen bonds defined for protein. 10974 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 113 hydrogen bonds 206 hydrogen bond angles 0 basepair planarities 47 basepair parallelities 128 stacking parallelities Total time for adding SS restraints: 43.10 Time building geometry restraints manager: 17.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 12467 1.31 - 1.44: 20867 1.44 - 1.58: 40883 1.58 - 1.71: 487 1.71 - 1.84: 449 Bond restraints: 75153 Sorted by residual: bond pdb=" N PRO W 89 " pdb=" CA PRO W 89 " ideal model delta sigma weight residual 1.469 1.690 -0.222 1.28e-02 6.10e+03 3.00e+02 bond pdb=" CA CYS A1002 " pdb=" C CYS A1002 " ideal model delta sigma weight residual 1.523 1.406 0.117 1.41e-02 5.03e+03 6.89e+01 bond pdb=" CA LYS A 769 " pdb=" C LYS A 769 " ideal model delta sigma weight residual 1.523 1.404 0.119 1.80e-02 3.09e+03 4.38e+01 bond pdb=" C ARG T 446 " pdb=" N SER T 447 " ideal model delta sigma weight residual 1.334 1.235 0.099 1.52e-02 4.33e+03 4.26e+01 bond pdb=" CB ASN T 426 " pdb=" CG ASN T 426 " ideal model delta sigma weight residual 1.516 1.371 0.145 2.50e-02 1.60e+03 3.36e+01 ... (remaining 75148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.83: 102114 3.83 - 7.66: 1119 7.66 - 11.48: 79 11.48 - 15.31: 16 15.31 - 19.14: 6 Bond angle restraints: 103334 Sorted by residual: angle pdb=" C ILE Q 786 " pdb=" N PRO Q 787 " pdb=" CA PRO Q 787 " ideal model delta sigma weight residual 119.76 138.90 -19.14 1.03e+00 9.43e-01 3.45e+02 angle pdb=" C GLY W 88 " pdb=" N PRO W 89 " pdb=" CA PRO W 89 " ideal model delta sigma weight residual 119.84 138.85 -19.01 1.25e+00 6.40e-01 2.31e+02 angle pdb=" N ALA C 400 " pdb=" CA ALA C 400 " pdb=" C ALA C 400 " ideal model delta sigma weight residual 113.28 98.31 14.97 1.22e+00 6.72e-01 1.51e+02 angle pdb=" N LYS T 187 " pdb=" CA LYS T 187 " pdb=" C LYS T 187 " ideal model delta sigma weight residual 112.72 123.43 -10.71 1.14e+00 7.69e-01 8.82e+01 angle pdb=" C PHE Q1110 " pdb=" N PRO Q1111 " pdb=" CA PRO Q1111 " ideal model delta sigma weight residual 118.85 127.77 -8.92 1.09e+00 8.42e-01 6.69e+01 ... (remaining 103329 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.51: 42691 35.51 - 71.03: 2714 71.03 - 106.54: 223 106.54 - 142.05: 17 142.05 - 177.57: 17 Dihedral angle restraints: 45662 sinusoidal: 18284 harmonic: 27378 Sorted by residual: dihedral pdb=" C4' U 3 95 " pdb=" C3' U 3 95 " pdb=" C2' U 3 95 " pdb=" C1' U 3 95 " ideal model delta sinusoidal sigma weight residual -35.00 32.75 -67.75 1 8.00e+00 1.56e-02 9.32e+01 dihedral pdb=" C5' U 3 95 " pdb=" C4' U 3 95 " pdb=" C3' U 3 95 " pdb=" O3' U 3 95 " ideal model delta sinusoidal sigma weight residual 147.00 80.82 66.18 1 8.00e+00 1.56e-02 8.94e+01 dihedral pdb=" CA LYS A1005 " pdb=" C LYS A1005 " pdb=" N PRO A1006 " pdb=" CA PRO A1006 " ideal model delta harmonic sigma weight residual 180.00 132.88 47.12 0 5.00e+00 4.00e-02 8.88e+01 ... (remaining 45659 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 11225 0.120 - 0.241: 682 0.241 - 0.361: 44 0.361 - 0.482: 5 0.482 - 0.602: 3 Chirality restraints: 11959 Sorted by residual: chirality pdb=" CA PRO W 89 " pdb=" N PRO W 89 " pdb=" C PRO W 89 " pdb=" CB PRO W 89 " both_signs ideal model delta sigma weight residual False 2.72 3.32 -0.60 2.00e-01 2.50e+01 9.07e+00 chirality pdb=" CB VAL A 175 " pdb=" CA VAL A 175 " pdb=" CG1 VAL A 175 " pdb=" CG2 VAL A 175 " both_signs ideal model delta sigma weight residual False -2.63 -2.04 -0.59 2.00e-01 2.50e+01 8.65e+00 chirality pdb=" CA HIS W 91 " pdb=" N HIS W 91 " pdb=" C HIS W 91 " pdb=" CB HIS W 91 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 6.90e+00 ... (remaining 11956 not shown) Planarity restraints: 12679 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C F 59 " 0.060 2.00e-02 2.50e+03 3.20e-02 2.31e+01 pdb=" N1 C F 59 " -0.066 2.00e-02 2.50e+03 pdb=" C2 C F 59 " -0.022 2.00e-02 2.50e+03 pdb=" O2 C F 59 " 0.000 2.00e-02 2.50e+03 pdb=" N3 C F 59 " 0.008 2.00e-02 2.50e+03 pdb=" C4 C F 59 " 0.023 2.00e-02 2.50e+03 pdb=" N4 C F 59 " 0.011 2.00e-02 2.50e+03 pdb=" C5 C F 59 " -0.007 2.00e-02 2.50e+03 pdb=" C6 C F 59 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A1005 " -0.078 5.00e-02 4.00e+02 1.20e-01 2.29e+01 pdb=" N PRO A1006 " 0.207 5.00e-02 4.00e+02 pdb=" CA PRO A1006 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO A1006 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 392 " 0.078 5.00e-02 4.00e+02 1.18e-01 2.22e+01 pdb=" N PRO C 393 " -0.204 5.00e-02 4.00e+02 pdb=" CA PRO C 393 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO C 393 " 0.064 5.00e-02 4.00e+02 ... (remaining 12676 not shown) Histogram of nonbonded interaction distances: 1.02 - 1.80: 13 1.80 - 2.57: 859 2.57 - 3.35: 93778 3.35 - 4.12: 191799 4.12 - 4.90: 328982 Nonbonded interactions: 615431 Sorted by model distance: nonbonded pdb=" NE2 GLN r 107 " pdb=" NE2 HIS s 108 " model vdw 1.019 3.200 nonbonded pdb=" OG SER C 193 " pdb="MG MG C1002 " model vdw 1.169 2.170 nonbonded pdb=" O HIS r 95 " pdb=" OE1 GLN r 99 " model vdw 1.252 3.040 nonbonded pdb=" NE2 GLN r 107 " pdb=" CE1 HIS s 108 " model vdw 1.331 3.340 nonbonded pdb=" CE1 TYR s 106 " pdb=" CG2 THR W 47 " model vdw 1.353 3.760 ... (remaining 615426 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 2.340 Check model and map are aligned: 0.420 Set scattering table: 0.510 Process input model: 165.880 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 190.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5560 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.222 75153 Z= 0.825 Angle : 1.093 19.138 103334 Z= 0.622 Chirality : 0.064 0.602 11959 Planarity : 0.007 0.120 12679 Dihedral : 21.437 177.566 27873 Min Nonbonded Distance : 1.019 Molprobity Statistics. All-atom Clashscore : 23.13 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.46 % Favored : 93.14 % Rotamer: Outliers : 13.19 % Allowed : 26.52 % Favored : 60.29 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.07), residues: 9287 helix: -1.76 (0.07), residues: 4180 sheet: -1.14 (0.15), residues: 1087 loop : -2.32 (0.09), residues: 4020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.005 TRP A 701 HIS 0.013 0.003 HIS K 28 PHE 0.051 0.004 PHE J 175 TYR 0.031 0.003 TYR J 192 ARG 0.019 0.001 ARG A 842 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18574 Ramachandran restraints generated. 9287 Oldfield, 0 Emsley, 9287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18574 Ramachandran restraints generated. 9287 Oldfield, 0 Emsley, 9287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1520 residues out of total 8096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 774 poor density : 746 time to evaluate : 5.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.7788 (mp) REVERT: A 252 MET cc_start: 0.8366 (ttp) cc_final: 0.7884 (ttp) REVERT: A 331 ILE cc_start: 0.4673 (OUTLIER) cc_final: 0.4361 (pp) REVERT: A 384 LYS cc_start: 0.4263 (OUTLIER) cc_final: 0.3988 (mmmt) REVERT: A 386 ARG cc_start: 0.4527 (OUTLIER) cc_final: 0.3090 (mpp80) REVERT: A 396 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7317 (mt) REVERT: A 478 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.7242 (mtt90) REVERT: A 544 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7690 (tttm) REVERT: A 589 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7407 (pttm) REVERT: A 668 MET cc_start: 0.7724 (ttt) cc_final: 0.7507 (ttp) REVERT: A 714 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8044 (ttm-80) REVERT: A 761 MET cc_start: 0.7110 (mmp) cc_final: 0.6860 (mmp) REVERT: A 882 GLU cc_start: 0.7473 (tt0) cc_final: 0.7198 (tt0) REVERT: A 980 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8415 (mtmm) REVERT: A 1005 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7635 (tptt) REVERT: A 1043 SER cc_start: 0.8751 (OUTLIER) cc_final: 0.8472 (t) REVERT: A 1248 ASN cc_start: 0.7535 (OUTLIER) cc_final: 0.7322 (m-40) REVERT: A 1278 TRP cc_start: 0.8652 (m-10) cc_final: 0.8399 (m-10) REVERT: A 1384 LYS cc_start: 0.7179 (mttt) cc_final: 0.6970 (mtpt) REVERT: A 1457 LYS cc_start: 0.4539 (OUTLIER) cc_final: 0.4119 (ptmt) REVERT: A 1461 LYS cc_start: 0.4425 (OUTLIER) cc_final: 0.3254 (tttt) REVERT: A 1729 GLN cc_start: 0.7335 (OUTLIER) cc_final: 0.7092 (pt0) REVERT: A 1791 ILE cc_start: 0.6873 (OUTLIER) cc_final: 0.6507 (pt) REVERT: A 1812 ARG cc_start: 0.7533 (mtt180) cc_final: 0.7309 (mtt180) REVERT: C 67 LEU cc_start: 0.6184 (pt) cc_final: 0.5940 (tm) REVERT: C 69 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.5725 (tt0) REVERT: C 119 ARG cc_start: 0.5174 (OUTLIER) cc_final: 0.3191 (mtp85) REVERT: C 186 ASP cc_start: 0.5917 (p0) cc_final: 0.5519 (p0) REVERT: C 421 ARG cc_start: 0.5764 (OUTLIER) cc_final: 0.5439 (ptp-170) REVERT: C 643 GLU cc_start: 0.3701 (OUTLIER) cc_final: 0.2816 (tm-30) REVERT: C 701 LYS cc_start: 0.3135 (OUTLIER) cc_final: 0.2688 (tmmm) REVERT: C 725 ASP cc_start: 0.3482 (OUTLIER) cc_final: 0.3242 (p0) REVERT: E 228 ASP cc_start: 0.5390 (OUTLIER) cc_final: 0.4912 (t0) REVERT: E 311 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.6463 (mtm110) REVERT: E 337 VAL cc_start: 0.4440 (OUTLIER) cc_final: 0.3999 (t) REVERT: E 342 LYS cc_start: 0.6255 (OUTLIER) cc_final: 0.5498 (mmtt) REVERT: q 113 ARG cc_start: 0.3300 (OUTLIER) cc_final: 0.2288 (ptm160) REVERT: r 57 LYS cc_start: 0.2407 (OUTLIER) cc_final: 0.1676 (tmtm) REVERT: r 84 MET cc_start: 0.2287 (tpt) cc_final: 0.1501 (mpp) REVERT: r 95 HIS cc_start: 0.1361 (OUTLIER) cc_final: 0.0175 (m170) REVERT: s 124 GLU cc_start: 0.3399 (OUTLIER) cc_final: 0.2995 (tp30) REVERT: a 19 GLU cc_start: 0.4706 (OUTLIER) cc_final: 0.3641 (mp0) REVERT: a 44 MET cc_start: 0.3955 (ttm) cc_final: 0.3514 (mpt) REVERT: e 35 ASP cc_start: 0.4057 (OUTLIER) cc_final: 0.3405 (p0) REVERT: e 55 GLU cc_start: 0.3966 (OUTLIER) cc_final: 0.3453 (tm-30) REVERT: e 62 LYS cc_start: 0.2684 (OUTLIER) cc_final: 0.1801 (ttmm) REVERT: c 1 MET cc_start: 0.3468 (mtt) cc_final: 0.2852 (tmm) REVERT: c 64 ASN cc_start: 0.0869 (OUTLIER) cc_final: -0.0179 (t160) REVERT: b 61 GLU cc_start: 0.2536 (OUTLIER) cc_final: 0.1440 (mm-30) REVERT: I 365 SER cc_start: -0.0429 (OUTLIER) cc_final: -0.0854 (m) REVERT: I 380 HIS cc_start: -0.0242 (m170) cc_final: -0.0590 (m-70) REVERT: I 408 LYS cc_start: 0.2856 (mmmt) cc_final: 0.2541 (tptt) REVERT: I 487 ARG cc_start: 0.3098 (OUTLIER) cc_final: 0.1775 (pmt170) REVERT: I 492 GLU cc_start: 0.4144 (mm-30) cc_final: 0.3765 (mm-30) REVERT: I 537 ILE cc_start: -0.0750 (OUTLIER) cc_final: -0.0996 (mt) REVERT: I 623 LYS cc_start: 0.4339 (OUTLIER) cc_final: 0.3037 (ttpp) REVERT: I 650 ARG cc_start: 0.1677 (mtt180) cc_final: 0.1431 (ttp80) REVERT: I 679 GLU cc_start: 0.1698 (mt-10) cc_final: 0.1125 (pp20) REVERT: I 712 ARG cc_start: 0.2216 (OUTLIER) cc_final: 0.1779 (mtt90) REVERT: I 748 LYS cc_start: 0.4810 (mmmt) cc_final: 0.4583 (ptpp) REVERT: J 144 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8240 (tpt90) REVERT: T 427 GLN cc_start: 0.7977 (mp10) cc_final: 0.7745 (mp10) REVERT: T 469 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8422 (mt) REVERT: O 111 GLU cc_start: 0.6116 (OUTLIER) cc_final: 0.5375 (mp0) REVERT: N 52 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.7881 (ttp-170) REVERT: R 191 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8285 (mm) REVERT: R 264 ASP cc_start: 0.5425 (OUTLIER) cc_final: 0.5177 (p0) REVERT: R 296 THR cc_start: 0.4745 (p) cc_final: 0.4529 (p) REVERT: S 82 LEU cc_start: 0.6110 (OUTLIER) cc_final: 0.5808 (mp) REVERT: S 133 ARG cc_start: 0.7509 (OUTLIER) cc_final: 0.6493 (ttt-90) REVERT: W 65 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7296 (mt) REVERT: W 139 ILE cc_start: 0.5078 (OUTLIER) cc_final: 0.4603 (tp) REVERT: W 171 ARG cc_start: 0.5944 (OUTLIER) cc_final: 0.2500 (tmt170) REVERT: W 181 ARG cc_start: 0.6511 (mtm-85) cc_final: 0.6308 (mtt180) REVERT: L 217 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.7844 (mt) REVERT: L 545 ARG cc_start: 0.3321 (OUTLIER) cc_final: 0.2638 (mtt180) REVERT: L 601 GLU cc_start: 0.3599 (OUTLIER) cc_final: 0.3124 (mm-30) REVERT: L 608 MET cc_start: 0.2744 (ptp) cc_final: 0.1760 (mmt) REVERT: L 614 HIS cc_start: 0.1681 (OUTLIER) cc_final: 0.1477 (t-90) REVERT: L 685 MET cc_start: 0.3159 (mtm) cc_final: 0.2004 (mtm) REVERT: L 699 ARG cc_start: 0.0529 (OUTLIER) cc_final: -0.0220 (mmm160) REVERT: L 780 GLU cc_start: 0.4310 (OUTLIER) cc_final: 0.2946 (tm-30) REVERT: L 817 ARG cc_start: 0.4023 (OUTLIER) cc_final: 0.2877 (mmp80) REVERT: K 59 THR cc_start: 0.3711 (OUTLIER) cc_final: 0.3477 (p) REVERT: K 86 GLU cc_start: 0.0359 (OUTLIER) cc_final: -0.0103 (mt-10) REVERT: K 104 TYR cc_start: 0.0583 (OUTLIER) cc_final: 0.0362 (m-10) REVERT: K 113 ARG cc_start: 0.3589 (tpt170) cc_final: 0.2813 (ttm-80) REVERT: K 134 GLN cc_start: 0.2161 (OUTLIER) cc_final: 0.1731 (tp-100) REVERT: K 144 LEU cc_start: 0.4835 (OUTLIER) cc_final: 0.4042 (tm) outliers start: 774 outliers final: 340 residues processed: 1425 average time/residue: 1.4466 time to fit residues: 2756.4361 Evaluate side-chains 1025 residues out of total 8096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 405 poor density : 620 time to evaluate : 5.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LYS Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 145 ARG Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 384 LYS Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 391 HIS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 544 LYS Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 589 LYS Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 619 LYS Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain A residue 643 GLN Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 706 ARG Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 714 ARG Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 899 ASP Chi-restraints excluded: chain A residue 909 ARG Chi-restraints excluded: chain A residue 923 SER Chi-restraints excluded: chain A residue 954 SER Chi-restraints excluded: chain A residue 978 LEU Chi-restraints excluded: chain A residue 980 LYS Chi-restraints excluded: chain A residue 993 GLU Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1005 LYS Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1026 VAL Chi-restraints excluded: chain A residue 1032 THR Chi-restraints excluded: chain A residue 1038 VAL Chi-restraints excluded: chain A residue 1043 SER Chi-restraints excluded: chain A residue 1059 ARG Chi-restraints excluded: chain A residue 1087 SER Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1131 CYS Chi-restraints excluded: chain A residue 1133 ASN Chi-restraints excluded: chain A residue 1153 SER Chi-restraints excluded: chain A residue 1157 ASN Chi-restraints excluded: chain A residue 1163 PHE Chi-restraints excluded: chain A residue 1164 ARG Chi-restraints excluded: chain A residue 1224 ARG Chi-restraints excluded: chain A residue 1230 THR Chi-restraints excluded: chain A residue 1231 THR Chi-restraints excluded: chain A residue 1240 SER Chi-restraints excluded: chain A residue 1248 ASN Chi-restraints excluded: chain A residue 1265 ARG Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1285 THR Chi-restraints excluded: chain A residue 1289 THR Chi-restraints excluded: chain A residue 1319 THR Chi-restraints excluded: chain A residue 1321 THR Chi-restraints excluded: chain A residue 1348 LEU Chi-restraints excluded: chain A residue 1351 LEU Chi-restraints excluded: chain A residue 1362 ARG Chi-restraints excluded: chain A residue 1365 ILE Chi-restraints excluded: chain A residue 1402 SER Chi-restraints excluded: chain A residue 1417 PHE Chi-restraints excluded: chain A residue 1428 LEU Chi-restraints excluded: chain A residue 1441 SER Chi-restraints excluded: chain A residue 1447 GLU Chi-restraints excluded: chain A residue 1456 LYS Chi-restraints excluded: chain A residue 1457 LYS Chi-restraints excluded: chain A residue 1461 LYS Chi-restraints excluded: chain A residue 1468 THR Chi-restraints excluded: chain A residue 1480 ILE Chi-restraints excluded: chain A residue 1491 ARG Chi-restraints excluded: chain A residue 1493 THR Chi-restraints excluded: chain A residue 1502 VAL Chi-restraints excluded: chain A residue 1512 THR Chi-restraints excluded: chain A residue 1514 MET Chi-restraints excluded: chain A residue 1538 VAL Chi-restraints excluded: chain A residue 1545 VAL Chi-restraints excluded: chain A residue 1557 THR Chi-restraints excluded: chain A residue 1592 GLN Chi-restraints excluded: chain A residue 1593 ILE Chi-restraints excluded: chain A residue 1605 THR Chi-restraints excluded: chain A residue 1626 MET Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1632 THR Chi-restraints excluded: chain A residue 1633 LEU Chi-restraints excluded: chain A residue 1645 LEU Chi-restraints excluded: chain A residue 1658 CYS Chi-restraints excluded: chain A residue 1683 SER Chi-restraints excluded: chain A residue 1712 THR Chi-restraints excluded: chain A residue 1713 ASN Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1728 VAL Chi-restraints excluded: chain A residue 1729 GLN Chi-restraints excluded: chain A residue 1757 SER Chi-restraints excluded: chain A residue 1783 PHE Chi-restraints excluded: chain A residue 1791 ILE Chi-restraints excluded: chain A residue 1807 LEU Chi-restraints excluded: chain A residue 1819 SER Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 119 ARG Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 306 CYS Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 421 ARG Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 485 CYS Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 600 GLN Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 627 VAL Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 643 GLU Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 701 LYS Chi-restraints excluded: chain C residue 725 ASP Chi-restraints excluded: chain C residue 726 MET Chi-restraints excluded: chain C residue 784 ILE Chi-restraints excluded: chain C residue 797 CYS Chi-restraints excluded: chain C residue 809 LEU Chi-restraints excluded: chain C residue 810 ASP Chi-restraints excluded: chain C residue 826 ILE Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 859 CYS Chi-restraints excluded: chain C residue 878 VAL Chi-restraints excluded: chain C residue 933 ILE Chi-restraints excluded: chain C residue 961 SER Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain E residue 130 LYS Chi-restraints excluded: chain E residue 157 CYS Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 200 PHE Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 302 SER Chi-restraints excluded: chain E residue 306 CYS Chi-restraints excluded: chain E residue 311 ARG Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 333 SER Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 342 LYS Chi-restraints excluded: chain q residue 4 SER Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain q residue 72 LEU Chi-restraints excluded: chain q residue 92 THR Chi-restraints excluded: chain q residue 113 ARG Chi-restraints excluded: chain r residue 2 PHE Chi-restraints excluded: chain r residue 9 VAL Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 17 THR Chi-restraints excluded: chain r residue 41 THR Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 55 VAL Chi-restraints excluded: chain r residue 57 LYS Chi-restraints excluded: chain r residue 59 VAL Chi-restraints excluded: chain r residue 63 THR Chi-restraints excluded: chain r residue 68 SER Chi-restraints excluded: chain r residue 95 HIS Chi-restraints excluded: chain r residue 113 ARG Chi-restraints excluded: chain r residue 115 ILE Chi-restraints excluded: chain s residue 85 LEU Chi-restraints excluded: chain s residue 124 GLU Chi-restraints excluded: chain t residue 90 THR Chi-restraints excluded: chain a residue 19 GLU Chi-restraints excluded: chain a residue 57 ASP Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain g residue 27 VAL Chi-restraints excluded: chain g residue 40 LEU Chi-restraints excluded: chain g residue 70 LEU Chi-restraints excluded: chain e residue 35 ASP Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 55 GLU Chi-restraints excluded: chain e residue 62 LYS Chi-restraints excluded: chain f residue 9 PRO Chi-restraints excluded: chain f residue 68 CYS Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 42 CYS Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 80 GLN Chi-restraints excluded: chain d residue 84 ARG Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain c residue 5 VAL Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 41 LEU Chi-restraints excluded: chain c residue 51 LYS Chi-restraints excluded: chain c residue 64 ASN Chi-restraints excluded: chain c residue 75 LEU Chi-restraints excluded: chain c residue 79 THR Chi-restraints excluded: chain b residue 36 ARG Chi-restraints excluded: chain b residue 61 GLU Chi-restraints excluded: chain b residue 105 ILE Chi-restraints excluded: chain I residue 346 VAL Chi-restraints excluded: chain I residue 356 LEU Chi-restraints excluded: chain I residue 365 SER Chi-restraints excluded: chain I residue 367 VAL Chi-restraints excluded: chain I residue 376 VAL Chi-restraints excluded: chain I residue 401 VAL Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain I residue 451 LEU Chi-restraints excluded: chain I residue 487 ARG Chi-restraints excluded: chain I residue 506 LEU Chi-restraints excluded: chain I residue 537 ILE Chi-restraints excluded: chain I residue 614 CYS Chi-restraints excluded: chain I residue 623 LYS Chi-restraints excluded: chain I residue 670 VAL Chi-restraints excluded: chain I residue 702 GLU Chi-restraints excluded: chain I residue 712 ARG Chi-restraints excluded: chain I residue 746 THR Chi-restraints excluded: chain J residue 61 SER Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 71 ARG Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain J residue 144 ARG Chi-restraints excluded: chain J residue 162 VAL Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain J residue 288 TYR Chi-restraints excluded: chain P residue 13 ILE Chi-restraints excluded: chain P residue 48 GLN Chi-restraints excluded: chain P residue 62 GLU Chi-restraints excluded: chain P residue 231 GLN Chi-restraints excluded: chain P residue 234 ILE Chi-restraints excluded: chain M residue 447 GLN Chi-restraints excluded: chain M residue 496 VAL Chi-restraints excluded: chain M residue 538 LYS Chi-restraints excluded: chain T residue 190 ARG Chi-restraints excluded: chain T residue 212 CYS Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 284 ILE Chi-restraints excluded: chain T residue 286 SER Chi-restraints excluded: chain T residue 314 VAL Chi-restraints excluded: chain T residue 324 VAL Chi-restraints excluded: chain T residue 377 SER Chi-restraints excluded: chain T residue 388 PHE Chi-restraints excluded: chain T residue 396 GLU Chi-restraints excluded: chain T residue 420 ILE Chi-restraints excluded: chain T residue 446 ARG Chi-restraints excluded: chain T residue 450 CYS Chi-restraints excluded: chain T residue 462 SER Chi-restraints excluded: chain T residue 465 SER Chi-restraints excluded: chain T residue 469 LEU Chi-restraints excluded: chain T residue 485 GLU Chi-restraints excluded: chain T residue 497 GLU Chi-restraints excluded: chain T residue 498 ASP Chi-restraints excluded: chain O residue 35 MET Chi-restraints excluded: chain O residue 38 ILE Chi-restraints excluded: chain O residue 49 ARG Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 83 CYS Chi-restraints excluded: chain O residue 111 GLU Chi-restraints excluded: chain O residue 165 VAL Chi-restraints excluded: chain O residue 180 CYS Chi-restraints excluded: chain O residue 206 ASN Chi-restraints excluded: chain O residue 217 VAL Chi-restraints excluded: chain O residue 224 THR Chi-restraints excluded: chain O residue 266 VAL Chi-restraints excluded: chain N residue 21 GLU Chi-restraints excluded: chain N residue 23 ILE Chi-restraints excluded: chain N residue 41 LYS Chi-restraints excluded: chain N residue 47 THR Chi-restraints excluded: chain N residue 50 ILE Chi-restraints excluded: chain N residue 52 ARG Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain N residue 82 GLU Chi-restraints excluded: chain N residue 118 SER Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain N residue 146 SER Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 83 ILE Chi-restraints excluded: chain R residue 88 LYS Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 118 VAL Chi-restraints excluded: chain R residue 136 LYS Chi-restraints excluded: chain R residue 146 GLU Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 168 SER Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 191 ILE Chi-restraints excluded: chain R residue 195 ASP Chi-restraints excluded: chain R residue 211 VAL Chi-restraints excluded: chain R residue 220 VAL Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 231 THR Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain R residue 264 ASP Chi-restraints excluded: chain R residue 286 THR Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 28 CYS Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain S residue 133 ARG Chi-restraints excluded: chain S residue 146 VAL Chi-restraints excluded: chain S residue 152 ILE Chi-restraints excluded: chain W residue 47 THR Chi-restraints excluded: chain W residue 51 LEU Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain W residue 72 LYS Chi-restraints excluded: chain W residue 74 MET Chi-restraints excluded: chain W residue 77 LEU Chi-restraints excluded: chain W residue 91 HIS Chi-restraints excluded: chain W residue 107 VAL Chi-restraints excluded: chain W residue 112 ASP Chi-restraints excluded: chain W residue 118 ILE Chi-restraints excluded: chain W residue 121 GLU Chi-restraints excluded: chain W residue 139 ILE Chi-restraints excluded: chain W residue 167 THR Chi-restraints excluded: chain W residue 168 THR Chi-restraints excluded: chain W residue 171 ARG Chi-restraints excluded: chain W residue 202 SER Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 161 THR Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain L residue 217 LEU Chi-restraints excluded: chain L residue 545 ARG Chi-restraints excluded: chain L residue 556 ILE Chi-restraints excluded: chain L residue 601 GLU Chi-restraints excluded: chain L residue 614 HIS Chi-restraints excluded: chain L residue 699 ARG Chi-restraints excluded: chain L residue 773 VAL Chi-restraints excluded: chain L residue 779 HIS Chi-restraints excluded: chain L residue 780 GLU Chi-restraints excluded: chain L residue 791 GLU Chi-restraints excluded: chain L residue 800 THR Chi-restraints excluded: chain L residue 805 VAL Chi-restraints excluded: chain L residue 817 ARG Chi-restraints excluded: chain L residue 828 LYS Chi-restraints excluded: chain K residue 28 HIS Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 86 GLU Chi-restraints excluded: chain K residue 104 TYR Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain K residue 134 GLN Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 2 TYR Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain V residue 658 THR Chi-restraints excluded: chain V residue 668 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 956 random chunks: chunk 807 optimal weight: 7.9990 chunk 724 optimal weight: 8.9990 chunk 402 optimal weight: 3.9990 chunk 247 optimal weight: 20.0000 chunk 488 optimal weight: 8.9990 chunk 387 optimal weight: 7.9990 chunk 749 optimal weight: 30.0000 chunk 289 optimal weight: 5.9990 chunk 455 optimal weight: 9.9990 chunk 557 optimal weight: 2.9990 chunk 868 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 HIS A 132 HIS A 269 HIS ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 HIS ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 GLN A 512 GLN A 521 ASN A 547 GLN A 581 HIS A 587 ASN A 625 ASN A 627 GLN A 648 HIS A 739 GLN A 744 HIS A 755 HIS A 852 GLN A 855 GLN A 968 HIS A1025 ASN A1033 ASN A1078 ASN A1133 ASN ** A1147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1157 ASN A1160 HIS A1175 GLN A1194 ASN A1223 ASN A1246 ASN A1282 ASN A1284 HIS A1325 ASN ** A1346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1360 GLN A1437 GLN A1488 GLN A1504 GLN A1521 HIS A1524 HIS A1595 ASN A1616 GLN A1639 GLN A1702 ASN C 68 HIS C 133 ASN ** C 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 GLN ** C 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 551 GLN ** C 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 757 GLN ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 944 GLN E 78 GLN E 100 ASN E 275 ASN ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 83 ASN q 99 GLN ** r 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 56 ASN r 95 HIS ** r 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 107 GLN a 47 GLN a 84 ASN g 62 ASN g 65 GLN e 21 GLN ** e 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 44 ASN ** d 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 80 GLN c 65 ASN I 374 HIS I 427 HIS I 432 ASN I 445 HIS I 453 HIS I 505 ASN I 512 HIS I 545 ASN I 743 ASN J 154 HIS J 225 ASN ** J 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 HIS P 212 GLN P 231 GLN M 540 GLN T 261 HIS T 347 GLN T 353 HIS O 45 HIS O 119 GLN O 152 GLN N 29 GLN N 35 ASN N 111 ASN N 119 HIS N 138 GLN N 172 ASN R 79 GLN R 80 GLN R 150 GLN R 235 GLN R 236 GLN R 274 ASN ** S 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 98 ASN S 138 GLN W 114 HIS W 119 HIS ** W 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 198 GLN L 29 GLN L 568 GLN L 688 HIS ** L 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 26 ASN K 28 HIS K 141 GLN ** K 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 189 HIS K 233 HIS ** V 674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 111 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4969 r_free = 0.4969 target = 0.276818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.246182 restraints weight = 84265.311| |-----------------------------------------------------------------------------| r_work (start): 0.4712 rms_B_bonded: 1.74 r_work: 0.4445 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.4409 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.4409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6209 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.132 75153 Z= 0.654 Angle : 0.908 15.950 103334 Z= 0.473 Chirality : 0.056 0.385 11959 Planarity : 0.007 0.111 12679 Dihedral : 18.637 179.156 14896 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.94 % Favored : 93.93 % Rotamer: Outliers : 11.95 % Allowed : 27.52 % Favored : 60.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 1.07 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.08), residues: 9287 helix: -0.71 (0.07), residues: 4284 sheet: -1.08 (0.15), residues: 1061 loop : -1.90 (0.09), residues: 3942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.004 TRP A 814 HIS 0.012 0.002 HIS W 128 PHE 0.043 0.003 PHE A 962 TYR 0.027 0.003 TYR J 192 ARG 0.020 0.001 ARG A 842 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18574 Ramachandran restraints generated. 9287 Oldfield, 0 Emsley, 9287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18574 Ramachandran restraints generated. 9287 Oldfield, 0 Emsley, 9287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1369 residues out of total 8096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 701 poor density : 668 time to evaluate : 5.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.7976 (ptt90) cc_final: 0.7688 (ptm160) REVERT: A 276 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7930 (ptmt) REVERT: A 331 ILE cc_start: 0.4481 (OUTLIER) cc_final: 0.4092 (pp) REVERT: A 386 ARG cc_start: 0.4598 (OUTLIER) cc_final: 0.3340 (mpp80) REVERT: A 396 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7483 (mt) REVERT: A 498 HIS cc_start: 0.4993 (OUTLIER) cc_final: 0.4122 (t-90) REVERT: A 526 ARG cc_start: 0.5808 (OUTLIER) cc_final: 0.5500 (ttm170) REVERT: A 619 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.7918 (tttp) REVERT: A 714 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8312 (ttm-80) REVERT: A 800 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7923 (tt0) REVERT: A 882 GLU cc_start: 0.7963 (tt0) cc_final: 0.7683 (tt0) REVERT: A 997 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.6438 (mtt90) REVERT: A 1043 SER cc_start: 0.8736 (OUTLIER) cc_final: 0.8515 (t) REVERT: A 1278 TRP cc_start: 0.8971 (m-10) cc_final: 0.8522 (m-10) REVERT: A 1307 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7776 (ttp-170) REVERT: A 1362 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.6797 (tpp80) REVERT: A 1384 LYS cc_start: 0.7664 (mttt) cc_final: 0.7408 (mtpt) REVERT: A 1491 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.7198 (mmp-170) REVERT: A 1626 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.8328 (mtm) REVERT: A 1659 GLN cc_start: 0.5981 (OUTLIER) cc_final: 0.5657 (tt0) REVERT: A 1754 ASP cc_start: 0.4730 (OUTLIER) cc_final: 0.4515 (t70) REVERT: A 1808 ARG cc_start: 0.7441 (mtt-85) cc_final: 0.7093 (mtt90) REVERT: C 67 LEU cc_start: 0.6433 (pt) cc_final: 0.6207 (tp) REVERT: C 69 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.6432 (tp30) REVERT: C 114 GLU cc_start: 0.3203 (OUTLIER) cc_final: 0.2842 (pm20) REVERT: C 188 GLN cc_start: 0.6848 (tp40) cc_final: 0.6484 (tm-30) REVERT: C 216 LEU cc_start: 0.5621 (OUTLIER) cc_final: 0.4950 (mt) REVERT: C 488 ARG cc_start: 0.4018 (OUTLIER) cc_final: 0.3100 (mtt90) REVERT: C 643 GLU cc_start: 0.3708 (OUTLIER) cc_final: 0.2606 (tm-30) REVERT: C 725 ASP cc_start: 0.3491 (OUTLIER) cc_final: 0.3192 (p0) REVERT: C 757 GLN cc_start: 0.5005 (pt0) cc_final: 0.4761 (mp10) REVERT: C 763 LEU cc_start: 0.1297 (OUTLIER) cc_final: 0.0764 (mt) REVERT: E 54 LEU cc_start: 0.6098 (OUTLIER) cc_final: 0.5602 (mt) REVERT: E 228 ASP cc_start: 0.5700 (OUTLIER) cc_final: 0.4985 (t0) REVERT: E 337 VAL cc_start: 0.4508 (OUTLIER) cc_final: 0.3956 (t) REVERT: r 84 MET cc_start: 0.2492 (tpt) cc_final: 0.1527 (mpp) REVERT: r 95 HIS cc_start: 0.1133 (OUTLIER) cc_final: 0.0494 (m170) REVERT: a 19 GLU cc_start: 0.4551 (OUTLIER) cc_final: 0.3646 (mp0) REVERT: a 56 ARG cc_start: 0.4045 (OUTLIER) cc_final: 0.3093 (mtm110) REVERT: g 70 LEU cc_start: 0.2580 (OUTLIER) cc_final: 0.1828 (mp) REVERT: e 55 GLU cc_start: 0.4134 (OUTLIER) cc_final: 0.3562 (tm-30) REVERT: e 62 LYS cc_start: 0.2495 (OUTLIER) cc_final: 0.1721 (ttmm) REVERT: e 66 ARG cc_start: 0.3911 (OUTLIER) cc_final: 0.2942 (ttm170) REVERT: d 68 GLU cc_start: 0.2516 (OUTLIER) cc_final: 0.1205 (pp20) REVERT: c 1 MET cc_start: 0.3181 (mtt) cc_final: 0.2357 (tmm) REVERT: c 10 LYS cc_start: 0.3967 (OUTLIER) cc_final: 0.3354 (tptp) REVERT: c 49 ARG cc_start: 0.3206 (OUTLIER) cc_final: 0.2308 (tpt170) REVERT: I 380 HIS cc_start: -0.0605 (m170) cc_final: -0.0946 (m-70) REVERT: I 384 LYS cc_start: 0.1551 (OUTLIER) cc_final: 0.1186 (mppt) REVERT: I 408 LYS cc_start: 0.2809 (mmmt) cc_final: 0.2529 (tptt) REVERT: I 417 TRP cc_start: 0.1179 (m100) cc_final: 0.0782 (m-90) REVERT: I 420 PHE cc_start: 0.1681 (OUTLIER) cc_final: 0.1219 (t80) REVERT: I 456 CYS cc_start: 0.3379 (OUTLIER) cc_final: 0.2864 (m) REVERT: I 487 ARG cc_start: 0.2978 (OUTLIER) cc_final: 0.1858 (pmt170) REVERT: I 492 GLU cc_start: 0.4375 (mm-30) cc_final: 0.3345 (pp20) REVERT: I 537 ILE cc_start: -0.0933 (OUTLIER) cc_final: -0.1158 (mt) REVERT: I 574 HIS cc_start: 0.2764 (OUTLIER) cc_final: 0.1697 (m-70) REVERT: I 601 LEU cc_start: 0.1350 (OUTLIER) cc_final: 0.1004 (mp) REVERT: I 623 LYS cc_start: 0.4595 (OUTLIER) cc_final: 0.3576 (ptpt) REVERT: I 650 ARG cc_start: 0.1981 (mtt180) cc_final: 0.1647 (ttp80) REVERT: I 679 GLU cc_start: 0.1487 (OUTLIER) cc_final: 0.1011 (pp20) REVERT: I 696 MET cc_start: 0.2450 (mmp) cc_final: 0.2147 (mmm) REVERT: I 748 LYS cc_start: 0.5274 (mmmt) cc_final: 0.4661 (ptpp) REVERT: J 71 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.7048 (ptp90) REVERT: J 306 GLN cc_start: 0.4230 (OUTLIER) cc_final: 0.3781 (mt0) REVERT: T 469 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8386 (mt) REVERT: T 498 ASP cc_start: 0.5369 (OUTLIER) cc_final: 0.5031 (p0) REVERT: O 111 GLU cc_start: 0.5895 (OUTLIER) cc_final: 0.5219 (mp0) REVERT: O 264 MET cc_start: 0.1561 (pmm) cc_final: 0.0889 (pmt) REVERT: N 6 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.8086 (pttt) REVERT: N 14 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6993 (tp30) REVERT: N 21 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6907 (tm-30) REVERT: N 52 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.8170 (ttp-170) REVERT: N 82 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7237 (mp0) REVERT: N 170 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.6824 (mt-10) REVERT: R 191 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8307 (mm) REVERT: R 205 LYS cc_start: 0.7556 (OUTLIER) cc_final: 0.6809 (mptt) REVERT: S 9 ASP cc_start: 0.6455 (OUTLIER) cc_final: 0.5933 (p0) REVERT: S 83 LYS cc_start: 0.6914 (OUTLIER) cc_final: 0.5691 (mtpp) REVERT: W 47 THR cc_start: 0.1229 (OUTLIER) cc_final: 0.0984 (t) REVERT: W 50 VAL cc_start: 0.3304 (OUTLIER) cc_final: 0.3062 (m) REVERT: L 24 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.8046 (tttp) REVERT: L 29 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.8023 (mm-40) REVERT: L 545 ARG cc_start: 0.3123 (OUTLIER) cc_final: 0.2595 (mtt180) REVERT: L 608 MET cc_start: 0.2766 (ptp) cc_final: 0.1436 (mmt) REVERT: L 614 HIS cc_start: 0.1507 (OUTLIER) cc_final: 0.0808 (t-90) REVERT: L 658 LEU cc_start: 0.2836 (OUTLIER) cc_final: 0.2520 (mp) REVERT: L 688 HIS cc_start: 0.1756 (OUTLIER) cc_final: 0.1394 (m-70) REVERT: L 757 ARG cc_start: 0.4682 (OUTLIER) cc_final: 0.3383 (ttt-90) REVERT: L 776 LYS cc_start: 0.5650 (ttpp) cc_final: 0.5148 (tptm) REVERT: L 780 GLU cc_start: 0.4276 (OUTLIER) cc_final: 0.3173 (tm-30) REVERT: L 817 ARG cc_start: 0.4263 (OUTLIER) cc_final: 0.3255 (mmp80) REVERT: K 27 GLU cc_start: 0.1807 (mp0) cc_final: 0.1390 (pp20) REVERT: K 59 THR cc_start: 0.3801 (OUTLIER) cc_final: 0.3499 (p) REVERT: K 65 TYR cc_start: 0.1715 (OUTLIER) cc_final: 0.1430 (m-80) REVERT: K 104 TYR cc_start: 0.0480 (OUTLIER) cc_final: -0.0136 (t80) REVERT: K 113 ARG cc_start: 0.3575 (OUTLIER) cc_final: 0.2796 (ttm-80) REVERT: K 144 LEU cc_start: 0.4316 (OUTLIER) cc_final: 0.3901 (tm) REVERT: V 657 ARG cc_start: 0.4057 (OUTLIER) cc_final: 0.3845 (tpt170) outliers start: 701 outliers final: 318 residues processed: 1275 average time/residue: 1.4482 time to fit residues: 2467.4979 Evaluate side-chains 1006 residues out of total 8096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 396 poor density : 610 time to evaluate : 5.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LYS Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 145 ARG Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 384 LYS Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 493 CYS Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 498 HIS Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 526 ARG Chi-restraints excluded: chain A residue 544 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 619 LYS Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 714 ARG Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 923 SER Chi-restraints excluded: chain A residue 978 LEU Chi-restraints excluded: chain A residue 997 ARG Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1026 VAL Chi-restraints excluded: chain A residue 1038 VAL Chi-restraints excluded: chain A residue 1043 SER Chi-restraints excluded: chain A residue 1059 ARG Chi-restraints excluded: chain A residue 1087 SER Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1163 PHE Chi-restraints excluded: chain A residue 1164 ARG Chi-restraints excluded: chain A residue 1224 ARG Chi-restraints excluded: chain A residue 1230 THR Chi-restraints excluded: chain A residue 1231 THR Chi-restraints excluded: chain A residue 1240 SER Chi-restraints excluded: chain A residue 1265 ARG Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1285 THR Chi-restraints excluded: chain A residue 1289 THR Chi-restraints excluded: chain A residue 1307 ARG Chi-restraints excluded: chain A residue 1319 THR Chi-restraints excluded: chain A residue 1321 THR Chi-restraints excluded: chain A residue 1351 LEU Chi-restraints excluded: chain A residue 1362 ARG Chi-restraints excluded: chain A residue 1365 ILE Chi-restraints excluded: chain A residue 1402 SER Chi-restraints excluded: chain A residue 1417 PHE Chi-restraints excluded: chain A residue 1428 LEU Chi-restraints excluded: chain A residue 1441 SER Chi-restraints excluded: chain A residue 1456 LYS Chi-restraints excluded: chain A residue 1465 ARG Chi-restraints excluded: chain A residue 1468 THR Chi-restraints excluded: chain A residue 1480 ILE Chi-restraints excluded: chain A residue 1483 ILE Chi-restraints excluded: chain A residue 1491 ARG Chi-restraints excluded: chain A residue 1493 THR Chi-restraints excluded: chain A residue 1502 VAL Chi-restraints excluded: chain A residue 1511 ILE Chi-restraints excluded: chain A residue 1512 THR Chi-restraints excluded: chain A residue 1514 MET Chi-restraints excluded: chain A residue 1538 VAL Chi-restraints excluded: chain A residue 1545 VAL Chi-restraints excluded: chain A residue 1557 THR Chi-restraints excluded: chain A residue 1593 ILE Chi-restraints excluded: chain A residue 1605 THR Chi-restraints excluded: chain A residue 1626 MET Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1632 THR Chi-restraints excluded: chain A residue 1635 ILE Chi-restraints excluded: chain A residue 1658 CYS Chi-restraints excluded: chain A residue 1659 GLN Chi-restraints excluded: chain A residue 1683 SER Chi-restraints excluded: chain A residue 1712 THR Chi-restraints excluded: chain A residue 1719 LYS Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1728 VAL Chi-restraints excluded: chain A residue 1747 LYS Chi-restraints excluded: chain A residue 1754 ASP Chi-restraints excluded: chain A residue 1757 SER Chi-restraints excluded: chain A residue 1783 PHE Chi-restraints excluded: chain A residue 1786 ILE Chi-restraints excluded: chain A residue 1807 LEU Chi-restraints excluded: chain A residue 1817 LEU Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 166 LYS Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 306 CYS Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 488 ARG Chi-restraints excluded: chain C residue 508 ASP Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain C residue 600 GLN Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 643 GLU Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 725 ASP Chi-restraints excluded: chain C residue 726 MET Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 809 LEU Chi-restraints excluded: chain C residue 810 ASP Chi-restraints excluded: chain C residue 820 ARG Chi-restraints excluded: chain C residue 826 ILE Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 878 VAL Chi-restraints excluded: chain C residue 901 GLU Chi-restraints excluded: chain C residue 902 THR Chi-restraints excluded: chain C residue 961 SER Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 79 CYS Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 145 LYS Chi-restraints excluded: chain E residue 157 CYS Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 200 PHE Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 306 CYS Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 333 SER Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 342 LYS Chi-restraints excluded: chain E residue 354 THR Chi-restraints excluded: chain q residue 26 SER Chi-restraints excluded: chain q residue 72 LEU Chi-restraints excluded: chain r residue 2 PHE Chi-restraints excluded: chain r residue 9 VAL Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain r residue 41 THR Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 63 THR Chi-restraints excluded: chain r residue 95 HIS Chi-restraints excluded: chain r residue 113 ARG Chi-restraints excluded: chain s residue 132 MET Chi-restraints excluded: chain a residue 19 GLU Chi-restraints excluded: chain a residue 56 ARG Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 87 MET Chi-restraints excluded: chain g residue 27 VAL Chi-restraints excluded: chain g residue 30 THR Chi-restraints excluded: chain g residue 38 MET Chi-restraints excluded: chain g residue 70 LEU Chi-restraints excluded: chain e residue 55 GLU Chi-restraints excluded: chain e residue 59 VAL Chi-restraints excluded: chain e residue 62 LYS Chi-restraints excluded: chain e residue 66 ARG Chi-restraints excluded: chain e residue 72 ILE Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 68 CYS Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 42 CYS Chi-restraints excluded: chain d residue 63 LEU Chi-restraints excluded: chain d residue 68 GLU Chi-restraints excluded: chain d residue 80 GLN Chi-restraints excluded: chain d residue 84 ARG Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain c residue 2 VAL Chi-restraints excluded: chain c residue 10 LYS Chi-restraints excluded: chain c residue 49 ARG Chi-restraints excluded: chain c residue 79 THR Chi-restraints excluded: chain c residue 85 ASP Chi-restraints excluded: chain b residue 36 ARG Chi-restraints excluded: chain b residue 40 LEU Chi-restraints excluded: chain b residue 105 ILE Chi-restraints excluded: chain I residue 356 LEU Chi-restraints excluded: chain I residue 367 VAL Chi-restraints excluded: chain I residue 384 LYS Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain I residue 420 PHE Chi-restraints excluded: chain I residue 435 ILE Chi-restraints excluded: chain I residue 456 CYS Chi-restraints excluded: chain I residue 480 THR Chi-restraints excluded: chain I residue 487 ARG Chi-restraints excluded: chain I residue 506 LEU Chi-restraints excluded: chain I residue 537 ILE Chi-restraints excluded: chain I residue 574 HIS Chi-restraints excluded: chain I residue 601 LEU Chi-restraints excluded: chain I residue 614 CYS Chi-restraints excluded: chain I residue 615 LYS Chi-restraints excluded: chain I residue 620 GLU Chi-restraints excluded: chain I residue 623 LYS Chi-restraints excluded: chain I residue 659 SER Chi-restraints excluded: chain I residue 667 ILE Chi-restraints excluded: chain I residue 670 VAL Chi-restraints excluded: chain I residue 679 GLU Chi-restraints excluded: chain I residue 687 SER Chi-restraints excluded: chain I residue 702 GLU Chi-restraints excluded: chain I residue 746 THR Chi-restraints excluded: chain J residue 61 SER Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 71 ARG Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain J residue 140 SER Chi-restraints excluded: chain J residue 144 ARG Chi-restraints excluded: chain J residue 196 ASP Chi-restraints excluded: chain J residue 228 VAL Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain J residue 260 GLU Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain J residue 306 GLN Chi-restraints excluded: chain P residue 13 ILE Chi-restraints excluded: chain P residue 62 GLU Chi-restraints excluded: chain P residue 231 GLN Chi-restraints excluded: chain P residue 234 ILE Chi-restraints excluded: chain M residue 447 GLN Chi-restraints excluded: chain M residue 496 VAL Chi-restraints excluded: chain T residue 190 ARG Chi-restraints excluded: chain T residue 198 LYS Chi-restraints excluded: chain T residue 212 CYS Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 286 SER Chi-restraints excluded: chain T residue 314 VAL Chi-restraints excluded: chain T residue 324 VAL Chi-restraints excluded: chain T residue 388 PHE Chi-restraints excluded: chain T residue 396 GLU Chi-restraints excluded: chain T residue 414 SER Chi-restraints excluded: chain T residue 422 SER Chi-restraints excluded: chain T residue 446 ARG Chi-restraints excluded: chain T residue 464 GLU Chi-restraints excluded: chain T residue 465 SER Chi-restraints excluded: chain T residue 469 LEU Chi-restraints excluded: chain T residue 498 ASP Chi-restraints excluded: chain O residue 22 VAL Chi-restraints excluded: chain O residue 35 MET Chi-restraints excluded: chain O residue 38 ILE Chi-restraints excluded: chain O residue 49 ARG Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 71 GLN Chi-restraints excluded: chain O residue 111 GLU Chi-restraints excluded: chain O residue 165 VAL Chi-restraints excluded: chain O residue 180 CYS Chi-restraints excluded: chain O residue 206 ASN Chi-restraints excluded: chain O residue 224 THR Chi-restraints excluded: chain O residue 248 VAL Chi-restraints excluded: chain O residue 266 VAL Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 14 GLU Chi-restraints excluded: chain N residue 21 GLU Chi-restraints excluded: chain N residue 52 ARG Chi-restraints excluded: chain N residue 82 GLU Chi-restraints excluded: chain N residue 118 SER Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain N residue 170 GLU Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 83 ILE Chi-restraints excluded: chain R residue 88 LYS Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 105 ARG Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 118 VAL Chi-restraints excluded: chain R residue 122 SER Chi-restraints excluded: chain R residue 136 LYS Chi-restraints excluded: chain R residue 152 LYS Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 191 ILE Chi-restraints excluded: chain R residue 195 ASP Chi-restraints excluded: chain R residue 205 LYS Chi-restraints excluded: chain R residue 211 VAL Chi-restraints excluded: chain R residue 220 VAL Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 231 THR Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain R residue 255 ILE Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain R residue 286 THR Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 6 VAL Chi-restraints excluded: chain S residue 9 ASP Chi-restraints excluded: chain S residue 28 CYS Chi-restraints excluded: chain S residue 83 LYS Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain S residue 92 MET Chi-restraints excluded: chain S residue 146 VAL Chi-restraints excluded: chain W residue 47 THR Chi-restraints excluded: chain W residue 50 VAL Chi-restraints excluded: chain W residue 72 LYS Chi-restraints excluded: chain W residue 77 LEU Chi-restraints excluded: chain W residue 81 ASP Chi-restraints excluded: chain W residue 86 VAL Chi-restraints excluded: chain W residue 87 LEU Chi-restraints excluded: chain W residue 91 HIS Chi-restraints excluded: chain W residue 107 VAL Chi-restraints excluded: chain W residue 112 ASP Chi-restraints excluded: chain W residue 118 ILE Chi-restraints excluded: chain W residue 121 GLU Chi-restraints excluded: chain W residue 137 SER Chi-restraints excluded: chain W residue 167 THR Chi-restraints excluded: chain W residue 168 THR Chi-restraints excluded: chain W residue 202 SER Chi-restraints excluded: chain L residue 24 LYS Chi-restraints excluded: chain L residue 29 GLN Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 161 THR Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain L residue 217 LEU Chi-restraints excluded: chain L residue 545 ARG Chi-restraints excluded: chain L residue 556 ILE Chi-restraints excluded: chain L residue 596 LEU Chi-restraints excluded: chain L residue 614 HIS Chi-restraints excluded: chain L residue 650 GLU Chi-restraints excluded: chain L residue 658 LEU Chi-restraints excluded: chain L residue 675 LEU Chi-restraints excluded: chain L residue 688 HIS Chi-restraints excluded: chain L residue 757 ARG Chi-restraints excluded: chain L residue 780 GLU Chi-restraints excluded: chain L residue 798 ASP Chi-restraints excluded: chain L residue 800 THR Chi-restraints excluded: chain L residue 806 ASP Chi-restraints excluded: chain L residue 817 ARG Chi-restraints excluded: chain K residue 28 HIS Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 65 TYR Chi-restraints excluded: chain K residue 66 LEU Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 104 TYR Chi-restraints excluded: chain K residue 113 ARG Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain K residue 205 GLN Chi-restraints excluded: chain K residue 217 ASP Chi-restraints excluded: chain U residue 2 TYR Chi-restraints excluded: chain U residue 8 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain V residue 657 ARG Chi-restraints excluded: chain V residue 668 ASP Chi-restraints excluded: chain V residue 677 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 956 random chunks: chunk 6 optimal weight: 0.7980 chunk 820 optimal weight: 8.9990 chunk 952 optimal weight: 5.9990 chunk 763 optimal weight: 6.9990 chunk 806 optimal weight: 4.9990 chunk 369 optimal weight: 30.0000 chunk 138 optimal weight: 0.7980 chunk 837 optimal weight: 9.9990 chunk 858 optimal weight: 50.0000 chunk 135 optimal weight: 2.9990 chunk 600 optimal weight: 1.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 269 HIS ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 GLN A 512 GLN A 587 ASN A 898 HIS A1025 ASN A1090 ASN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1246 ASN A1344 HIS ** A1346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1595 ASN A1616 GLN A1659 GLN A1687 ASN C 68 HIS ** C 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 HIS ** C 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 261 ASN ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 83 ASN ** q 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 96 GLN r 99 GLN ** r 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 27 GLN c 64 ASN I 505 ASN I 723 HIS P 212 GLN N 29 GLN R 80 GLN S 30 ASN W 126 ASN W 198 GLN L 779 HIS K 141 GLN ** K 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4989 r_free = 0.4989 target = 0.279723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.250226 restraints weight = 85015.224| |-----------------------------------------------------------------------------| r_work (start): 0.4743 rms_B_bonded: 1.71 r_work: 0.4468 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.4439 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.4439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6139 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 75153 Z= 0.332 Angle : 0.735 13.197 103334 Z= 0.382 Chirality : 0.047 0.292 11959 Planarity : 0.006 0.095 12679 Dihedral : 17.858 179.855 14603 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.46 % Favored : 95.45 % Rotamer: Outliers : 9.22 % Allowed : 29.45 % Favored : 61.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.08), residues: 9287 helix: 0.15 (0.08), residues: 4300 sheet: -0.91 (0.15), residues: 1104 loop : -1.51 (0.10), residues: 3883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP A1701 HIS 0.013 0.001 HIS W 128 PHE 0.027 0.002 PHE A 962 TYR 0.030 0.002 TYR J 272 ARG 0.010 0.001 ARG J 273 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18574 Ramachandran restraints generated. 9287 Oldfield, 0 Emsley, 9287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18574 Ramachandran restraints generated. 9287 Oldfield, 0 Emsley, 9287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1205 residues out of total 8096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 541 poor density : 664 time to evaluate : 5.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.7919 (ptt90) cc_final: 0.7617 (ptm160) REVERT: A 252 MET cc_start: 0.8493 (ttp) cc_final: 0.8078 (mtp) REVERT: A 276 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7920 (ptmt) REVERT: A 331 ILE cc_start: 0.4613 (OUTLIER) cc_final: 0.4130 (pp) REVERT: A 386 ARG cc_start: 0.4254 (OUTLIER) cc_final: 0.2971 (mpp80) REVERT: A 498 HIS cc_start: 0.4917 (OUTLIER) cc_final: 0.4030 (t-90) REVERT: A 1215 ARG cc_start: 0.7873 (mtt-85) cc_final: 0.7631 (mtp180) REVERT: A 1224 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8626 (mtt180) REVERT: A 1266 MET cc_start: 0.6815 (ttm) cc_final: 0.6494 (ttp) REVERT: A 1278 TRP cc_start: 0.8927 (m-10) cc_final: 0.8543 (m-10) REVERT: A 1362 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.6482 (tpt90) REVERT: A 1384 LYS cc_start: 0.7583 (mttt) cc_final: 0.7368 (mtpt) REVERT: A 1417 PHE cc_start: 0.4717 (OUTLIER) cc_final: 0.4456 (p90) REVERT: A 1435 TYR cc_start: 0.8010 (m-80) cc_final: 0.7638 (m-80) REVERT: A 1480 ILE cc_start: 0.6846 (OUTLIER) cc_final: 0.6454 (tp) REVERT: A 1491 ARG cc_start: 0.7455 (OUTLIER) cc_final: 0.7151 (mmp-170) REVERT: A 1626 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.8220 (mtm) REVERT: A 1658 CYS cc_start: 0.5497 (OUTLIER) cc_final: 0.5191 (t) REVERT: A 1708 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7092 (tt) REVERT: A 1789 LEU cc_start: 0.4159 (OUTLIER) cc_final: 0.3572 (tp) REVERT: A 1808 ARG cc_start: 0.7181 (mtt-85) cc_final: 0.6939 (mtt90) REVERT: C 69 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6200 (tp30) REVERT: C 106 LYS cc_start: 0.4955 (OUTLIER) cc_final: 0.4599 (mmtt) REVERT: C 177 GLN cc_start: 0.4645 (OUTLIER) cc_final: 0.4079 (tt0) REVERT: C 188 GLN cc_start: 0.6518 (tp40) cc_final: 0.6208 (tm-30) REVERT: C 216 LEU cc_start: 0.5561 (OUTLIER) cc_final: 0.4969 (mt) REVERT: C 488 ARG cc_start: 0.4021 (OUTLIER) cc_final: 0.2970 (mtt90) REVERT: C 527 LEU cc_start: 0.4174 (OUTLIER) cc_final: 0.3365 (mp) REVERT: C 550 TYR cc_start: 0.4150 (OUTLIER) cc_final: 0.3734 (t80) REVERT: C 639 GLU cc_start: 0.1672 (OUTLIER) cc_final: 0.0768 (pm20) REVERT: C 643 GLU cc_start: 0.3759 (OUTLIER) cc_final: 0.2816 (tm-30) REVERT: C 725 ASP cc_start: 0.3598 (OUTLIER) cc_final: 0.3302 (p0) REVERT: C 763 LEU cc_start: 0.1517 (OUTLIER) cc_final: 0.0887 (mt) REVERT: E 228 ASP cc_start: 0.5312 (OUTLIER) cc_final: 0.4834 (t0) REVERT: E 337 VAL cc_start: 0.4297 (OUTLIER) cc_final: 0.3821 (t) REVERT: E 342 LYS cc_start: 0.6709 (OUTLIER) cc_final: 0.5730 (mmtt) REVERT: r 12 GLN cc_start: 0.3115 (OUTLIER) cc_final: 0.2884 (pm20) REVERT: r 84 MET cc_start: 0.2246 (tpt) cc_final: 0.1474 (mpp) REVERT: r 95 HIS cc_start: 0.1234 (OUTLIER) cc_final: 0.0577 (m170) REVERT: a 19 GLU cc_start: 0.4260 (OUTLIER) cc_final: 0.3434 (mp0) REVERT: a 56 ARG cc_start: 0.4038 (OUTLIER) cc_final: 0.3126 (mtm110) REVERT: a 82 LEU cc_start: 0.5851 (OUTLIER) cc_final: 0.5306 (mp) REVERT: g 70 LEU cc_start: 0.2200 (OUTLIER) cc_final: 0.1357 (mp) REVERT: e 49 MET cc_start: 0.1675 (mmt) cc_final: 0.0471 (mtt) REVERT: e 55 GLU cc_start: 0.4118 (OUTLIER) cc_final: 0.3794 (tm-30) REVERT: d 68 GLU cc_start: 0.2409 (OUTLIER) cc_final: 0.1090 (pp20) REVERT: c 1 MET cc_start: 0.3314 (mtt) cc_final: 0.2437 (tmm) REVERT: I 344 ASN cc_start: 0.3149 (OUTLIER) cc_final: 0.2888 (m-40) REVERT: I 370 ARG cc_start: 0.3505 (OUTLIER) cc_final: 0.2011 (mmt180) REVERT: I 380 HIS cc_start: -0.0873 (m170) cc_final: -0.1121 (m-70) REVERT: I 417 TRP cc_start: 0.1087 (m100) cc_final: 0.0672 (m-90) REVERT: I 424 TYR cc_start: 0.0222 (m-10) cc_final: -0.0475 (m-10) REVERT: I 461 MET cc_start: 0.0558 (tmm) cc_final: -0.0089 (ptp) REVERT: I 487 ARG cc_start: 0.2827 (OUTLIER) cc_final: 0.1799 (pmt170) REVERT: I 492 GLU cc_start: 0.4415 (mm-30) cc_final: 0.3411 (pp20) REVERT: I 574 HIS cc_start: 0.2783 (OUTLIER) cc_final: 0.1770 (m-70) REVERT: I 601 LEU cc_start: 0.1501 (OUTLIER) cc_final: 0.1024 (mp) REVERT: I 625 GLU cc_start: 0.3007 (OUTLIER) cc_final: 0.1645 (pt0) REVERT: I 650 ARG cc_start: 0.1871 (mtt180) cc_final: 0.1654 (ttp80) REVERT: I 679 GLU cc_start: 0.1340 (OUTLIER) cc_final: 0.1052 (pp20) REVERT: I 748 LYS cc_start: 0.5058 (mmmt) cc_final: 0.4537 (ptpp) REVERT: I 750 MET cc_start: 0.2217 (mtp) cc_final: 0.1252 (mmt) REVERT: J 71 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.7232 (ptp90) REVERT: M 510 LYS cc_start: 0.4689 (OUTLIER) cc_final: 0.3955 (tmmt) REVERT: T 469 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8262 (mt) REVERT: T 498 ASP cc_start: 0.5380 (OUTLIER) cc_final: 0.5044 (p0) REVERT: O 264 MET cc_start: 0.0886 (pmm) cc_final: 0.0453 (pmt) REVERT: N 6 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.8067 (pttt) REVERT: N 21 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6559 (tm-30) REVERT: N 52 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8139 (ttp-170) REVERT: R 154 SER cc_start: 0.7566 (t) cc_final: 0.7350 (m) REVERT: R 205 LYS cc_start: 0.7550 (OUTLIER) cc_final: 0.6830 (mptt) REVERT: R 259 LYS cc_start: 0.7038 (ttmm) cc_final: 0.6623 (tttm) REVERT: R 292 ARG cc_start: 0.6186 (OUTLIER) cc_final: 0.5416 (tpp-160) REVERT: S 9 ASP cc_start: 0.6385 (OUTLIER) cc_final: 0.5990 (p0) REVERT: S 81 ASP cc_start: 0.4137 (t70) cc_final: 0.3919 (t70) REVERT: W 77 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7898 (mt) REVERT: W 202 SER cc_start: 0.6549 (OUTLIER) cc_final: 0.6267 (p) REVERT: L 545 ARG cc_start: 0.2917 (OUTLIER) cc_final: 0.2536 (mtt180) REVERT: L 601 GLU cc_start: 0.3073 (OUTLIER) cc_final: 0.2790 (mm-30) REVERT: L 608 MET cc_start: 0.2489 (ptp) cc_final: 0.1299 (mmt) REVERT: L 614 HIS cc_start: 0.1798 (OUTLIER) cc_final: 0.1018 (t-90) REVERT: L 650 GLU cc_start: 0.2441 (OUTLIER) cc_final: 0.1540 (tt0) REVERT: L 688 HIS cc_start: 0.0101 (OUTLIER) cc_final: -0.0672 (t-170) REVERT: L 776 LYS cc_start: 0.5707 (ttpp) cc_final: 0.5202 (tptm) REVERT: L 817 ARG cc_start: 0.4144 (OUTLIER) cc_final: 0.3278 (mmp80) REVERT: K 59 THR cc_start: 0.3882 (OUTLIER) cc_final: 0.3607 (p) REVERT: K 104 TYR cc_start: 0.0428 (OUTLIER) cc_final: -0.0155 (t80) REVERT: K 113 ARG cc_start: 0.3578 (OUTLIER) cc_final: 0.2844 (ttm-80) REVERT: K 144 LEU cc_start: 0.4178 (OUTLIER) cc_final: 0.3910 (tm) REVERT: K 145 LEU cc_start: 0.2649 (OUTLIER) cc_final: 0.2345 (pp) REVERT: K 146 LYS cc_start: 0.2904 (OUTLIER) cc_final: 0.2139 (pptt) REVERT: V 678 LYS cc_start: 0.4750 (OUTLIER) cc_final: 0.3315 (ptpt) outliers start: 541 outliers final: 239 residues processed: 1121 average time/residue: 1.4605 time to fit residues: 2185.5409 Evaluate side-chains 910 residues out of total 8096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 306 poor density : 604 time to evaluate : 5.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 493 CYS Chi-restraints excluded: chain A residue 498 HIS Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 544 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 550 GLU Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 909 ARG Chi-restraints excluded: chain A residue 923 SER Chi-restraints excluded: chain A residue 978 LEU Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1026 VAL Chi-restraints excluded: chain A residue 1059 ARG Chi-restraints excluded: chain A residue 1087 SER Chi-restraints excluded: chain A residue 1091 SER Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1131 CYS Chi-restraints excluded: chain A residue 1140 ASP Chi-restraints excluded: chain A residue 1153 SER Chi-restraints excluded: chain A residue 1224 ARG Chi-restraints excluded: chain A residue 1231 THR Chi-restraints excluded: chain A residue 1240 SER Chi-restraints excluded: chain A residue 1246 ASN Chi-restraints excluded: chain A residue 1285 THR Chi-restraints excluded: chain A residue 1289 THR Chi-restraints excluded: chain A residue 1307 ARG Chi-restraints excluded: chain A residue 1319 THR Chi-restraints excluded: chain A residue 1321 THR Chi-restraints excluded: chain A residue 1362 ARG Chi-restraints excluded: chain A residue 1365 ILE Chi-restraints excluded: chain A residue 1385 GLU Chi-restraints excluded: chain A residue 1402 SER Chi-restraints excluded: chain A residue 1417 PHE Chi-restraints excluded: chain A residue 1428 LEU Chi-restraints excluded: chain A residue 1447 GLU Chi-restraints excluded: chain A residue 1480 ILE Chi-restraints excluded: chain A residue 1491 ARG Chi-restraints excluded: chain A residue 1502 VAL Chi-restraints excluded: chain A residue 1511 ILE Chi-restraints excluded: chain A residue 1512 THR Chi-restraints excluded: chain A residue 1538 VAL Chi-restraints excluded: chain A residue 1545 VAL Chi-restraints excluded: chain A residue 1593 ILE Chi-restraints excluded: chain A residue 1605 THR Chi-restraints excluded: chain A residue 1626 MET Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1635 ILE Chi-restraints excluded: chain A residue 1658 CYS Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1712 THR Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1728 VAL Chi-restraints excluded: chain A residue 1747 LYS Chi-restraints excluded: chain A residue 1757 SER Chi-restraints excluded: chain A residue 1783 PHE Chi-restraints excluded: chain A residue 1786 ILE Chi-restraints excluded: chain A residue 1789 LEU Chi-restraints excluded: chain A residue 1807 LEU Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 106 LYS Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 257 ARG Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 306 CYS Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 488 ARG Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 550 TYR Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain C residue 600 GLN Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 639 GLU Chi-restraints excluded: chain C residue 643 GLU Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 725 ASP Chi-restraints excluded: chain C residue 726 MET Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 809 LEU Chi-restraints excluded: chain C residue 810 ASP Chi-restraints excluded: chain C residue 820 ARG Chi-restraints excluded: chain C residue 826 ILE Chi-restraints excluded: chain C residue 902 THR Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 79 CYS Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 200 PHE Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 306 CYS Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain E residue 333 SER Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 342 LYS Chi-restraints excluded: chain E residue 354 THR Chi-restraints excluded: chain q residue 46 SER Chi-restraints excluded: chain q residue 72 LEU Chi-restraints excluded: chain r residue 2 PHE Chi-restraints excluded: chain r residue 9 VAL Chi-restraints excluded: chain r residue 12 GLN Chi-restraints excluded: chain r residue 41 THR Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain r residue 63 THR Chi-restraints excluded: chain r residue 95 HIS Chi-restraints excluded: chain r residue 113 ARG Chi-restraints excluded: chain s residue 85 LEU Chi-restraints excluded: chain a residue 10 ILE Chi-restraints excluded: chain a residue 19 GLU Chi-restraints excluded: chain a residue 56 ARG Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 82 LEU Chi-restraints excluded: chain g residue 38 MET Chi-restraints excluded: chain g residue 70 LEU Chi-restraints excluded: chain e residue 55 GLU Chi-restraints excluded: chain e residue 72 ILE Chi-restraints excluded: chain f residue 22 ILE Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 48 SER Chi-restraints excluded: chain d residue 17 GLU Chi-restraints excluded: chain d residue 42 CYS Chi-restraints excluded: chain d residue 68 GLU Chi-restraints excluded: chain d residue 84 ARG Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 98 ARG Chi-restraints excluded: chain c residue 2 VAL Chi-restraints excluded: chain b residue 40 LEU Chi-restraints excluded: chain I residue 344 ASN Chi-restraints excluded: chain I residue 356 LEU Chi-restraints excluded: chain I residue 367 VAL Chi-restraints excluded: chain I residue 370 ARG Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain I residue 487 ARG Chi-restraints excluded: chain I residue 506 LEU Chi-restraints excluded: chain I residue 574 HIS Chi-restraints excluded: chain I residue 601 LEU Chi-restraints excluded: chain I residue 614 CYS Chi-restraints excluded: chain I residue 615 LYS Chi-restraints excluded: chain I residue 625 GLU Chi-restraints excluded: chain I residue 655 ASP Chi-restraints excluded: chain I residue 670 VAL Chi-restraints excluded: chain I residue 679 GLU Chi-restraints excluded: chain I residue 687 SER Chi-restraints excluded: chain I residue 702 GLU Chi-restraints excluded: chain I residue 746 THR Chi-restraints excluded: chain J residue 61 SER Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 71 ARG Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain J residue 144 ARG Chi-restraints excluded: chain J residue 202 PHE Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain P residue 13 ILE Chi-restraints excluded: chain P residue 231 GLN Chi-restraints excluded: chain M residue 447 GLN Chi-restraints excluded: chain M residue 496 VAL Chi-restraints excluded: chain M residue 510 LYS Chi-restraints excluded: chain T residue 190 ARG Chi-restraints excluded: chain T residue 212 CYS Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 286 SER Chi-restraints excluded: chain T residue 314 VAL Chi-restraints excluded: chain T residue 324 VAL Chi-restraints excluded: chain T residue 388 PHE Chi-restraints excluded: chain T residue 396 GLU Chi-restraints excluded: chain T residue 422 SER Chi-restraints excluded: chain T residue 446 ARG Chi-restraints excluded: chain T residue 465 SER Chi-restraints excluded: chain T residue 469 LEU Chi-restraints excluded: chain T residue 498 ASP Chi-restraints excluded: chain O residue 22 VAL Chi-restraints excluded: chain O residue 35 MET Chi-restraints excluded: chain O residue 38 ILE Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 71 GLN Chi-restraints excluded: chain O residue 165 VAL Chi-restraints excluded: chain O residue 184 HIS Chi-restraints excluded: chain O residue 206 ASN Chi-restraints excluded: chain O residue 224 THR Chi-restraints excluded: chain O residue 248 VAL Chi-restraints excluded: chain O residue 267 LYS Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 11 LYS Chi-restraints excluded: chain N residue 21 GLU Chi-restraints excluded: chain N residue 52 ARG Chi-restraints excluded: chain N residue 82 GLU Chi-restraints excluded: chain R residue 83 ILE Chi-restraints excluded: chain R residue 88 LYS Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 118 VAL Chi-restraints excluded: chain R residue 136 LYS Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 168 SER Chi-restraints excluded: chain R residue 195 ASP Chi-restraints excluded: chain R residue 205 LYS Chi-restraints excluded: chain R residue 211 VAL Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 231 THR Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain R residue 255 ILE Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain R residue 292 ARG Chi-restraints excluded: chain S residue 6 VAL Chi-restraints excluded: chain S residue 9 ASP Chi-restraints excluded: chain S residue 28 CYS Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain S residue 92 MET Chi-restraints excluded: chain S residue 146 VAL Chi-restraints excluded: chain S residue 152 ILE Chi-restraints excluded: chain W residue 77 LEU Chi-restraints excluded: chain W residue 81 ASP Chi-restraints excluded: chain W residue 87 LEU Chi-restraints excluded: chain W residue 91 HIS Chi-restraints excluded: chain W residue 107 VAL Chi-restraints excluded: chain W residue 112 ASP Chi-restraints excluded: chain W residue 118 ILE Chi-restraints excluded: chain W residue 121 GLU Chi-restraints excluded: chain W residue 167 THR Chi-restraints excluded: chain W residue 202 SER Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 161 THR Chi-restraints excluded: chain L residue 217 LEU Chi-restraints excluded: chain L residue 545 ARG Chi-restraints excluded: chain L residue 556 ILE Chi-restraints excluded: chain L residue 596 LEU Chi-restraints excluded: chain L residue 601 GLU Chi-restraints excluded: chain L residue 614 HIS Chi-restraints excluded: chain L residue 650 GLU Chi-restraints excluded: chain L residue 688 HIS Chi-restraints excluded: chain L residue 798 ASP Chi-restraints excluded: chain L residue 800 THR Chi-restraints excluded: chain L residue 806 ASP Chi-restraints excluded: chain L residue 817 ARG Chi-restraints excluded: chain K residue 28 HIS Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 104 TYR Chi-restraints excluded: chain K residue 113 ARG Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain K residue 145 LEU Chi-restraints excluded: chain K residue 146 LYS Chi-restraints excluded: chain K residue 217 ASP Chi-restraints excluded: chain U residue 2 TYR Chi-restraints excluded: chain U residue 8 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 23 LYS Chi-restraints excluded: chain V residue 668 ASP Chi-restraints excluded: chain V residue 678 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 956 random chunks: chunk 936 optimal weight: 7.9990 chunk 403 optimal weight: 6.9990 chunk 752 optimal weight: 20.0000 chunk 713 optimal weight: 50.0000 chunk 170 optimal weight: 0.9980 chunk 478 optimal weight: 20.0000 chunk 435 optimal weight: 10.0000 chunk 364 optimal weight: 5.9990 chunk 569 optimal weight: 0.7980 chunk 614 optimal weight: 0.1980 chunk 489 optimal weight: 7.9990 overall best weight: 2.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 269 HIS ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 476 ASN A 512 GLN A 587 ASN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1344 HIS ** A1346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1484 ASN A1729 GLN C 68 HIS ** C 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 83 ASN ** r 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 96 GLN r 99 GLN ** r 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 47 GLN ** d 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 505 ASN P 45 GLN P 212 GLN ** O 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 29 GLN R 80 GLN W 91 HIS W 198 GLN K 141 GLN ** K 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4984 r_free = 0.4984 target = 0.279266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.249767 restraints weight = 84703.135| |-----------------------------------------------------------------------------| r_work (start): 0.4739 rms_B_bonded: 1.63 r_work: 0.4470 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.4440 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.4440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6144 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 75153 Z= 0.397 Angle : 0.738 14.210 103334 Z= 0.381 Chirality : 0.048 0.287 11959 Planarity : 0.006 0.098 12679 Dihedral : 17.485 178.667 14452 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.08 % Favored : 94.84 % Rotamer: Outliers : 9.30 % Allowed : 29.38 % Favored : 61.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.09), residues: 9287 helix: 0.42 (0.08), residues: 4323 sheet: -0.84 (0.15), residues: 1101 loop : -1.40 (0.10), residues: 3863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP A1701 HIS 0.010 0.002 HIS W 128 PHE 0.030 0.002 PHE J 175 TYR 0.026 0.002 TYR A1751 ARG 0.011 0.001 ARG S 153 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18574 Ramachandran restraints generated. 9287 Oldfield, 0 Emsley, 9287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18574 Ramachandran restraints generated. 9287 Oldfield, 0 Emsley, 9287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1171 residues out of total 8096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 546 poor density : 625 time to evaluate : 5.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.7934 (ptt90) cc_final: 0.7655 (ptm160) REVERT: A 276 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7918 (ptmt) REVERT: A 331 ILE cc_start: 0.4678 (OUTLIER) cc_final: 0.4228 (pp) REVERT: A 498 HIS cc_start: 0.4875 (OUTLIER) cc_final: 0.4286 (t-90) REVERT: A 589 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.7510 (pttm) REVERT: A 809 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8709 (tm-30) REVERT: A 1233 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7299 (tp30) REVERT: A 1266 MET cc_start: 0.6826 (ttm) cc_final: 0.6465 (ttp) REVERT: A 1278 TRP cc_start: 0.8940 (m-10) cc_final: 0.8556 (m-10) REVERT: A 1362 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.6309 (tpp80) REVERT: A 1384 LYS cc_start: 0.7610 (mttt) cc_final: 0.7391 (mtpt) REVERT: A 1417 PHE cc_start: 0.4864 (OUTLIER) cc_final: 0.4595 (p90) REVERT: A 1435 TYR cc_start: 0.8000 (m-80) cc_final: 0.7675 (m-80) REVERT: A 1480 ILE cc_start: 0.7006 (OUTLIER) cc_final: 0.6600 (tp) REVERT: A 1626 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8229 (mtm) REVERT: A 1658 CYS cc_start: 0.5289 (OUTLIER) cc_final: 0.4988 (t) REVERT: A 1789 LEU cc_start: 0.4201 (OUTLIER) cc_final: 0.3691 (tp) REVERT: C 69 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6168 (tp30) REVERT: C 188 GLN cc_start: 0.6508 (tp40) cc_final: 0.6257 (tm-30) REVERT: C 216 LEU cc_start: 0.5555 (OUTLIER) cc_final: 0.4949 (mt) REVERT: C 257 ARG cc_start: 0.5493 (OUTLIER) cc_final: 0.4243 (mpt-90) REVERT: C 359 ARG cc_start: 0.2978 (OUTLIER) cc_final: 0.2067 (mtp85) REVERT: C 527 LEU cc_start: 0.4064 (OUTLIER) cc_final: 0.3285 (mp) REVERT: C 550 TYR cc_start: 0.4049 (OUTLIER) cc_final: 0.3569 (t80) REVERT: C 639 GLU cc_start: 0.1759 (OUTLIER) cc_final: 0.0932 (pm20) REVERT: C 725 ASP cc_start: 0.3624 (OUTLIER) cc_final: 0.3351 (p0) REVERT: C 763 LEU cc_start: 0.1479 (OUTLIER) cc_final: 0.0828 (mt) REVERT: C 789 TRP cc_start: 0.3154 (OUTLIER) cc_final: 0.2603 (t60) REVERT: E 54 LEU cc_start: 0.5730 (OUTLIER) cc_final: 0.5348 (mt) REVERT: E 228 ASP cc_start: 0.5403 (OUTLIER) cc_final: 0.4937 (t0) REVERT: E 330 HIS cc_start: 0.7781 (OUTLIER) cc_final: 0.7530 (m-70) REVERT: E 337 VAL cc_start: 0.4376 (OUTLIER) cc_final: 0.3796 (t) REVERT: E 342 LYS cc_start: 0.6715 (OUTLIER) cc_final: 0.5765 (mmtt) REVERT: r 84 MET cc_start: 0.2340 (tpt) cc_final: 0.1531 (mpp) REVERT: r 95 HIS cc_start: 0.1257 (OUTLIER) cc_final: 0.0554 (m170) REVERT: a 56 ARG cc_start: 0.4137 (OUTLIER) cc_final: 0.3193 (mtm110) REVERT: a 82 LEU cc_start: 0.5859 (OUTLIER) cc_final: 0.5348 (mp) REVERT: g 70 LEU cc_start: 0.2068 (OUTLIER) cc_final: 0.1238 (mp) REVERT: e 49 MET cc_start: 0.1599 (mmt) cc_final: 0.0557 (mtt) REVERT: e 55 GLU cc_start: 0.4124 (OUTLIER) cc_final: 0.3777 (tm-30) REVERT: e 61 MET cc_start: 0.2453 (OUTLIER) cc_final: 0.0527 (ppp) REVERT: e 66 ARG cc_start: 0.3822 (OUTLIER) cc_final: 0.2894 (ttm170) REVERT: d 68 GLU cc_start: 0.2502 (OUTLIER) cc_final: 0.1156 (pp20) REVERT: c 1 MET cc_start: 0.3424 (mtt) cc_final: 0.2484 (tmm) REVERT: c 9 MET cc_start: 0.1772 (mmt) cc_final: 0.0258 (tmm) REVERT: c 10 LYS cc_start: 0.3819 (OUTLIER) cc_final: 0.2452 (tptp) REVERT: c 49 ARG cc_start: 0.3501 (OUTLIER) cc_final: 0.2277 (tpt170) REVERT: c 75 LEU cc_start: 0.1339 (OUTLIER) cc_final: 0.0825 (mt) REVERT: I 417 TRP cc_start: 0.1050 (m100) cc_final: 0.0663 (m-90) REVERT: I 461 MET cc_start: 0.0660 (tmm) cc_final: 0.0024 (ptm) REVERT: I 473 ASP cc_start: 0.2661 (OUTLIER) cc_final: 0.2213 (t70) REVERT: I 492 GLU cc_start: 0.4472 (mm-30) cc_final: 0.3435 (pp20) REVERT: I 574 HIS cc_start: 0.2813 (OUTLIER) cc_final: 0.1818 (m-70) REVERT: I 625 GLU cc_start: 0.2848 (OUTLIER) cc_final: 0.1567 (pt0) REVERT: I 679 GLU cc_start: 0.1356 (mt-10) cc_final: 0.1102 (pp20) REVERT: I 748 LYS cc_start: 0.5092 (mmmt) cc_final: 0.4553 (ptpp) REVERT: I 750 MET cc_start: 0.2162 (mtp) cc_final: 0.0677 (mmp) REVERT: J 71 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.7113 (ptp90) REVERT: P 62 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7818 (mt-10) REVERT: M 510 LYS cc_start: 0.4503 (OUTLIER) cc_final: 0.3633 (pptt) REVERT: T 469 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8308 (mt) REVERT: O 264 MET cc_start: 0.0831 (OUTLIER) cc_final: 0.0369 (pmt) REVERT: N 6 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.8080 (pttt) REVERT: N 21 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6507 (tm-30) REVERT: N 52 ARG cc_start: 0.9074 (OUTLIER) cc_final: 0.8171 (ttp-170) REVERT: N 82 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7212 (mp0) REVERT: R 191 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8211 (mm) REVERT: R 205 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.6893 (mptt) REVERT: R 259 LYS cc_start: 0.7046 (ttmm) cc_final: 0.6651 (tttm) REVERT: S 9 ASP cc_start: 0.6579 (OUTLIER) cc_final: 0.6042 (p0) REVERT: W 77 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7769 (mt) REVERT: W 202 SER cc_start: 0.6465 (m) cc_final: 0.6249 (p) REVERT: L 150 MET cc_start: 0.6360 (ttm) cc_final: 0.6008 (tmm) REVERT: L 188 ARG cc_start: 0.4168 (OUTLIER) cc_final: 0.3965 (ttp-170) REVERT: L 241 ARG cc_start: 0.2946 (OUTLIER) cc_final: 0.2456 (pmt170) REVERT: L 601 GLU cc_start: 0.3160 (OUTLIER) cc_final: 0.2787 (mm-30) REVERT: L 608 MET cc_start: 0.2474 (ptp) cc_final: 0.1313 (mmt) REVERT: L 614 HIS cc_start: 0.1748 (OUTLIER) cc_final: 0.0938 (t-90) REVERT: L 650 GLU cc_start: 0.2633 (OUTLIER) cc_final: 0.1689 (tt0) REVERT: L 688 HIS cc_start: 0.0690 (OUTLIER) cc_final: -0.0434 (t-170) REVERT: L 776 LYS cc_start: 0.5641 (ttpp) cc_final: 0.5126 (tptm) REVERT: L 817 ARG cc_start: 0.4171 (OUTLIER) cc_final: 0.3517 (mmp80) REVERT: K 28 HIS cc_start: 0.4158 (OUTLIER) cc_final: 0.2583 (p-80) REVERT: K 104 TYR cc_start: 0.0381 (OUTLIER) cc_final: -0.0182 (t80) REVERT: K 113 ARG cc_start: 0.3551 (OUTLIER) cc_final: 0.2851 (ttm-80) REVERT: K 145 LEU cc_start: 0.2506 (OUTLIER) cc_final: 0.2253 (pp) REVERT: K 146 LYS cc_start: 0.2756 (OUTLIER) cc_final: 0.2366 (pptt) outliers start: 546 outliers final: 267 residues processed: 1087 average time/residue: 1.4278 time to fit residues: 2082.4143 Evaluate side-chains 918 residues out of total 8096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 332 poor density : 586 time to evaluate : 5.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 493 CYS Chi-restraints excluded: chain A residue 498 HIS Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain A residue 544 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 589 LYS Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 809 GLN Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 909 ARG Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 923 SER Chi-restraints excluded: chain A residue 954 SER Chi-restraints excluded: chain A residue 978 LEU Chi-restraints excluded: chain A residue 995 ASP Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1026 VAL Chi-restraints excluded: chain A residue 1038 VAL Chi-restraints excluded: chain A residue 1059 ARG Chi-restraints excluded: chain A residue 1087 SER Chi-restraints excluded: chain A residue 1091 SER Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1131 CYS Chi-restraints excluded: chain A residue 1140 ASP Chi-restraints excluded: chain A residue 1153 SER Chi-restraints excluded: chain A residue 1231 THR Chi-restraints excluded: chain A residue 1233 GLU Chi-restraints excluded: chain A residue 1240 SER Chi-restraints excluded: chain A residue 1285 THR Chi-restraints excluded: chain A residue 1289 THR Chi-restraints excluded: chain A residue 1307 ARG Chi-restraints excluded: chain A residue 1319 THR Chi-restraints excluded: chain A residue 1321 THR Chi-restraints excluded: chain A residue 1351 LEU Chi-restraints excluded: chain A residue 1362 ARG Chi-restraints excluded: chain A residue 1365 ILE Chi-restraints excluded: chain A residue 1385 GLU Chi-restraints excluded: chain A residue 1402 SER Chi-restraints excluded: chain A residue 1417 PHE Chi-restraints excluded: chain A residue 1428 LEU Chi-restraints excluded: chain A residue 1480 ILE Chi-restraints excluded: chain A residue 1493 THR Chi-restraints excluded: chain A residue 1502 VAL Chi-restraints excluded: chain A residue 1511 ILE Chi-restraints excluded: chain A residue 1512 THR Chi-restraints excluded: chain A residue 1538 VAL Chi-restraints excluded: chain A residue 1545 VAL Chi-restraints excluded: chain A residue 1557 THR Chi-restraints excluded: chain A residue 1605 THR Chi-restraints excluded: chain A residue 1626 MET Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1635 ILE Chi-restraints excluded: chain A residue 1658 CYS Chi-restraints excluded: chain A residue 1712 THR Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1728 VAL Chi-restraints excluded: chain A residue 1747 LYS Chi-restraints excluded: chain A residue 1757 SER Chi-restraints excluded: chain A residue 1783 PHE Chi-restraints excluded: chain A residue 1786 ILE Chi-restraints excluded: chain A residue 1789 LEU Chi-restraints excluded: chain A residue 1807 LEU Chi-restraints excluded: chain A residue 1820 SER Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 257 ARG Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 306 CYS Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 550 TYR Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 600 GLN Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 639 GLU Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 725 ASP Chi-restraints excluded: chain C residue 726 MET Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 789 TRP Chi-restraints excluded: chain C residue 797 CYS Chi-restraints excluded: chain C residue 809 LEU Chi-restraints excluded: chain C residue 810 ASP Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 820 ARG Chi-restraints excluded: chain C residue 826 ILE Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 874 VAL Chi-restraints excluded: chain C residue 902 THR Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 79 CYS Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 200 PHE Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 306 CYS Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain E residue 330 HIS Chi-restraints excluded: chain E residue 333 SER Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 342 LYS Chi-restraints excluded: chain E residue 354 THR Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain q residue 46 SER Chi-restraints excluded: chain q residue 72 LEU Chi-restraints excluded: chain r residue 2 PHE Chi-restraints excluded: chain r residue 9 VAL Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain r residue 41 THR Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain r residue 95 HIS Chi-restraints excluded: chain r residue 101 LEU Chi-restraints excluded: chain s residue 132 MET Chi-restraints excluded: chain a residue 19 GLU Chi-restraints excluded: chain a residue 56 ARG Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 82 LEU Chi-restraints excluded: chain g residue 38 MET Chi-restraints excluded: chain g residue 70 LEU Chi-restraints excluded: chain e residue 37 ARG Chi-restraints excluded: chain e residue 55 GLU Chi-restraints excluded: chain e residue 61 MET Chi-restraints excluded: chain e residue 66 ARG Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain f residue 22 ILE Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 48 SER Chi-restraints excluded: chain d residue 42 CYS Chi-restraints excluded: chain d residue 51 ARG Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 68 GLU Chi-restraints excluded: chain d residue 80 GLN Chi-restraints excluded: chain d residue 84 ARG Chi-restraints excluded: chain c residue 2 VAL Chi-restraints excluded: chain c residue 10 LYS Chi-restraints excluded: chain c residue 49 ARG Chi-restraints excluded: chain c residue 75 LEU Chi-restraints excluded: chain c residue 79 THR Chi-restraints excluded: chain b residue 36 ARG Chi-restraints excluded: chain b residue 40 LEU Chi-restraints excluded: chain b residue 105 ILE Chi-restraints excluded: chain I residue 356 LEU Chi-restraints excluded: chain I residue 367 VAL Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain I residue 473 ASP Chi-restraints excluded: chain I residue 574 HIS Chi-restraints excluded: chain I residue 614 CYS Chi-restraints excluded: chain I residue 625 GLU Chi-restraints excluded: chain I residue 670 VAL Chi-restraints excluded: chain I residue 687 SER Chi-restraints excluded: chain I residue 702 GLU Chi-restraints excluded: chain I residue 737 PHE Chi-restraints excluded: chain I residue 746 THR Chi-restraints excluded: chain J residue 61 SER Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 71 ARG Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain J residue 144 ARG Chi-restraints excluded: chain J residue 196 ASP Chi-restraints excluded: chain J residue 202 PHE Chi-restraints excluded: chain J residue 228 VAL Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain J residue 318 GLU Chi-restraints excluded: chain P residue 13 ILE Chi-restraints excluded: chain P residue 231 GLN Chi-restraints excluded: chain M residue 496 VAL Chi-restraints excluded: chain M residue 510 LYS Chi-restraints excluded: chain T residue 190 ARG Chi-restraints excluded: chain T residue 212 CYS Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 286 SER Chi-restraints excluded: chain T residue 292 SER Chi-restraints excluded: chain T residue 314 VAL Chi-restraints excluded: chain T residue 324 VAL Chi-restraints excluded: chain T residue 388 PHE Chi-restraints excluded: chain T residue 396 GLU Chi-restraints excluded: chain T residue 422 SER Chi-restraints excluded: chain T residue 446 ARG Chi-restraints excluded: chain T residue 465 SER Chi-restraints excluded: chain T residue 469 LEU Chi-restraints excluded: chain O residue 22 VAL Chi-restraints excluded: chain O residue 35 MET Chi-restraints excluded: chain O residue 38 ILE Chi-restraints excluded: chain O residue 49 ARG Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 71 GLN Chi-restraints excluded: chain O residue 165 VAL Chi-restraints excluded: chain O residue 184 HIS Chi-restraints excluded: chain O residue 224 THR Chi-restraints excluded: chain O residue 248 VAL Chi-restraints excluded: chain O residue 264 MET Chi-restraints excluded: chain O residue 267 LYS Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 11 LYS Chi-restraints excluded: chain N residue 21 GLU Chi-restraints excluded: chain N residue 52 ARG Chi-restraints excluded: chain N residue 82 GLU Chi-restraints excluded: chain R residue 83 ILE Chi-restraints excluded: chain R residue 88 LYS Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 118 VAL Chi-restraints excluded: chain R residue 152 LYS Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 168 SER Chi-restraints excluded: chain R residue 191 ILE Chi-restraints excluded: chain R residue 195 ASP Chi-restraints excluded: chain R residue 205 LYS Chi-restraints excluded: chain R residue 211 VAL Chi-restraints excluded: chain R residue 220 VAL Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 231 THR Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain R residue 255 ILE Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain S residue 6 VAL Chi-restraints excluded: chain S residue 9 ASP Chi-restraints excluded: chain S residue 28 CYS Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain S residue 92 MET Chi-restraints excluded: chain S residue 134 LEU Chi-restraints excluded: chain S residue 146 VAL Chi-restraints excluded: chain W residue 77 LEU Chi-restraints excluded: chain W residue 81 ASP Chi-restraints excluded: chain W residue 87 LEU Chi-restraints excluded: chain W residue 91 HIS Chi-restraints excluded: chain W residue 107 VAL Chi-restraints excluded: chain W residue 112 ASP Chi-restraints excluded: chain W residue 118 ILE Chi-restraints excluded: chain W residue 121 GLU Chi-restraints excluded: chain W residue 167 THR Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 161 THR Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain L residue 188 ARG Chi-restraints excluded: chain L residue 207 VAL Chi-restraints excluded: chain L residue 217 LEU Chi-restraints excluded: chain L residue 241 ARG Chi-restraints excluded: chain L residue 601 GLU Chi-restraints excluded: chain L residue 614 HIS Chi-restraints excluded: chain L residue 650 GLU Chi-restraints excluded: chain L residue 688 HIS Chi-restraints excluded: chain L residue 798 ASP Chi-restraints excluded: chain L residue 800 THR Chi-restraints excluded: chain L residue 817 ARG Chi-restraints excluded: chain K residue 28 HIS Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 66 LEU Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 104 TYR Chi-restraints excluded: chain K residue 113 ARG Chi-restraints excluded: chain K residue 145 LEU Chi-restraints excluded: chain K residue 146 LYS Chi-restraints excluded: chain K residue 217 ASP Chi-restraints excluded: chain U residue 2 TYR Chi-restraints excluded: chain U residue 8 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 23 LYS Chi-restraints excluded: chain V residue 668 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 956 random chunks: chunk 780 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 78 optimal weight: 8.9990 chunk 859 optimal weight: 9.9990 chunk 353 optimal weight: 20.0000 chunk 728 optimal weight: 20.0000 chunk 285 optimal weight: 7.9990 chunk 264 optimal weight: 10.0000 chunk 222 optimal weight: 0.0670 chunk 833 optimal weight: 6.9990 chunk 913 optimal weight: 50.0000 overall best weight: 4.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 269 HIS ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 HIS A 512 GLN ** A 939 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1246 ASN ** A1346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1729 GLN C 68 HIS ** C 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 96 GLN r 99 GLN ** s 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 108 HIS a 47 GLN ** d 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 28 GLN P 45 GLN P 212 GLN ** O 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 80 GLN W 198 GLN K 141 GLN ** K 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4973 r_free = 0.4973 target = 0.278032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.247160 restraints weight = 84430.418| |-----------------------------------------------------------------------------| r_work (start): 0.4716 rms_B_bonded: 1.76 r_work: 0.4452 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.4419 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.4419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6189 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.111 75153 Z= 0.525 Angle : 0.787 13.674 103334 Z= 0.407 Chirality : 0.051 0.337 11959 Planarity : 0.006 0.094 12679 Dihedral : 17.441 178.211 14401 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.57 % Favored : 94.36 % Rotamer: Outliers : 9.59 % Allowed : 29.00 % Favored : 61.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.09), residues: 9287 helix: 0.38 (0.08), residues: 4342 sheet: -0.87 (0.15), residues: 1098 loop : -1.43 (0.10), residues: 3847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.003 TRP A1701 HIS 0.010 0.002 HIS C 145 PHE 0.034 0.003 PHE A 962 TYR 0.026 0.002 TYR A1751 ARG 0.011 0.001 ARG C 905 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18574 Ramachandran restraints generated. 9287 Oldfield, 0 Emsley, 9287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18574 Ramachandran restraints generated. 9287 Oldfield, 0 Emsley, 9287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1182 residues out of total 8096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 563 poor density : 619 time to evaluate : 5.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.7999 (ptt90) cc_final: 0.7727 (ptm160) REVERT: A 252 MET cc_start: 0.8427 (ttp) cc_final: 0.8125 (ttp) REVERT: A 276 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7982 (ptmt) REVERT: A 331 ILE cc_start: 0.4435 (OUTLIER) cc_final: 0.4022 (pp) REVERT: A 498 HIS cc_start: 0.4902 (OUTLIER) cc_final: 0.4297 (t-90) REVERT: A 526 ARG cc_start: 0.5393 (OUTLIER) cc_final: 0.4112 (ttp-170) REVERT: A 589 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.7537 (pttm) REVERT: A 800 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7931 (tt0) REVERT: A 802 MET cc_start: 0.8858 (ttp) cc_final: 0.8649 (ttp) REVERT: A 1046 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6933 (mm-30) REVERT: A 1233 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7372 (tp30) REVERT: A 1266 MET cc_start: 0.7039 (ttm) cc_final: 0.6816 (ttm) REVERT: A 1278 TRP cc_start: 0.8953 (m-10) cc_final: 0.8527 (m-10) REVERT: A 1362 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.6708 (tpp80) REVERT: A 1384 LYS cc_start: 0.7612 (mttt) cc_final: 0.7393 (mtpt) REVERT: A 1465 ARG cc_start: 0.4640 (OUTLIER) cc_final: 0.4226 (tmm-80) REVERT: A 1480 ILE cc_start: 0.7259 (OUTLIER) cc_final: 0.6911 (tp) REVERT: A 1626 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.8262 (mtm) REVERT: A 1627 HIS cc_start: 0.8847 (OUTLIER) cc_final: 0.8408 (m-70) REVERT: A 1658 CYS cc_start: 0.5525 (OUTLIER) cc_final: 0.5192 (t) REVERT: A 1742 ARG cc_start: 0.7228 (ttp-170) cc_final: 0.6992 (ttp-170) REVERT: A 1783 PHE cc_start: 0.3187 (OUTLIER) cc_final: 0.1765 (p90) REVERT: A 1789 LEU cc_start: 0.4261 (OUTLIER) cc_final: 0.3736 (tp) REVERT: C 69 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6355 (tp30) REVERT: C 177 GLN cc_start: 0.4258 (OUTLIER) cc_final: 0.3733 (tt0) REVERT: C 188 GLN cc_start: 0.6590 (tp40) cc_final: 0.6302 (tm-30) REVERT: C 216 LEU cc_start: 0.5653 (OUTLIER) cc_final: 0.5009 (mt) REVERT: C 359 ARG cc_start: 0.3073 (OUTLIER) cc_final: 0.2786 (mmt180) REVERT: C 550 TYR cc_start: 0.4155 (OUTLIER) cc_final: 0.3580 (t80) REVERT: C 639 GLU cc_start: 0.1458 (OUTLIER) cc_final: 0.0818 (pm20) REVERT: C 643 GLU cc_start: 0.3442 (OUTLIER) cc_final: 0.2754 (tm-30) REVERT: C 725 ASP cc_start: 0.3521 (OUTLIER) cc_final: 0.3269 (p0) REVERT: C 763 LEU cc_start: 0.1456 (OUTLIER) cc_final: 0.0797 (mt) REVERT: C 789 TRP cc_start: 0.3119 (OUTLIER) cc_final: 0.2593 (t60) REVERT: C 892 LEU cc_start: 0.5768 (OUTLIER) cc_final: 0.5348 (tt) REVERT: E 54 LEU cc_start: 0.5722 (OUTLIER) cc_final: 0.5315 (mt) REVERT: E 200 PHE cc_start: 0.4611 (OUTLIER) cc_final: 0.3736 (t80) REVERT: E 228 ASP cc_start: 0.5658 (OUTLIER) cc_final: 0.4970 (t0) REVERT: E 330 HIS cc_start: 0.7773 (OUTLIER) cc_final: 0.7495 (m-70) REVERT: E 337 VAL cc_start: 0.4590 (OUTLIER) cc_final: 0.4044 (t) REVERT: E 342 LYS cc_start: 0.6726 (OUTLIER) cc_final: 0.5801 (mmtt) REVERT: r 84 MET cc_start: 0.2274 (tpt) cc_final: 0.1483 (mpp) REVERT: r 95 HIS cc_start: 0.1290 (OUTLIER) cc_final: 0.0633 (m170) REVERT: t 123 ASP cc_start: 0.1920 (OUTLIER) cc_final: 0.1309 (t70) REVERT: a 44 MET cc_start: 0.5936 (OUTLIER) cc_final: 0.5080 (tmm) REVERT: a 56 ARG cc_start: 0.4119 (OUTLIER) cc_final: 0.3078 (mtm110) REVERT: a 82 LEU cc_start: 0.6111 (OUTLIER) cc_final: 0.5603 (mp) REVERT: g 48 GLU cc_start: 0.4445 (OUTLIER) cc_final: 0.3356 (tm-30) REVERT: g 70 LEU cc_start: 0.2163 (OUTLIER) cc_final: 0.1336 (mp) REVERT: e 9 MET cc_start: 0.2842 (ttt) cc_final: 0.1586 (pmm) REVERT: e 49 MET cc_start: 0.0892 (mmt) cc_final: -0.0064 (mtt) REVERT: e 55 GLU cc_start: 0.3961 (OUTLIER) cc_final: 0.3496 (tm-30) REVERT: d 22 THR cc_start: 0.3393 (OUTLIER) cc_final: 0.3157 (p) REVERT: d 68 GLU cc_start: 0.2614 (OUTLIER) cc_final: 0.1209 (pp20) REVERT: c 1 MET cc_start: 0.3396 (mtt) cc_final: 0.2474 (tmm) REVERT: c 9 MET cc_start: 0.1430 (mmp) cc_final: 0.0411 (ttm) REVERT: c 10 LYS cc_start: 0.3808 (OUTLIER) cc_final: 0.2437 (tptp) REVERT: c 49 ARG cc_start: 0.3765 (OUTLIER) cc_final: 0.3560 (tpt170) REVERT: c 75 LEU cc_start: 0.1132 (OUTLIER) cc_final: 0.0504 (mt) REVERT: b 32 MET cc_start: 0.3935 (mmm) cc_final: 0.3613 (mmm) REVERT: I 417 TRP cc_start: 0.0929 (m100) cc_final: 0.0453 (m-90) REVERT: I 424 TYR cc_start: 0.0503 (m-10) cc_final: -0.0173 (m-10) REVERT: I 456 CYS cc_start: 0.3365 (OUTLIER) cc_final: 0.2867 (m) REVERT: I 461 MET cc_start: 0.0648 (tmm) cc_final: 0.0086 (ptp) REVERT: I 473 ASP cc_start: 0.2546 (OUTLIER) cc_final: 0.2163 (t70) REVERT: I 487 ARG cc_start: 0.2908 (OUTLIER) cc_final: 0.1764 (pmt170) REVERT: I 492 GLU cc_start: 0.4603 (mm-30) cc_final: 0.3502 (pp20) REVERT: I 574 HIS cc_start: 0.2748 (OUTLIER) cc_final: 0.1764 (m-70) REVERT: I 625 GLU cc_start: 0.2888 (OUTLIER) cc_final: 0.1620 (pt0) REVERT: I 672 GLU cc_start: 0.2924 (mt-10) cc_final: 0.2183 (tt0) REVERT: I 748 LYS cc_start: 0.4989 (mmmt) cc_final: 0.4628 (ptpp) REVERT: I 750 MET cc_start: 0.2145 (mtp) cc_final: 0.0607 (mmp) REVERT: J 71 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.7052 (ptp90) REVERT: P 62 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7873 (mt-10) REVERT: M 452 ARG cc_start: 0.6572 (ptm160) cc_final: 0.6193 (ptp-170) REVERT: M 510 LYS cc_start: 0.4526 (OUTLIER) cc_final: 0.3458 (pptt) REVERT: T 469 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8345 (mt) REVERT: T 497 GLU cc_start: 0.5317 (OUTLIER) cc_final: 0.4868 (pp20) REVERT: O 264 MET cc_start: 0.1086 (pmm) cc_final: 0.0609 (pmt) REVERT: N 6 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8100 (pttt) REVERT: N 21 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6692 (tm-30) REVERT: N 52 ARG cc_start: 0.9062 (OUTLIER) cc_final: 0.8193 (ttp-170) REVERT: N 82 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7472 (mp0) REVERT: N 170 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7019 (mt-10) REVERT: R 191 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8363 (mm) REVERT: R 205 LYS cc_start: 0.7559 (OUTLIER) cc_final: 0.6911 (mptt) REVERT: R 259 LYS cc_start: 0.7055 (ttmm) cc_final: 0.6646 (tttm) REVERT: S 9 ASP cc_start: 0.6652 (OUTLIER) cc_final: 0.6084 (p0) REVERT: W 218 ILE cc_start: 0.2306 (OUTLIER) cc_final: 0.2036 (mt) REVERT: L 150 MET cc_start: 0.6307 (ttm) cc_final: 0.5978 (tmm) REVERT: L 188 ARG cc_start: 0.4225 (OUTLIER) cc_final: 0.4001 (ttp-170) REVERT: L 241 ARG cc_start: 0.2918 (OUTLIER) cc_final: 0.2315 (pmt170) REVERT: L 601 GLU cc_start: 0.3003 (OUTLIER) cc_final: 0.2611 (mm-30) REVERT: L 608 MET cc_start: 0.2608 (ptp) cc_final: 0.1429 (mmt) REVERT: L 614 HIS cc_start: 0.1900 (OUTLIER) cc_final: 0.1081 (t-90) REVERT: L 650 GLU cc_start: 0.2637 (OUTLIER) cc_final: 0.1726 (tt0) REVERT: L 662 GLU cc_start: 0.2140 (OUTLIER) cc_final: 0.1872 (pm20) REVERT: L 776 LYS cc_start: 0.5681 (ttpp) cc_final: 0.5150 (tptm) REVERT: K 104 TYR cc_start: 0.0139 (OUTLIER) cc_final: -0.0445 (t80) REVERT: K 113 ARG cc_start: 0.3419 (OUTLIER) cc_final: 0.2781 (ttm-80) REVERT: K 144 LEU cc_start: 0.3884 (OUTLIER) cc_final: 0.3292 (mm) REVERT: K 145 LEU cc_start: 0.2587 (OUTLIER) cc_final: 0.2313 (pp) REVERT: K 146 LYS cc_start: 0.2643 (OUTLIER) cc_final: 0.2196 (ptpt) REVERT: V 678 LYS cc_start: 0.5155 (OUTLIER) cc_final: 0.3286 (ptpt) outliers start: 563 outliers final: 289 residues processed: 1096 average time/residue: 1.4484 time to fit residues: 2129.5957 Evaluate side-chains 966 residues out of total 8096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 366 poor density : 600 time to evaluate : 5.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 493 CYS Chi-restraints excluded: chain A residue 498 HIS Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 526 ARG Chi-restraints excluded: chain A residue 544 LYS Chi-restraints excluded: chain A residue 589 LYS Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 909 ARG Chi-restraints excluded: chain A residue 912 GLU Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 954 SER Chi-restraints excluded: chain A residue 978 LEU Chi-restraints excluded: chain A residue 995 ASP Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1026 VAL Chi-restraints excluded: chain A residue 1038 VAL Chi-restraints excluded: chain A residue 1046 GLU Chi-restraints excluded: chain A residue 1059 ARG Chi-restraints excluded: chain A residue 1087 SER Chi-restraints excluded: chain A residue 1091 SER Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1131 CYS Chi-restraints excluded: chain A residue 1140 ASP Chi-restraints excluded: chain A residue 1153 SER Chi-restraints excluded: chain A residue 1231 THR Chi-restraints excluded: chain A residue 1233 GLU Chi-restraints excluded: chain A residue 1240 SER Chi-restraints excluded: chain A residue 1285 THR Chi-restraints excluded: chain A residue 1289 THR Chi-restraints excluded: chain A residue 1307 ARG Chi-restraints excluded: chain A residue 1319 THR Chi-restraints excluded: chain A residue 1321 THR Chi-restraints excluded: chain A residue 1351 LEU Chi-restraints excluded: chain A residue 1362 ARG Chi-restraints excluded: chain A residue 1365 ILE Chi-restraints excluded: chain A residue 1385 GLU Chi-restraints excluded: chain A residue 1402 SER Chi-restraints excluded: chain A residue 1417 PHE Chi-restraints excluded: chain A residue 1428 LEU Chi-restraints excluded: chain A residue 1465 ARG Chi-restraints excluded: chain A residue 1480 ILE Chi-restraints excluded: chain A residue 1493 THR Chi-restraints excluded: chain A residue 1502 VAL Chi-restraints excluded: chain A residue 1511 ILE Chi-restraints excluded: chain A residue 1512 THR Chi-restraints excluded: chain A residue 1538 VAL Chi-restraints excluded: chain A residue 1545 VAL Chi-restraints excluded: chain A residue 1557 THR Chi-restraints excluded: chain A residue 1593 ILE Chi-restraints excluded: chain A residue 1605 THR Chi-restraints excluded: chain A residue 1626 MET Chi-restraints excluded: chain A residue 1627 HIS Chi-restraints excluded: chain A residue 1635 ILE Chi-restraints excluded: chain A residue 1658 CYS Chi-restraints excluded: chain A residue 1712 THR Chi-restraints excluded: chain A residue 1719 LYS Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1728 VAL Chi-restraints excluded: chain A residue 1747 LYS Chi-restraints excluded: chain A residue 1757 SER Chi-restraints excluded: chain A residue 1783 PHE Chi-restraints excluded: chain A residue 1786 ILE Chi-restraints excluded: chain A residue 1789 LEU Chi-restraints excluded: chain A residue 1807 LEU Chi-restraints excluded: chain A residue 1820 SER Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 257 ARG Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 306 CYS Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 485 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 550 TYR Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 600 GLN Chi-restraints excluded: chain C residue 639 GLU Chi-restraints excluded: chain C residue 643 GLU Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 725 ASP Chi-restraints excluded: chain C residue 726 MET Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 771 THR Chi-restraints excluded: chain C residue 789 TRP Chi-restraints excluded: chain C residue 797 CYS Chi-restraints excluded: chain C residue 809 LEU Chi-restraints excluded: chain C residue 810 ASP Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 820 ARG Chi-restraints excluded: chain C residue 826 ILE Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 874 VAL Chi-restraints excluded: chain C residue 892 LEU Chi-restraints excluded: chain C residue 902 THR Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 79 CYS Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 200 PHE Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 306 CYS Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain E residue 330 HIS Chi-restraints excluded: chain E residue 333 SER Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 342 LYS Chi-restraints excluded: chain E residue 354 THR Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain q residue 46 SER Chi-restraints excluded: chain q residue 72 LEU Chi-restraints excluded: chain q residue 114 VAL Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 2 PHE Chi-restraints excluded: chain r residue 9 VAL Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain r residue 41 THR Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain r residue 63 THR Chi-restraints excluded: chain r residue 95 HIS Chi-restraints excluded: chain r residue 101 LEU Chi-restraints excluded: chain t residue 123 ASP Chi-restraints excluded: chain a residue 19 GLU Chi-restraints excluded: chain a residue 44 MET Chi-restraints excluded: chain a residue 56 ARG Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 82 LEU Chi-restraints excluded: chain g residue 27 VAL Chi-restraints excluded: chain g residue 38 MET Chi-restraints excluded: chain g residue 48 GLU Chi-restraints excluded: chain g residue 70 LEU Chi-restraints excluded: chain e residue 10 THR Chi-restraints excluded: chain e residue 37 ARG Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 55 GLU Chi-restraints excluded: chain e residue 68 THR Chi-restraints excluded: chain e residue 72 ILE Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain f residue 22 ILE Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 48 SER Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 42 CYS Chi-restraints excluded: chain d residue 51 ARG Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 68 GLU Chi-restraints excluded: chain d residue 80 GLN Chi-restraints excluded: chain d residue 84 ARG Chi-restraints excluded: chain d residue 98 ARG Chi-restraints excluded: chain c residue 2 VAL Chi-restraints excluded: chain c residue 10 LYS Chi-restraints excluded: chain c residue 49 ARG Chi-restraints excluded: chain c residue 75 LEU Chi-restraints excluded: chain c residue 79 THR Chi-restraints excluded: chain b residue 36 ARG Chi-restraints excluded: chain b residue 40 LEU Chi-restraints excluded: chain b residue 45 SER Chi-restraints excluded: chain b residue 105 ILE Chi-restraints excluded: chain I residue 356 LEU Chi-restraints excluded: chain I residue 366 SER Chi-restraints excluded: chain I residue 367 VAL Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain I residue 435 ILE Chi-restraints excluded: chain I residue 438 GLN Chi-restraints excluded: chain I residue 456 CYS Chi-restraints excluded: chain I residue 473 ASP Chi-restraints excluded: chain I residue 480 THR Chi-restraints excluded: chain I residue 487 ARG Chi-restraints excluded: chain I residue 574 HIS Chi-restraints excluded: chain I residue 599 ARG Chi-restraints excluded: chain I residue 614 CYS Chi-restraints excluded: chain I residue 625 GLU Chi-restraints excluded: chain I residue 667 ILE Chi-restraints excluded: chain I residue 670 VAL Chi-restraints excluded: chain I residue 687 SER Chi-restraints excluded: chain I residue 702 GLU Chi-restraints excluded: chain I residue 737 PHE Chi-restraints excluded: chain I residue 746 THR Chi-restraints excluded: chain J residue 61 SER Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 71 ARG Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain J residue 144 ARG Chi-restraints excluded: chain J residue 167 GLN Chi-restraints excluded: chain J residue 196 ASP Chi-restraints excluded: chain J residue 228 VAL Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain P residue 13 ILE Chi-restraints excluded: chain P residue 62 GLU Chi-restraints excluded: chain P residue 231 GLN Chi-restraints excluded: chain M residue 496 VAL Chi-restraints excluded: chain M residue 510 LYS Chi-restraints excluded: chain M residue 538 LYS Chi-restraints excluded: chain T residue 190 ARG Chi-restraints excluded: chain T residue 212 CYS Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 286 SER Chi-restraints excluded: chain T residue 314 VAL Chi-restraints excluded: chain T residue 324 VAL Chi-restraints excluded: chain T residue 388 PHE Chi-restraints excluded: chain T residue 396 GLU Chi-restraints excluded: chain T residue 414 SER Chi-restraints excluded: chain T residue 422 SER Chi-restraints excluded: chain T residue 446 ARG Chi-restraints excluded: chain T residue 465 SER Chi-restraints excluded: chain T residue 469 LEU Chi-restraints excluded: chain T residue 497 GLU Chi-restraints excluded: chain O residue 22 VAL Chi-restraints excluded: chain O residue 35 MET Chi-restraints excluded: chain O residue 38 ILE Chi-restraints excluded: chain O residue 49 ARG Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 120 MET Chi-restraints excluded: chain O residue 165 VAL Chi-restraints excluded: chain O residue 184 HIS Chi-restraints excluded: chain O residue 224 THR Chi-restraints excluded: chain O residue 239 VAL Chi-restraints excluded: chain O residue 248 VAL Chi-restraints excluded: chain O residue 267 LYS Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 11 LYS Chi-restraints excluded: chain N residue 21 GLU Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 52 ARG Chi-restraints excluded: chain N residue 82 GLU Chi-restraints excluded: chain N residue 170 GLU Chi-restraints excluded: chain R residue 83 ILE Chi-restraints excluded: chain R residue 88 LYS Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 118 VAL Chi-restraints excluded: chain R residue 122 SER Chi-restraints excluded: chain R residue 152 LYS Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 168 SER Chi-restraints excluded: chain R residue 191 ILE Chi-restraints excluded: chain R residue 195 ASP Chi-restraints excluded: chain R residue 205 LYS Chi-restraints excluded: chain R residue 211 VAL Chi-restraints excluded: chain R residue 220 VAL Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 231 THR Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain R residue 255 ILE Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain S residue 6 VAL Chi-restraints excluded: chain S residue 9 ASP Chi-restraints excluded: chain S residue 23 HIS Chi-restraints excluded: chain S residue 28 CYS Chi-restraints excluded: chain S residue 34 LEU Chi-restraints excluded: chain S residue 50 ARG Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain S residue 92 MET Chi-restraints excluded: chain S residue 134 LEU Chi-restraints excluded: chain S residue 146 VAL Chi-restraints excluded: chain S residue 152 ILE Chi-restraints excluded: chain W residue 81 ASP Chi-restraints excluded: chain W residue 87 LEU Chi-restraints excluded: chain W residue 91 HIS Chi-restraints excluded: chain W residue 107 VAL Chi-restraints excluded: chain W residue 112 ASP Chi-restraints excluded: chain W residue 118 ILE Chi-restraints excluded: chain W residue 121 GLU Chi-restraints excluded: chain W residue 167 THR Chi-restraints excluded: chain W residue 168 THR Chi-restraints excluded: chain W residue 218 ILE Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 130 ASN Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain L residue 188 ARG Chi-restraints excluded: chain L residue 207 VAL Chi-restraints excluded: chain L residue 217 LEU Chi-restraints excluded: chain L residue 241 ARG Chi-restraints excluded: chain L residue 601 GLU Chi-restraints excluded: chain L residue 614 HIS Chi-restraints excluded: chain L residue 650 GLU Chi-restraints excluded: chain L residue 662 GLU Chi-restraints excluded: chain L residue 798 ASP Chi-restraints excluded: chain L residue 800 THR Chi-restraints excluded: chain K residue 28 HIS Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 104 TYR Chi-restraints excluded: chain K residue 113 ARG Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain K residue 145 LEU Chi-restraints excluded: chain K residue 146 LYS Chi-restraints excluded: chain K residue 217 ASP Chi-restraints excluded: chain U residue 2 TYR Chi-restraints excluded: chain U residue 8 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 23 LYS Chi-restraints excluded: chain V residue 668 ASP Chi-restraints excluded: chain V residue 678 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 956 random chunks: chunk 98 optimal weight: 0.9980 chunk 522 optimal weight: 10.0000 chunk 165 optimal weight: 1.9990 chunk 709 optimal weight: 40.0000 chunk 307 optimal weight: 3.9990 chunk 254 optimal weight: 8.9990 chunk 846 optimal weight: 30.0000 chunk 670 optimal weight: 30.0000 chunk 563 optimal weight: 0.7980 chunk 895 optimal weight: 8.9990 chunk 870 optimal weight: 10.0000 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 269 HIS ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 HIS A 512 GLN A 587 ASN ** A 809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 939 HIS ** A1147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1246 ASN A1616 GLN A1729 GLN C 68 HIS C 124 ASN ** C 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 HIS ** C 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 96 GLN r 99 GLN ** s 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 47 GLN ** c 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 225 ASN P 45 GLN P 212 GLN ** O 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 29 GLN R 80 GLN ** R 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 198 GLN K 141 GLN K 187 GLN ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4980 r_free = 0.4980 target = 0.278920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.248647 restraints weight = 84617.238| |-----------------------------------------------------------------------------| r_work (start): 0.4729 rms_B_bonded: 1.75 r_work: 0.4464 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.4429 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.4429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6168 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 75153 Z= 0.424 Angle : 0.735 12.917 103334 Z= 0.378 Chirality : 0.048 0.302 11959 Planarity : 0.006 0.092 12679 Dihedral : 17.255 178.379 14384 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.20 % Favored : 94.72 % Rotamer: Outliers : 8.98 % Allowed : 29.75 % Favored : 61.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.09), residues: 9287 helix: 0.60 (0.08), residues: 4333 sheet: -0.81 (0.16), residues: 1093 loop : -1.39 (0.10), residues: 3861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP A1701 HIS 0.010 0.002 HIS C 145 PHE 0.032 0.002 PHE A 962 TYR 0.025 0.002 TYR A1751 ARG 0.011 0.001 ARG A 842 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18574 Ramachandran restraints generated. 9287 Oldfield, 0 Emsley, 9287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18574 Ramachandran restraints generated. 9287 Oldfield, 0 Emsley, 9287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1139 residues out of total 8096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 527 poor density : 612 time to evaluate : 5.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.7953 (ptt90) cc_final: 0.7707 (ptm160) REVERT: A 276 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7918 (ptmt) REVERT: A 331 ILE cc_start: 0.4606 (OUTLIER) cc_final: 0.4177 (pp) REVERT: A 498 HIS cc_start: 0.4734 (OUTLIER) cc_final: 0.4122 (t-90) REVERT: A 526 ARG cc_start: 0.5393 (OUTLIER) cc_final: 0.4216 (ttp-170) REVERT: A 589 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.7534 (pttm) REVERT: A 800 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7938 (tt0) REVERT: A 1046 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6989 (mm-30) REVERT: A 1233 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7370 (tp30) REVERT: A 1266 MET cc_start: 0.6998 (ttm) cc_final: 0.6780 (ttm) REVERT: A 1278 TRP cc_start: 0.8946 (m-10) cc_final: 0.8562 (m-10) REVERT: A 1362 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.6385 (tpp80) REVERT: A 1417 PHE cc_start: 0.4778 (OUTLIER) cc_final: 0.4497 (p90) REVERT: A 1435 TYR cc_start: 0.8021 (m-80) cc_final: 0.7579 (m-80) REVERT: A 1465 ARG cc_start: 0.4487 (OUTLIER) cc_final: 0.4103 (tmm-80) REVERT: A 1480 ILE cc_start: 0.7060 (OUTLIER) cc_final: 0.6600 (tp) REVERT: A 1597 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.7386 (ttp-110) REVERT: A 1626 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8262 (mtm) REVERT: A 1630 ILE cc_start: 0.7910 (OUTLIER) cc_final: 0.7501 (mt) REVERT: A 1658 CYS cc_start: 0.5428 (OUTLIER) cc_final: 0.5153 (t) REVERT: A 1705 LYS cc_start: 0.6222 (OUTLIER) cc_final: 0.5922 (ttmt) REVERT: A 1742 ARG cc_start: 0.7225 (OUTLIER) cc_final: 0.6995 (ttp-170) REVERT: A 1754 ASP cc_start: 0.4814 (OUTLIER) cc_final: 0.4607 (t70) REVERT: A 1783 PHE cc_start: 0.3218 (OUTLIER) cc_final: 0.1743 (p90) REVERT: A 1789 LEU cc_start: 0.4170 (OUTLIER) cc_final: 0.3765 (tp) REVERT: C 69 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.6304 (tp30) REVERT: C 177 GLN cc_start: 0.4360 (OUTLIER) cc_final: 0.3851 (tt0) REVERT: C 216 LEU cc_start: 0.5582 (OUTLIER) cc_final: 0.4990 (mt) REVERT: C 257 ARG cc_start: 0.5719 (OUTLIER) cc_final: 0.4463 (mpt-90) REVERT: C 359 ARG cc_start: 0.3031 (OUTLIER) cc_final: 0.2747 (mmt180) REVERT: C 379 ARG cc_start: 0.4375 (mtt90) cc_final: 0.4172 (mtt-85) REVERT: C 527 LEU cc_start: 0.3806 (OUTLIER) cc_final: 0.3071 (mp) REVERT: C 550 TYR cc_start: 0.4184 (OUTLIER) cc_final: 0.3569 (t80) REVERT: C 639 GLU cc_start: 0.1300 (OUTLIER) cc_final: 0.0717 (pm20) REVERT: C 643 GLU cc_start: 0.3440 (OUTLIER) cc_final: 0.2734 (tm-30) REVERT: C 763 LEU cc_start: 0.1264 (OUTLIER) cc_final: 0.0714 (mt) REVERT: C 789 TRP cc_start: 0.3017 (OUTLIER) cc_final: 0.2511 (t60) REVERT: C 820 ARG cc_start: 0.2899 (OUTLIER) cc_final: 0.2052 (ptt90) REVERT: C 892 LEU cc_start: 0.5647 (OUTLIER) cc_final: 0.5255 (tt) REVERT: E 54 LEU cc_start: 0.5660 (OUTLIER) cc_final: 0.5281 (mt) REVERT: E 200 PHE cc_start: 0.4589 (OUTLIER) cc_final: 0.3620 (t80) REVERT: E 228 ASP cc_start: 0.5419 (OUTLIER) cc_final: 0.4864 (t0) REVERT: E 342 LYS cc_start: 0.6631 (OUTLIER) cc_final: 0.5754 (mmtt) REVERT: r 51 LEU cc_start: 0.2614 (OUTLIER) cc_final: 0.2390 (tm) REVERT: r 84 MET cc_start: 0.2205 (tpt) cc_final: 0.1474 (mpp) REVERT: r 95 HIS cc_start: 0.1507 (OUTLIER) cc_final: 0.0866 (m170) REVERT: t 105 LEU cc_start: 0.1216 (OUTLIER) cc_final: 0.0659 (tt) REVERT: a 44 MET cc_start: 0.5740 (OUTLIER) cc_final: 0.5275 (tmm) REVERT: g 48 GLU cc_start: 0.4359 (OUTLIER) cc_final: 0.3269 (tm-30) REVERT: g 70 LEU cc_start: 0.2172 (OUTLIER) cc_final: 0.1369 (mp) REVERT: e 49 MET cc_start: 0.0551 (mmt) cc_final: -0.0044 (mtt) REVERT: e 55 GLU cc_start: 0.3892 (OUTLIER) cc_final: 0.3522 (tm-30) REVERT: e 58 GLU cc_start: 0.2468 (OUTLIER) cc_final: 0.1151 (mp0) REVERT: f 29 MET cc_start: 0.3619 (ttm) cc_final: 0.1811 (mpm) REVERT: d 68 GLU cc_start: 0.2572 (OUTLIER) cc_final: 0.1219 (pp20) REVERT: c 1 MET cc_start: 0.3441 (mtt) cc_final: 0.2551 (tmm) REVERT: c 9 MET cc_start: 0.1031 (mmp) cc_final: 0.0434 (ttm) REVERT: c 10 LYS cc_start: 0.3789 (OUTLIER) cc_final: 0.2454 (tptp) REVERT: c 37 MET cc_start: 0.3884 (mpp) cc_final: 0.2622 (pmm) REVERT: c 75 LEU cc_start: 0.1309 (OUTLIER) cc_final: 0.0617 (mt) REVERT: b 32 MET cc_start: 0.3698 (mmm) cc_final: 0.3424 (mmm) REVERT: I 356 LEU cc_start: 0.1645 (OUTLIER) cc_final: 0.0928 (mt) REVERT: I 417 TRP cc_start: 0.0884 (m100) cc_final: 0.0408 (m-90) REVERT: I 456 CYS cc_start: 0.3185 (OUTLIER) cc_final: 0.2828 (m) REVERT: I 461 MET cc_start: 0.0857 (tmm) cc_final: 0.0213 (ptm) REVERT: I 473 ASP cc_start: 0.2533 (OUTLIER) cc_final: 0.2151 (t70) REVERT: I 492 GLU cc_start: 0.4601 (mm-30) cc_final: 0.3501 (pp20) REVERT: I 574 HIS cc_start: 0.2782 (OUTLIER) cc_final: 0.1809 (m-70) REVERT: I 625 GLU cc_start: 0.2842 (OUTLIER) cc_final: 0.1595 (pt0) REVERT: I 650 ARG cc_start: 0.2134 (mpt-90) cc_final: 0.1712 (mmm160) REVERT: I 672 GLU cc_start: 0.2978 (mt-10) cc_final: 0.2247 (tt0) REVERT: I 697 ARG cc_start: 0.2516 (OUTLIER) cc_final: 0.1764 (mmt-90) REVERT: I 747 PHE cc_start: 0.1091 (OUTLIER) cc_final: 0.0863 (m-10) REVERT: I 748 LYS cc_start: 0.4947 (mmmt) cc_final: 0.4657 (ptpp) REVERT: I 750 MET cc_start: 0.2023 (mtp) cc_final: 0.0543 (mmp) REVERT: J 71 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.7178 (ptp90) REVERT: P 62 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7831 (mt-10) REVERT: M 510 LYS cc_start: 0.4436 (OUTLIER) cc_final: 0.3544 (pptt) REVERT: T 187 LYS cc_start: 0.8377 (pttt) cc_final: 0.8106 (pttm) REVERT: T 469 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8349 (mt) REVERT: T 497 GLU cc_start: 0.5285 (OUTLIER) cc_final: 0.4894 (pp20) REVERT: O 264 MET cc_start: 0.0990 (OUTLIER) cc_final: 0.0504 (pmt) REVERT: N 6 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.8079 (pttt) REVERT: N 21 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6552 (tm-30) REVERT: N 52 ARG cc_start: 0.9067 (OUTLIER) cc_final: 0.8177 (ttp-170) REVERT: N 82 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7339 (mp0) REVERT: N 170 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.6932 (mt-10) REVERT: R 205 LYS cc_start: 0.7566 (OUTLIER) cc_final: 0.6921 (mptt) REVERT: R 251 LYS cc_start: 0.6263 (OUTLIER) cc_final: 0.5701 (mtmp) REVERT: R 259 LYS cc_start: 0.7033 (ttmm) cc_final: 0.6646 (tttm) REVERT: S 9 ASP cc_start: 0.6562 (OUTLIER) cc_final: 0.5958 (p0) REVERT: L 150 MET cc_start: 0.6319 (ttm) cc_final: 0.5972 (tmm) REVERT: L 188 ARG cc_start: 0.4115 (OUTLIER) cc_final: 0.3903 (ttp-170) REVERT: L 241 ARG cc_start: 0.2927 (OUTLIER) cc_final: 0.2260 (pmt170) REVERT: L 545 ARG cc_start: 0.2918 (OUTLIER) cc_final: 0.2254 (mtt90) REVERT: L 557 GLU cc_start: 0.3015 (OUTLIER) cc_final: 0.2674 (tm-30) REVERT: L 601 GLU cc_start: 0.2943 (OUTLIER) cc_final: 0.2561 (mm-30) REVERT: L 608 MET cc_start: 0.2518 (ptp) cc_final: 0.1383 (mmt) REVERT: L 614 HIS cc_start: 0.1899 (OUTLIER) cc_final: 0.1049 (t-90) REVERT: L 650 GLU cc_start: 0.2621 (OUTLIER) cc_final: 0.1694 (tt0) REVERT: L 662 GLU cc_start: 0.2134 (OUTLIER) cc_final: 0.1931 (pm20) REVERT: L 776 LYS cc_start: 0.5696 (ttpp) cc_final: 0.5177 (tptm) REVERT: L 798 ASP cc_start: 0.3397 (OUTLIER) cc_final: 0.2233 (t70) REVERT: K 28 HIS cc_start: 0.4097 (OUTLIER) cc_final: 0.2840 (p-80) REVERT: K 104 TYR cc_start: 0.0159 (OUTLIER) cc_final: -0.0427 (t80) REVERT: K 113 ARG cc_start: 0.3466 (OUTLIER) cc_final: 0.2912 (ttm-80) REVERT: K 144 LEU cc_start: 0.3818 (OUTLIER) cc_final: 0.3185 (mm) REVERT: K 145 LEU cc_start: 0.2777 (OUTLIER) cc_final: 0.2498 (pp) REVERT: K 146 LYS cc_start: 0.2431 (OUTLIER) cc_final: 0.1902 (pptt) outliers start: 527 outliers final: 281 residues processed: 1066 average time/residue: 1.4553 time to fit residues: 2102.3546 Evaluate side-chains 957 residues out of total 8096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 365 poor density : 592 time to evaluate : 5.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 493 CYS Chi-restraints excluded: chain A residue 498 HIS Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 526 ARG Chi-restraints excluded: chain A residue 544 LYS Chi-restraints excluded: chain A residue 589 LYS Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 909 ARG Chi-restraints excluded: chain A residue 912 GLU Chi-restraints excluded: chain A residue 954 SER Chi-restraints excluded: chain A residue 978 LEU Chi-restraints excluded: chain A residue 995 ASP Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1026 VAL Chi-restraints excluded: chain A residue 1038 VAL Chi-restraints excluded: chain A residue 1042 GLN Chi-restraints excluded: chain A residue 1046 GLU Chi-restraints excluded: chain A residue 1059 ARG Chi-restraints excluded: chain A residue 1087 SER Chi-restraints excluded: chain A residue 1091 SER Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1131 CYS Chi-restraints excluded: chain A residue 1153 SER Chi-restraints excluded: chain A residue 1231 THR Chi-restraints excluded: chain A residue 1233 GLU Chi-restraints excluded: chain A residue 1240 SER Chi-restraints excluded: chain A residue 1285 THR Chi-restraints excluded: chain A residue 1289 THR Chi-restraints excluded: chain A residue 1307 ARG Chi-restraints excluded: chain A residue 1319 THR Chi-restraints excluded: chain A residue 1321 THR Chi-restraints excluded: chain A residue 1351 LEU Chi-restraints excluded: chain A residue 1362 ARG Chi-restraints excluded: chain A residue 1365 ILE Chi-restraints excluded: chain A residue 1385 GLU Chi-restraints excluded: chain A residue 1402 SER Chi-restraints excluded: chain A residue 1417 PHE Chi-restraints excluded: chain A residue 1428 LEU Chi-restraints excluded: chain A residue 1465 ARG Chi-restraints excluded: chain A residue 1480 ILE Chi-restraints excluded: chain A residue 1493 THR Chi-restraints excluded: chain A residue 1502 VAL Chi-restraints excluded: chain A residue 1511 ILE Chi-restraints excluded: chain A residue 1512 THR Chi-restraints excluded: chain A residue 1538 VAL Chi-restraints excluded: chain A residue 1557 THR Chi-restraints excluded: chain A residue 1593 ILE Chi-restraints excluded: chain A residue 1597 ARG Chi-restraints excluded: chain A residue 1605 THR Chi-restraints excluded: chain A residue 1626 MET Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1635 ILE Chi-restraints excluded: chain A residue 1658 CYS Chi-restraints excluded: chain A residue 1688 SER Chi-restraints excluded: chain A residue 1705 LYS Chi-restraints excluded: chain A residue 1712 THR Chi-restraints excluded: chain A residue 1719 LYS Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1728 VAL Chi-restraints excluded: chain A residue 1742 ARG Chi-restraints excluded: chain A residue 1747 LYS Chi-restraints excluded: chain A residue 1754 ASP Chi-restraints excluded: chain A residue 1757 SER Chi-restraints excluded: chain A residue 1783 PHE Chi-restraints excluded: chain A residue 1789 LEU Chi-restraints excluded: chain A residue 1807 LEU Chi-restraints excluded: chain A residue 1820 SER Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 257 ARG Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 306 CYS Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 550 TYR Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 639 GLU Chi-restraints excluded: chain C residue 643 GLU Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 726 MET Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 771 THR Chi-restraints excluded: chain C residue 789 TRP Chi-restraints excluded: chain C residue 797 CYS Chi-restraints excluded: chain C residue 809 LEU Chi-restraints excluded: chain C residue 810 ASP Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 820 ARG Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 874 VAL Chi-restraints excluded: chain C residue 892 LEU Chi-restraints excluded: chain C residue 902 THR Chi-restraints excluded: chain C residue 930 ASP Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 79 CYS Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 200 PHE Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain E residue 259 MET Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 306 CYS Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 333 SER Chi-restraints excluded: chain E residue 342 LYS Chi-restraints excluded: chain E residue 354 THR Chi-restraints excluded: chain q residue 26 SER Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain q residue 46 SER Chi-restraints excluded: chain q residue 114 VAL Chi-restraints excluded: chain r residue 2 PHE Chi-restraints excluded: chain r residue 9 VAL Chi-restraints excluded: chain r residue 41 THR Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain r residue 51 LEU Chi-restraints excluded: chain r residue 55 VAL Chi-restraints excluded: chain r residue 63 THR Chi-restraints excluded: chain r residue 95 HIS Chi-restraints excluded: chain r residue 101 LEU Chi-restraints excluded: chain r residue 113 ARG Chi-restraints excluded: chain t residue 105 LEU Chi-restraints excluded: chain a residue 19 GLU Chi-restraints excluded: chain a residue 44 MET Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain g residue 27 VAL Chi-restraints excluded: chain g residue 38 MET Chi-restraints excluded: chain g residue 48 GLU Chi-restraints excluded: chain g residue 70 LEU Chi-restraints excluded: chain e residue 10 THR Chi-restraints excluded: chain e residue 37 ARG Chi-restraints excluded: chain e residue 55 GLU Chi-restraints excluded: chain e residue 58 GLU Chi-restraints excluded: chain e residue 68 THR Chi-restraints excluded: chain e residue 72 ILE Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain f residue 22 ILE Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 48 SER Chi-restraints excluded: chain d residue 42 CYS Chi-restraints excluded: chain d residue 51 ARG Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 68 GLU Chi-restraints excluded: chain d residue 80 GLN Chi-restraints excluded: chain d residue 84 ARG Chi-restraints excluded: chain c residue 2 VAL Chi-restraints excluded: chain c residue 10 LYS Chi-restraints excluded: chain c residue 75 LEU Chi-restraints excluded: chain c residue 79 THR Chi-restraints excluded: chain b residue 36 ARG Chi-restraints excluded: chain b residue 45 SER Chi-restraints excluded: chain b residue 105 ILE Chi-restraints excluded: chain I residue 356 LEU Chi-restraints excluded: chain I residue 367 VAL Chi-restraints excluded: chain I residue 380 HIS Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain I residue 456 CYS Chi-restraints excluded: chain I residue 473 ASP Chi-restraints excluded: chain I residue 476 THR Chi-restraints excluded: chain I residue 484 ARG Chi-restraints excluded: chain I residue 574 HIS Chi-restraints excluded: chain I residue 599 ARG Chi-restraints excluded: chain I residue 625 GLU Chi-restraints excluded: chain I residue 670 VAL Chi-restraints excluded: chain I residue 687 SER Chi-restraints excluded: chain I residue 697 ARG Chi-restraints excluded: chain I residue 702 GLU Chi-restraints excluded: chain I residue 737 PHE Chi-restraints excluded: chain I residue 746 THR Chi-restraints excluded: chain I residue 747 PHE Chi-restraints excluded: chain J residue 61 SER Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 71 ARG Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain J residue 144 ARG Chi-restraints excluded: chain J residue 196 ASP Chi-restraints excluded: chain J residue 223 MET Chi-restraints excluded: chain J residue 225 ASN Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain P residue 13 ILE Chi-restraints excluded: chain P residue 231 GLN Chi-restraints excluded: chain M residue 496 VAL Chi-restraints excluded: chain M residue 510 LYS Chi-restraints excluded: chain M residue 538 LYS Chi-restraints excluded: chain T residue 190 ARG Chi-restraints excluded: chain T residue 212 CYS Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 286 SER Chi-restraints excluded: chain T residue 292 SER Chi-restraints excluded: chain T residue 314 VAL Chi-restraints excluded: chain T residue 324 VAL Chi-restraints excluded: chain T residue 388 PHE Chi-restraints excluded: chain T residue 396 GLU Chi-restraints excluded: chain T residue 414 SER Chi-restraints excluded: chain T residue 422 SER Chi-restraints excluded: chain T residue 446 ARG Chi-restraints excluded: chain T residue 465 SER Chi-restraints excluded: chain T residue 469 LEU Chi-restraints excluded: chain T residue 485 GLU Chi-restraints excluded: chain T residue 497 GLU Chi-restraints excluded: chain O residue 22 VAL Chi-restraints excluded: chain O residue 38 ILE Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 120 MET Chi-restraints excluded: chain O residue 165 VAL Chi-restraints excluded: chain O residue 184 HIS Chi-restraints excluded: chain O residue 224 THR Chi-restraints excluded: chain O residue 239 VAL Chi-restraints excluded: chain O residue 248 VAL Chi-restraints excluded: chain O residue 264 MET Chi-restraints excluded: chain O residue 267 LYS Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 11 LYS Chi-restraints excluded: chain N residue 19 ILE Chi-restraints excluded: chain N residue 21 GLU Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 52 ARG Chi-restraints excluded: chain N residue 82 GLU Chi-restraints excluded: chain N residue 170 GLU Chi-restraints excluded: chain R residue 83 ILE Chi-restraints excluded: chain R residue 88 LYS Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 118 VAL Chi-restraints excluded: chain R residue 152 LYS Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 168 SER Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 195 ASP Chi-restraints excluded: chain R residue 205 LYS Chi-restraints excluded: chain R residue 211 VAL Chi-restraints excluded: chain R residue 220 VAL Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 231 THR Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 251 LYS Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain R residue 255 ILE Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 6 VAL Chi-restraints excluded: chain S residue 9 ASP Chi-restraints excluded: chain S residue 23 HIS Chi-restraints excluded: chain S residue 28 CYS Chi-restraints excluded: chain S residue 34 LEU Chi-restraints excluded: chain S residue 50 ARG Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain S residue 92 MET Chi-restraints excluded: chain S residue 134 LEU Chi-restraints excluded: chain S residue 146 VAL Chi-restraints excluded: chain S residue 152 ILE Chi-restraints excluded: chain W residue 87 LEU Chi-restraints excluded: chain W residue 91 HIS Chi-restraints excluded: chain W residue 107 VAL Chi-restraints excluded: chain W residue 112 ASP Chi-restraints excluded: chain W residue 118 ILE Chi-restraints excluded: chain W residue 121 GLU Chi-restraints excluded: chain W residue 167 THR Chi-restraints excluded: chain W residue 168 THR Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 130 ASN Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain L residue 188 ARG Chi-restraints excluded: chain L residue 207 VAL Chi-restraints excluded: chain L residue 217 LEU Chi-restraints excluded: chain L residue 241 ARG Chi-restraints excluded: chain L residue 545 ARG Chi-restraints excluded: chain L residue 557 GLU Chi-restraints excluded: chain L residue 601 GLU Chi-restraints excluded: chain L residue 614 HIS Chi-restraints excluded: chain L residue 650 GLU Chi-restraints excluded: chain L residue 662 GLU Chi-restraints excluded: chain L residue 696 SER Chi-restraints excluded: chain L residue 791 GLU Chi-restraints excluded: chain L residue 798 ASP Chi-restraints excluded: chain L residue 800 THR Chi-restraints excluded: chain K residue 28 HIS Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 66 LEU Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 104 TYR Chi-restraints excluded: chain K residue 113 ARG Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain K residue 145 LEU Chi-restraints excluded: chain K residue 146 LYS Chi-restraints excluded: chain K residue 217 ASP Chi-restraints excluded: chain U residue 2 TYR Chi-restraints excluded: chain U residue 8 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 23 LYS Chi-restraints excluded: chain V residue 655 LEU Chi-restraints excluded: chain V residue 668 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 956 random chunks: chunk 671 optimal weight: 30.0000 chunk 928 optimal weight: 7.9990 chunk 903 optimal weight: 10.0000 chunk 933 optimal weight: 50.0000 chunk 477 optimal weight: 30.0000 chunk 734 optimal weight: 50.0000 chunk 662 optimal weight: 0.7980 chunk 474 optimal weight: 8.9990 chunk 183 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 449 optimal weight: 3.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 269 HIS ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 GLN A 939 HIS A 943 GLN ** A1147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1246 ASN A1325 ASN A1616 GLN A1729 GLN C 68 HIS ** C 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 96 GLN r 99 GLN ** s 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 47 GLN c 64 ASN I 465 HIS ** I 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 278 HIS P 45 GLN P 212 GLN R 80 GLN ** R 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 130 ASN ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 141 GLN ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4965 r_free = 0.4965 target = 0.277153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.246216 restraints weight = 84090.722| |-----------------------------------------------------------------------------| r_work (start): 0.4708 rms_B_bonded: 1.90 r_work: 0.4426 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.4387 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.4387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6257 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.131 75153 Z= 0.641 Angle : 0.838 13.895 103334 Z= 0.432 Chirality : 0.054 0.384 11959 Planarity : 0.006 0.095 12679 Dihedral : 17.399 179.988 14362 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.14 % Favored : 93.78 % Rotamer: Outliers : 9.19 % Allowed : 29.91 % Favored : 60.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.09), residues: 9287 helix: 0.40 (0.08), residues: 4314 sheet: -0.94 (0.15), residues: 1087 loop : -1.48 (0.10), residues: 3886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.004 TRP A1701 HIS 0.013 0.002 HIS A 744 PHE 0.039 0.003 PHE A 962 TYR 0.037 0.003 TYR J 272 ARG 0.013 0.001 ARG A 842 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18574 Ramachandran restraints generated. 9287 Oldfield, 0 Emsley, 9287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18574 Ramachandran restraints generated. 9287 Oldfield, 0 Emsley, 9287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1148 residues out of total 8096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 539 poor density : 609 time to evaluate : 6.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.7955 (ptt90) cc_final: 0.7731 (ptm160) REVERT: A 276 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7973 (ptmt) REVERT: A 331 ILE cc_start: 0.4738 (OUTLIER) cc_final: 0.4319 (pp) REVERT: A 589 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.7570 (pttm) REVERT: A 800 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.7970 (tt0) REVERT: A 997 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.6928 (mtt90) REVERT: A 1046 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6933 (mm-30) REVERT: A 1233 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7388 (tp30) REVERT: A 1266 MET cc_start: 0.7038 (ttm) cc_final: 0.6700 (ttm) REVERT: A 1278 TRP cc_start: 0.8977 (m-10) cc_final: 0.8535 (m-10) REVERT: A 1307 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7699 (ttp-170) REVERT: A 1362 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.6693 (tpp80) REVERT: A 1444 MET cc_start: 0.7613 (OUTLIER) cc_final: 0.6953 (mtp) REVERT: A 1465 ARG cc_start: 0.4528 (OUTLIER) cc_final: 0.4144 (tmm-80) REVERT: A 1480 ILE cc_start: 0.7433 (OUTLIER) cc_final: 0.7199 (tp) REVERT: A 1626 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8360 (mtm) REVERT: A 1627 HIS cc_start: 0.8912 (OUTLIER) cc_final: 0.8509 (m-70) REVERT: A 1630 ILE cc_start: 0.7903 (OUTLIER) cc_final: 0.7490 (mt) REVERT: A 1658 CYS cc_start: 0.5782 (OUTLIER) cc_final: 0.5420 (t) REVERT: A 1704 SER cc_start: 0.5864 (OUTLIER) cc_final: 0.5606 (t) REVERT: A 1742 ARG cc_start: 0.7264 (OUTLIER) cc_final: 0.7036 (ttp-170) REVERT: A 1789 LEU cc_start: 0.4354 (OUTLIER) cc_final: 0.3976 (tp) REVERT: C 177 GLN cc_start: 0.4174 (OUTLIER) cc_final: 0.3691 (tt0) REVERT: C 216 LEU cc_start: 0.5770 (OUTLIER) cc_final: 0.5123 (mt) REVERT: C 354 ARG cc_start: 0.5309 (OUTLIER) cc_final: 0.3143 (mmm160) REVERT: C 374 ARG cc_start: 0.6052 (mmm160) cc_final: 0.5789 (mmp80) REVERT: C 550 TYR cc_start: 0.4418 (OUTLIER) cc_final: 0.3645 (t80) REVERT: C 568 LEU cc_start: 0.3465 (OUTLIER) cc_final: 0.2821 (mt) REVERT: C 639 GLU cc_start: 0.1622 (OUTLIER) cc_final: 0.0912 (pm20) REVERT: C 643 GLU cc_start: 0.3472 (OUTLIER) cc_final: 0.2745 (tm-30) REVERT: C 763 LEU cc_start: 0.1374 (OUTLIER) cc_final: 0.0814 (mt) REVERT: C 789 TRP cc_start: 0.3093 (OUTLIER) cc_final: 0.2589 (t60) REVERT: C 820 ARG cc_start: 0.3130 (OUTLIER) cc_final: 0.2219 (ptt90) REVERT: C 892 LEU cc_start: 0.5730 (OUTLIER) cc_final: 0.5374 (tt) REVERT: C 951 MET cc_start: 0.3879 (ttp) cc_final: 0.3624 (tmm) REVERT: E 54 LEU cc_start: 0.5654 (OUTLIER) cc_final: 0.5233 (mt) REVERT: E 228 ASP cc_start: 0.6101 (OUTLIER) cc_final: 0.5178 (t0) REVERT: E 311 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.6820 (mtm180) REVERT: E 337 VAL cc_start: 0.4662 (OUTLIER) cc_final: 0.4160 (t) REVERT: E 342 LYS cc_start: 0.6606 (OUTLIER) cc_final: 0.5761 (mmtt) REVERT: r 51 LEU cc_start: 0.2639 (OUTLIER) cc_final: 0.2365 (tm) REVERT: r 84 MET cc_start: 0.2245 (tpt) cc_final: 0.1427 (mpp) REVERT: r 95 HIS cc_start: 0.1707 (OUTLIER) cc_final: 0.1241 (m170) REVERT: t 84 MET cc_start: 0.2985 (OUTLIER) cc_final: 0.2772 (tpp) REVERT: t 105 LEU cc_start: 0.1309 (OUTLIER) cc_final: 0.0734 (tt) REVERT: t 121 GLU cc_start: 0.1875 (OUTLIER) cc_final: 0.0194 (tt0) REVERT: t 123 ASP cc_start: 0.1833 (OUTLIER) cc_final: 0.1261 (t70) REVERT: a 44 MET cc_start: 0.5703 (OUTLIER) cc_final: 0.4843 (tmm) REVERT: g 48 GLU cc_start: 0.4407 (OUTLIER) cc_final: 0.3316 (tm-30) REVERT: e 9 MET cc_start: 0.3714 (OUTLIER) cc_final: 0.1527 (pmm) REVERT: e 49 MET cc_start: 0.0288 (mmp) cc_final: -0.0258 (mtt) REVERT: e 55 GLU cc_start: 0.4106 (OUTLIER) cc_final: 0.3578 (tm-30) REVERT: f 29 MET cc_start: 0.3547 (ttm) cc_final: 0.1722 (mpm) REVERT: d 68 GLU cc_start: 0.2764 (OUTLIER) cc_final: 0.1374 (pp20) REVERT: c 1 MET cc_start: 0.3417 (mtt) cc_final: 0.2487 (tmm) REVERT: c 9 MET cc_start: 0.1019 (mmp) cc_final: 0.0472 (ttm) REVERT: c 41 LEU cc_start: 0.3422 (OUTLIER) cc_final: 0.3216 (mp) REVERT: c 49 ARG cc_start: 0.3862 (OUTLIER) cc_final: 0.2449 (tpt170) REVERT: c 75 LEU cc_start: 0.1379 (OUTLIER) cc_final: 0.0675 (mt) REVERT: b 32 MET cc_start: 0.3536 (mmm) cc_final: 0.3252 (mmm) REVERT: b 61 GLU cc_start: 0.2249 (OUTLIER) cc_final: 0.1079 (mm-30) REVERT: I 360 ARG cc_start: 0.3542 (mmm-85) cc_final: 0.3302 (mmm160) REVERT: I 412 LYS cc_start: 0.2347 (OUTLIER) cc_final: 0.1882 (mtpp) REVERT: I 417 TRP cc_start: 0.0951 (m100) cc_final: 0.0476 (m-10) REVERT: I 420 PHE cc_start: 0.2292 (OUTLIER) cc_final: 0.1841 (t80) REVERT: I 461 MET cc_start: 0.0622 (tmm) cc_final: 0.0118 (ptm) REVERT: I 487 ARG cc_start: 0.3053 (OUTLIER) cc_final: 0.1918 (pmt170) REVERT: I 574 HIS cc_start: 0.2955 (OUTLIER) cc_final: 0.1923 (m-70) REVERT: I 623 LYS cc_start: 0.4279 (OUTLIER) cc_final: 0.3516 (ptpt) REVERT: I 625 GLU cc_start: 0.2873 (OUTLIER) cc_final: 0.1642 (pt0) REVERT: I 650 ARG cc_start: 0.2295 (OUTLIER) cc_final: 0.1761 (mmm160) REVERT: I 672 GLU cc_start: 0.3005 (mt-10) cc_final: 0.2516 (tt0) REVERT: I 697 ARG cc_start: 0.2466 (OUTLIER) cc_final: 0.1646 (mmt-90) REVERT: I 747 PHE cc_start: 0.1165 (OUTLIER) cc_final: 0.0938 (m-10) REVERT: I 748 LYS cc_start: 0.5105 (mmmt) cc_final: 0.4707 (ptpp) REVERT: I 750 MET cc_start: 0.1947 (mtp) cc_final: 0.0487 (mmp) REVERT: J 71 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.7013 (ptp90) REVERT: P 60 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7840 (ttm-80) REVERT: P 62 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7897 (mt-10) REVERT: M 510 LYS cc_start: 0.4442 (OUTLIER) cc_final: 0.3467 (tmmt) REVERT: T 469 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8400 (mt) REVERT: T 497 GLU cc_start: 0.5511 (OUTLIER) cc_final: 0.4855 (pp20) REVERT: O 264 MET cc_start: 0.1208 (pmm) cc_final: 0.0700 (pmt) REVERT: N 6 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8131 (pttt) REVERT: N 21 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6830 (tm-30) REVERT: N 52 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.8202 (ttp-170) REVERT: N 82 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7479 (mp0) REVERT: N 170 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7016 (mt-10) REVERT: R 161 LEU cc_start: 0.3851 (OUTLIER) cc_final: 0.3265 (mt) REVERT: R 191 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8417 (mm) REVERT: R 205 LYS cc_start: 0.7602 (OUTLIER) cc_final: 0.6928 (mptt) REVERT: R 236 GLN cc_start: 0.6867 (OUTLIER) cc_final: 0.6635 (mp10) REVERT: R 251 LYS cc_start: 0.6278 (OUTLIER) cc_final: 0.5888 (mtmt) REVERT: S 9 ASP cc_start: 0.6746 (OUTLIER) cc_final: 0.6111 (p0) REVERT: S 67 GLU cc_start: 0.6678 (mp0) cc_final: 0.6039 (mm-30) REVERT: L 150 MET cc_start: 0.6288 (ttm) cc_final: 0.5944 (tmm) REVERT: L 188 ARG cc_start: 0.4178 (OUTLIER) cc_final: 0.3025 (ttp-170) REVERT: L 241 ARG cc_start: 0.3276 (OUTLIER) cc_final: 0.2505 (pmt170) REVERT: L 545 ARG cc_start: 0.3130 (OUTLIER) cc_final: 0.2224 (mtt90) REVERT: L 557 GLU cc_start: 0.3086 (OUTLIER) cc_final: 0.2735 (tm-30) REVERT: L 601 GLU cc_start: 0.3071 (OUTLIER) cc_final: 0.2651 (mm-30) REVERT: L 608 MET cc_start: 0.2508 (ptp) cc_final: 0.1376 (mmt) REVERT: L 614 HIS cc_start: 0.1775 (OUTLIER) cc_final: 0.0921 (t-90) REVERT: L 618 LYS cc_start: 0.2766 (OUTLIER) cc_final: 0.1533 (tmtt) REVERT: L 646 GLU cc_start: 0.3287 (OUTLIER) cc_final: 0.2075 (mm-30) REVERT: L 650 GLU cc_start: 0.2678 (OUTLIER) cc_final: 0.1768 (tt0) REVERT: L 662 GLU cc_start: 0.2094 (OUTLIER) cc_final: 0.1845 (pm20) REVERT: L 744 LEU cc_start: 0.0017 (OUTLIER) cc_final: -0.0360 (pp) REVERT: L 776 LYS cc_start: 0.5736 (ttpp) cc_final: 0.5189 (tptm) REVERT: L 795 GLU cc_start: 0.5200 (OUTLIER) cc_final: 0.4873 (mm-30) REVERT: K 104 TYR cc_start: 0.0103 (OUTLIER) cc_final: -0.0515 (t80) REVERT: K 113 ARG cc_start: 0.3630 (OUTLIER) cc_final: 0.2949 (ttm-80) outliers start: 539 outliers final: 312 residues processed: 1072 average time/residue: 1.4402 time to fit residues: 2071.5824 Evaluate side-chains 990 residues out of total 8096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 402 poor density : 588 time to evaluate : 5.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 493 CYS Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 544 LYS Chi-restraints excluded: chain A residue 589 LYS Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 909 ARG Chi-restraints excluded: chain A residue 912 GLU Chi-restraints excluded: chain A residue 954 SER Chi-restraints excluded: chain A residue 978 LEU Chi-restraints excluded: chain A residue 995 ASP Chi-restraints excluded: chain A residue 997 ARG Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1026 VAL Chi-restraints excluded: chain A residue 1038 VAL Chi-restraints excluded: chain A residue 1042 GLN Chi-restraints excluded: chain A residue 1046 GLU Chi-restraints excluded: chain A residue 1059 ARG Chi-restraints excluded: chain A residue 1087 SER Chi-restraints excluded: chain A residue 1091 SER Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1131 CYS Chi-restraints excluded: chain A residue 1153 SER Chi-restraints excluded: chain A residue 1201 ASP Chi-restraints excluded: chain A residue 1231 THR Chi-restraints excluded: chain A residue 1233 GLU Chi-restraints excluded: chain A residue 1240 SER Chi-restraints excluded: chain A residue 1285 THR Chi-restraints excluded: chain A residue 1289 THR Chi-restraints excluded: chain A residue 1307 ARG Chi-restraints excluded: chain A residue 1319 THR Chi-restraints excluded: chain A residue 1351 LEU Chi-restraints excluded: chain A residue 1362 ARG Chi-restraints excluded: chain A residue 1365 ILE Chi-restraints excluded: chain A residue 1385 GLU Chi-restraints excluded: chain A residue 1402 SER Chi-restraints excluded: chain A residue 1417 PHE Chi-restraints excluded: chain A residue 1428 LEU Chi-restraints excluded: chain A residue 1433 TYR Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain A residue 1465 ARG Chi-restraints excluded: chain A residue 1480 ILE Chi-restraints excluded: chain A residue 1493 THR Chi-restraints excluded: chain A residue 1502 VAL Chi-restraints excluded: chain A residue 1511 ILE Chi-restraints excluded: chain A residue 1512 THR Chi-restraints excluded: chain A residue 1538 VAL Chi-restraints excluded: chain A residue 1557 THR Chi-restraints excluded: chain A residue 1593 ILE Chi-restraints excluded: chain A residue 1605 THR Chi-restraints excluded: chain A residue 1626 MET Chi-restraints excluded: chain A residue 1627 HIS Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1635 ILE Chi-restraints excluded: chain A residue 1658 CYS Chi-restraints excluded: chain A residue 1688 SER Chi-restraints excluded: chain A residue 1704 SER Chi-restraints excluded: chain A residue 1712 THR Chi-restraints excluded: chain A residue 1719 LYS Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1728 VAL Chi-restraints excluded: chain A residue 1742 ARG Chi-restraints excluded: chain A residue 1747 LYS Chi-restraints excluded: chain A residue 1754 ASP Chi-restraints excluded: chain A residue 1757 SER Chi-restraints excluded: chain A residue 1783 PHE Chi-restraints excluded: chain A residue 1789 LEU Chi-restraints excluded: chain A residue 1807 LEU Chi-restraints excluded: chain A residue 1820 SER Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 257 ARG Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 306 CYS Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 354 ARG Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 485 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 550 TYR Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 639 GLU Chi-restraints excluded: chain C residue 643 GLU Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 726 MET Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 771 THR Chi-restraints excluded: chain C residue 789 TRP Chi-restraints excluded: chain C residue 797 CYS Chi-restraints excluded: chain C residue 809 LEU Chi-restraints excluded: chain C residue 810 ASP Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 820 ARG Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 874 VAL Chi-restraints excluded: chain C residue 878 VAL Chi-restraints excluded: chain C residue 892 LEU Chi-restraints excluded: chain C residue 902 THR Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 79 CYS Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 200 PHE Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 306 CYS Chi-restraints excluded: chain E residue 311 ARG Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 333 SER Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 342 LYS Chi-restraints excluded: chain E residue 354 THR Chi-restraints excluded: chain q residue 26 SER Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain q residue 46 SER Chi-restraints excluded: chain q residue 114 VAL Chi-restraints excluded: chain r residue 2 PHE Chi-restraints excluded: chain r residue 9 VAL Chi-restraints excluded: chain r residue 41 THR Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain r residue 51 LEU Chi-restraints excluded: chain r residue 55 VAL Chi-restraints excluded: chain r residue 63 THR Chi-restraints excluded: chain r residue 95 HIS Chi-restraints excluded: chain r residue 101 LEU Chi-restraints excluded: chain r residue 113 ARG Chi-restraints excluded: chain s residue 85 LEU Chi-restraints excluded: chain t residue 84 MET Chi-restraints excluded: chain t residue 105 LEU Chi-restraints excluded: chain t residue 121 GLU Chi-restraints excluded: chain t residue 123 ASP Chi-restraints excluded: chain a residue 19 GLU Chi-restraints excluded: chain a residue 44 MET Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain g residue 27 VAL Chi-restraints excluded: chain g residue 38 MET Chi-restraints excluded: chain g residue 48 GLU Chi-restraints excluded: chain e residue 9 MET Chi-restraints excluded: chain e residue 10 THR Chi-restraints excluded: chain e residue 37 ARG Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 55 GLU Chi-restraints excluded: chain e residue 68 THR Chi-restraints excluded: chain e residue 72 ILE Chi-restraints excluded: chain f residue 22 ILE Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 48 SER Chi-restraints excluded: chain d residue 42 CYS Chi-restraints excluded: chain d residue 51 ARG Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 68 GLU Chi-restraints excluded: chain d residue 80 GLN Chi-restraints excluded: chain d residue 84 ARG Chi-restraints excluded: chain c residue 2 VAL Chi-restraints excluded: chain c residue 10 LYS Chi-restraints excluded: chain c residue 41 LEU Chi-restraints excluded: chain c residue 49 ARG Chi-restraints excluded: chain c residue 75 LEU Chi-restraints excluded: chain c residue 79 THR Chi-restraints excluded: chain b residue 36 ARG Chi-restraints excluded: chain b residue 61 GLU Chi-restraints excluded: chain b residue 105 ILE Chi-restraints excluded: chain I residue 356 LEU Chi-restraints excluded: chain I residue 366 SER Chi-restraints excluded: chain I residue 367 VAL Chi-restraints excluded: chain I residue 380 HIS Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain I residue 412 LYS Chi-restraints excluded: chain I residue 420 PHE Chi-restraints excluded: chain I residue 456 CYS Chi-restraints excluded: chain I residue 473 ASP Chi-restraints excluded: chain I residue 476 THR Chi-restraints excluded: chain I residue 480 THR Chi-restraints excluded: chain I residue 484 ARG Chi-restraints excluded: chain I residue 487 ARG Chi-restraints excluded: chain I residue 506 LEU Chi-restraints excluded: chain I residue 574 HIS Chi-restraints excluded: chain I residue 599 ARG Chi-restraints excluded: chain I residue 623 LYS Chi-restraints excluded: chain I residue 625 GLU Chi-restraints excluded: chain I residue 650 ARG Chi-restraints excluded: chain I residue 667 ILE Chi-restraints excluded: chain I residue 670 VAL Chi-restraints excluded: chain I residue 687 SER Chi-restraints excluded: chain I residue 697 ARG Chi-restraints excluded: chain I residue 702 GLU Chi-restraints excluded: chain I residue 737 PHE Chi-restraints excluded: chain I residue 746 THR Chi-restraints excluded: chain I residue 747 PHE Chi-restraints excluded: chain J residue 61 SER Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 71 ARG Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain J residue 144 ARG Chi-restraints excluded: chain J residue 167 GLN Chi-restraints excluded: chain J residue 195 VAL Chi-restraints excluded: chain J residue 196 ASP Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 276 LEU Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain J residue 296 LYS Chi-restraints excluded: chain P residue 13 ILE Chi-restraints excluded: chain P residue 60 ARG Chi-restraints excluded: chain P residue 62 GLU Chi-restraints excluded: chain P residue 231 GLN Chi-restraints excluded: chain M residue 496 VAL Chi-restraints excluded: chain M residue 510 LYS Chi-restraints excluded: chain M residue 538 LYS Chi-restraints excluded: chain T residue 212 CYS Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 286 SER Chi-restraints excluded: chain T residue 314 VAL Chi-restraints excluded: chain T residue 324 VAL Chi-restraints excluded: chain T residue 388 PHE Chi-restraints excluded: chain T residue 396 GLU Chi-restraints excluded: chain T residue 414 SER Chi-restraints excluded: chain T residue 422 SER Chi-restraints excluded: chain T residue 446 ARG Chi-restraints excluded: chain T residue 465 SER Chi-restraints excluded: chain T residue 469 LEU Chi-restraints excluded: chain T residue 485 GLU Chi-restraints excluded: chain T residue 497 GLU Chi-restraints excluded: chain O residue 22 VAL Chi-restraints excluded: chain O residue 38 ILE Chi-restraints excluded: chain O residue 49 ARG Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 120 MET Chi-restraints excluded: chain O residue 165 VAL Chi-restraints excluded: chain O residue 184 HIS Chi-restraints excluded: chain O residue 224 THR Chi-restraints excluded: chain O residue 248 VAL Chi-restraints excluded: chain O residue 266 VAL Chi-restraints excluded: chain O residue 267 LYS Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 19 ILE Chi-restraints excluded: chain N residue 21 GLU Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 52 ARG Chi-restraints excluded: chain N residue 82 GLU Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain N residue 170 GLU Chi-restraints excluded: chain R residue 83 ILE Chi-restraints excluded: chain R residue 88 LYS Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 118 VAL Chi-restraints excluded: chain R residue 122 SER Chi-restraints excluded: chain R residue 152 LYS Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 168 SER Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 191 ILE Chi-restraints excluded: chain R residue 195 ASP Chi-restraints excluded: chain R residue 205 LYS Chi-restraints excluded: chain R residue 211 VAL Chi-restraints excluded: chain R residue 220 VAL Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 231 THR Chi-restraints excluded: chain R residue 236 GLN Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 251 LYS Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain R residue 255 ILE Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 6 VAL Chi-restraints excluded: chain S residue 9 ASP Chi-restraints excluded: chain S residue 23 HIS Chi-restraints excluded: chain S residue 28 CYS Chi-restraints excluded: chain S residue 50 ARG Chi-restraints excluded: chain S residue 76 ASP Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain S residue 92 MET Chi-restraints excluded: chain S residue 134 LEU Chi-restraints excluded: chain S residue 146 VAL Chi-restraints excluded: chain S residue 152 ILE Chi-restraints excluded: chain W residue 87 LEU Chi-restraints excluded: chain W residue 91 HIS Chi-restraints excluded: chain W residue 107 VAL Chi-restraints excluded: chain W residue 112 ASP Chi-restraints excluded: chain W residue 118 ILE Chi-restraints excluded: chain W residue 121 GLU Chi-restraints excluded: chain W residue 167 THR Chi-restraints excluded: chain W residue 168 THR Chi-restraints excluded: chain W residue 218 ILE Chi-restraints excluded: chain L residue 23 MET Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain L residue 188 ARG Chi-restraints excluded: chain L residue 207 VAL Chi-restraints excluded: chain L residue 217 LEU Chi-restraints excluded: chain L residue 241 ARG Chi-restraints excluded: chain L residue 545 ARG Chi-restraints excluded: chain L residue 557 GLU Chi-restraints excluded: chain L residue 601 GLU Chi-restraints excluded: chain L residue 614 HIS Chi-restraints excluded: chain L residue 618 LYS Chi-restraints excluded: chain L residue 646 GLU Chi-restraints excluded: chain L residue 650 GLU Chi-restraints excluded: chain L residue 662 GLU Chi-restraints excluded: chain L residue 696 SER Chi-restraints excluded: chain L residue 744 LEU Chi-restraints excluded: chain L residue 791 GLU Chi-restraints excluded: chain L residue 795 GLU Chi-restraints excluded: chain L residue 798 ASP Chi-restraints excluded: chain L residue 800 THR Chi-restraints excluded: chain K residue 28 HIS Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 66 LEU Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 104 TYR Chi-restraints excluded: chain K residue 113 ARG Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain K residue 217 ASP Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 2 TYR Chi-restraints excluded: chain U residue 8 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 23 LYS Chi-restraints excluded: chain V residue 655 LEU Chi-restraints excluded: chain V residue 661 LEU Chi-restraints excluded: chain V residue 668 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 956 random chunks: chunk 124 optimal weight: 0.8980 chunk 925 optimal weight: 50.0000 chunk 478 optimal weight: 8.9990 chunk 765 optimal weight: 20.0000 chunk 116 optimal weight: 0.8980 chunk 568 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 898 optimal weight: 0.0980 chunk 379 optimal weight: 5.9990 chunk 464 optimal weight: 10.0000 chunk 943 optimal weight: 50.0000 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 269 HIS A 512 GLN A 587 ASN A 939 HIS ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1246 ASN A1423 HIS A1616 GLN C 68 HIS ** C 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 GLN ** C 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 21 HIS r 96 GLN r 99 GLN ** s 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 21 HIS a 47 GLN I 380 HIS ** I 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 278 HIS P 45 GLN P 212 GLN R 80 GLN ** R 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 198 GLN K 141 GLN ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4994 r_free = 0.4994 target = 0.280536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.250893 restraints weight = 85183.982| |-----------------------------------------------------------------------------| r_work (start): 0.4748 rms_B_bonded: 1.71 r_work: 0.4475 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.4443 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.4443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6128 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 75153 Z= 0.225 Angle : 0.676 12.888 103334 Z= 0.346 Chirality : 0.044 0.259 11959 Planarity : 0.005 0.094 12679 Dihedral : 17.056 178.929 14355 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.31 % Favored : 95.63 % Rotamer: Outliers : 6.70 % Allowed : 32.24 % Favored : 61.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.09), residues: 9287 helix: 0.85 (0.08), residues: 4348 sheet: -0.87 (0.15), residues: 1127 loop : -1.26 (0.10), residues: 3812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.002 TRP A1701 HIS 0.009 0.001 HIS C 145 PHE 0.027 0.002 PHE W 217 TYR 0.032 0.002 TYR A1433 ARG 0.011 0.001 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18574 Ramachandran restraints generated. 9287 Oldfield, 0 Emsley, 9287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18574 Ramachandran restraints generated. 9287 Oldfield, 0 Emsley, 9287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1002 residues out of total 8096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 393 poor density : 609 time to evaluate : 5.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.7932 (ptt90) cc_final: 0.7720 (ptm160) REVERT: A 276 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7841 (ptmt) REVERT: A 331 ILE cc_start: 0.4691 (OUTLIER) cc_final: 0.4321 (pp) REVERT: A 498 HIS cc_start: 0.4736 (OUTLIER) cc_final: 0.4104 (t-90) REVERT: A 589 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.7604 (pttm) REVERT: A 1046 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6884 (mm-30) REVERT: A 1215 ARG cc_start: 0.7875 (mtt-85) cc_final: 0.7648 (mtp180) REVERT: A 1233 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7253 (tp30) REVERT: A 1266 MET cc_start: 0.6731 (ttm) cc_final: 0.6485 (ttm) REVERT: A 1273 ASN cc_start: 0.1972 (OUTLIER) cc_final: 0.1594 (p0) REVERT: A 1362 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.6497 (tpt90) REVERT: A 1417 PHE cc_start: 0.4721 (OUTLIER) cc_final: 0.4371 (p90) REVERT: A 1465 ARG cc_start: 0.4424 (OUTLIER) cc_final: 0.4101 (tmm-80) REVERT: A 1480 ILE cc_start: 0.7014 (OUTLIER) cc_final: 0.6562 (tp) REVERT: A 1626 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.8156 (mtm) REVERT: A 1630 ILE cc_start: 0.7901 (OUTLIER) cc_final: 0.7489 (mt) REVERT: A 1742 ARG cc_start: 0.7141 (OUTLIER) cc_final: 0.6915 (ttp-170) REVERT: A 1783 PHE cc_start: 0.2305 (OUTLIER) cc_final: 0.1396 (p90) REVERT: A 1789 LEU cc_start: 0.4136 (OUTLIER) cc_final: 0.3841 (tp) REVERT: C 69 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6312 (tp30) REVERT: C 106 LYS cc_start: 0.5065 (OUTLIER) cc_final: 0.4749 (mtpm) REVERT: C 177 GLN cc_start: 0.4237 (OUTLIER) cc_final: 0.3840 (tt0) REVERT: C 216 LEU cc_start: 0.5527 (OUTLIER) cc_final: 0.4894 (mt) REVERT: C 227 GLU cc_start: 0.6588 (OUTLIER) cc_final: 0.5907 (mm-30) REVERT: C 257 ARG cc_start: 0.5545 (OUTLIER) cc_final: 0.4119 (mpt-90) REVERT: C 550 TYR cc_start: 0.4313 (OUTLIER) cc_final: 0.3655 (t80) REVERT: C 639 GLU cc_start: 0.1089 (OUTLIER) cc_final: 0.0660 (pm20) REVERT: C 643 GLU cc_start: 0.3420 (OUTLIER) cc_final: 0.2920 (tm-30) REVERT: C 789 TRP cc_start: 0.3133 (OUTLIER) cc_final: 0.2616 (t60) REVERT: C 892 LEU cc_start: 0.5638 (OUTLIER) cc_final: 0.5328 (tt) REVERT: E 200 PHE cc_start: 0.4623 (OUTLIER) cc_final: 0.3507 (t80) REVERT: E 228 ASP cc_start: 0.5159 (OUTLIER) cc_final: 0.4707 (t0) REVERT: E 337 VAL cc_start: 0.4347 (OUTLIER) cc_final: 0.4017 (t) REVERT: E 342 LYS cc_start: 0.6515 (OUTLIER) cc_final: 0.5686 (mmtt) REVERT: r 18 LYS cc_start: 0.2800 (OUTLIER) cc_final: 0.1467 (mttt) REVERT: r 84 MET cc_start: 0.2148 (tpt) cc_final: 0.1467 (mpp) REVERT: r 95 HIS cc_start: 0.1674 (OUTLIER) cc_final: 0.1244 (m170) REVERT: t 105 LEU cc_start: 0.1150 (OUTLIER) cc_final: 0.0629 (tt) REVERT: a 44 MET cc_start: 0.5666 (OUTLIER) cc_final: 0.5158 (tmm) REVERT: e 9 MET cc_start: 0.3286 (OUTLIER) cc_final: 0.1351 (pmm) REVERT: e 49 MET cc_start: 0.0595 (mmp) cc_final: 0.0076 (mtt) REVERT: e 55 GLU cc_start: 0.3987 (OUTLIER) cc_final: 0.3753 (tm-30) REVERT: f 29 MET cc_start: 0.3364 (ttm) cc_final: 0.1550 (mpm) REVERT: d 68 GLU cc_start: 0.2492 (OUTLIER) cc_final: 0.1163 (pp20) REVERT: c 1 MET cc_start: 0.3255 (mtt) cc_final: 0.2377 (tmm) REVERT: c 10 LYS cc_start: 0.3783 (OUTLIER) cc_final: 0.2402 (tptp) REVERT: c 37 MET cc_start: 0.3532 (mpp) cc_final: 0.2672 (pmm) REVERT: c 75 LEU cc_start: 0.1226 (OUTLIER) cc_final: 0.0518 (mt) REVERT: b 32 MET cc_start: 0.3432 (mmm) cc_final: 0.3047 (mmm) REVERT: I 356 LEU cc_start: 0.1442 (OUTLIER) cc_final: 0.0802 (mt) REVERT: I 360 ARG cc_start: 0.3383 (mmm-85) cc_final: 0.3175 (mmm160) REVERT: I 366 SER cc_start: 0.1340 (OUTLIER) cc_final: 0.0908 (t) REVERT: I 412 LYS cc_start: 0.2032 (OUTLIER) cc_final: 0.1540 (mtpp) REVERT: I 417 TRP cc_start: 0.0700 (m100) cc_final: 0.0262 (m-90) REVERT: I 456 CYS cc_start: 0.2981 (OUTLIER) cc_final: 0.2744 (m) REVERT: I 461 MET cc_start: 0.0499 (tmm) cc_final: 0.0087 (ptm) REVERT: I 492 GLU cc_start: 0.4553 (mm-30) cc_final: 0.3705 (pp20) REVERT: I 574 HIS cc_start: 0.2767 (OUTLIER) cc_final: 0.1746 (m-70) REVERT: I 625 GLU cc_start: 0.2681 (OUTLIER) cc_final: 0.1491 (pt0) REVERT: I 650 ARG cc_start: 0.2228 (OUTLIER) cc_final: 0.1793 (mmm160) REVERT: I 672 GLU cc_start: 0.2843 (mt-10) cc_final: 0.2159 (tt0) REVERT: I 697 ARG cc_start: 0.2523 (OUTLIER) cc_final: 0.1764 (mmt-90) REVERT: I 747 PHE cc_start: 0.1190 (OUTLIER) cc_final: 0.0891 (m-10) REVERT: I 748 LYS cc_start: 0.4936 (mmmt) cc_final: 0.4621 (ptpp) REVERT: I 750 MET cc_start: 0.1867 (mtp) cc_final: 0.0396 (mmp) REVERT: J 71 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.7220 (ptp90) REVERT: J 318 GLU cc_start: 0.3059 (OUTLIER) cc_final: 0.2254 (tm-30) REVERT: P 62 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7797 (mt-10) REVERT: M 476 PHE cc_start: 0.5466 (OUTLIER) cc_final: 0.5215 (p90) REVERT: M 510 LYS cc_start: 0.4137 (OUTLIER) cc_final: 0.3489 (pptt) REVERT: T 190 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7626 (mtp-110) REVERT: O 264 MET cc_start: 0.0963 (OUTLIER) cc_final: 0.0466 (pmt) REVERT: O 267 LYS cc_start: 0.2378 (OUTLIER) cc_final: 0.1411 (ptmt) REVERT: N 6 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.8032 (pttt) REVERT: N 21 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6469 (tt0) REVERT: N 52 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8165 (ttp-170) REVERT: N 82 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7155 (mp0) REVERT: N 170 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.6966 (mt-10) REVERT: R 191 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8407 (mm) REVERT: R 205 LYS cc_start: 0.7499 (OUTLIER) cc_final: 0.6839 (mptt) REVERT: R 259 LYS cc_start: 0.6824 (ttmm) cc_final: 0.6467 (tttm) REVERT: S 67 GLU cc_start: 0.6628 (mp0) cc_final: 0.5951 (mm-30) REVERT: W 77 LEU cc_start: 0.8129 (mp) cc_final: 0.7913 (mt) REVERT: L 150 MET cc_start: 0.6271 (ttm) cc_final: 0.5884 (tmm) REVERT: L 188 ARG cc_start: 0.4093 (OUTLIER) cc_final: 0.3036 (ttp80) REVERT: L 236 MET cc_start: 0.7839 (mtt) cc_final: 0.7522 (mtt) REVERT: L 241 ARG cc_start: 0.3084 (OUTLIER) cc_final: 0.2412 (pmt170) REVERT: L 545 ARG cc_start: 0.3192 (OUTLIER) cc_final: 0.2168 (mtt90) REVERT: L 557 GLU cc_start: 0.2992 (OUTLIER) cc_final: 0.2757 (tm-30) REVERT: L 601 GLU cc_start: 0.3012 (OUTLIER) cc_final: 0.2588 (mm-30) REVERT: L 608 MET cc_start: 0.2350 (ptp) cc_final: 0.1273 (mmt) REVERT: L 614 HIS cc_start: 0.1421 (OUTLIER) cc_final: 0.0630 (t-90) REVERT: L 618 LYS cc_start: 0.2876 (OUTLIER) cc_final: 0.1622 (tmtt) REVERT: L 646 GLU cc_start: 0.3016 (OUTLIER) cc_final: 0.1836 (mm-30) REVERT: L 650 GLU cc_start: 0.2669 (OUTLIER) cc_final: 0.1717 (tt0) REVERT: L 744 LEU cc_start: -0.0196 (OUTLIER) cc_final: -0.0570 (pp) REVERT: L 765 VAL cc_start: 0.2230 (m) cc_final: 0.1995 (t) REVERT: L 776 LYS cc_start: 0.5697 (ttpp) cc_final: 0.5190 (tptm) REVERT: L 798 ASP cc_start: 0.3470 (OUTLIER) cc_final: 0.2309 (t70) REVERT: K 28 HIS cc_start: 0.3649 (OUTLIER) cc_final: 0.2824 (p-80) REVERT: K 87 TYR cc_start: 0.2233 (OUTLIER) cc_final: 0.0625 (t80) REVERT: K 104 TYR cc_start: -0.0028 (OUTLIER) cc_final: -0.0610 (t80) REVERT: K 113 ARG cc_start: 0.3506 (OUTLIER) cc_final: 0.2968 (ttm-80) REVERT: K 144 LEU cc_start: 0.3618 (OUTLIER) cc_final: 0.2988 (mm) REVERT: V 678 LYS cc_start: 0.5435 (OUTLIER) cc_final: 0.3644 (ptpt) outliers start: 393 outliers final: 204 residues processed: 940 average time/residue: 1.5863 time to fit residues: 2029.4450 Evaluate side-chains 868 residues out of total 8096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 284 poor density : 584 time to evaluate : 5.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 493 CYS Chi-restraints excluded: chain A residue 498 HIS Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 544 LYS Chi-restraints excluded: chain A residue 589 LYS Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 912 GLU Chi-restraints excluded: chain A residue 978 LEU Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1026 VAL Chi-restraints excluded: chain A residue 1046 GLU Chi-restraints excluded: chain A residue 1059 ARG Chi-restraints excluded: chain A residue 1087 SER Chi-restraints excluded: chain A residue 1091 SER Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1131 CYS Chi-restraints excluded: chain A residue 1231 THR Chi-restraints excluded: chain A residue 1233 GLU Chi-restraints excluded: chain A residue 1240 SER Chi-restraints excluded: chain A residue 1246 ASN Chi-restraints excluded: chain A residue 1273 ASN Chi-restraints excluded: chain A residue 1285 THR Chi-restraints excluded: chain A residue 1289 THR Chi-restraints excluded: chain A residue 1307 ARG Chi-restraints excluded: chain A residue 1319 THR Chi-restraints excluded: chain A residue 1351 LEU Chi-restraints excluded: chain A residue 1362 ARG Chi-restraints excluded: chain A residue 1365 ILE Chi-restraints excluded: chain A residue 1385 GLU Chi-restraints excluded: chain A residue 1402 SER Chi-restraints excluded: chain A residue 1417 PHE Chi-restraints excluded: chain A residue 1428 LEU Chi-restraints excluded: chain A residue 1465 ARG Chi-restraints excluded: chain A residue 1480 ILE Chi-restraints excluded: chain A residue 1493 THR Chi-restraints excluded: chain A residue 1502 VAL Chi-restraints excluded: chain A residue 1512 THR Chi-restraints excluded: chain A residue 1538 VAL Chi-restraints excluded: chain A residue 1557 THR Chi-restraints excluded: chain A residue 1593 ILE Chi-restraints excluded: chain A residue 1605 THR Chi-restraints excluded: chain A residue 1626 MET Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1635 ILE Chi-restraints excluded: chain A residue 1671 GLU Chi-restraints excluded: chain A residue 1688 SER Chi-restraints excluded: chain A residue 1712 THR Chi-restraints excluded: chain A residue 1719 LYS Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1728 VAL Chi-restraints excluded: chain A residue 1742 ARG Chi-restraints excluded: chain A residue 1747 LYS Chi-restraints excluded: chain A residue 1757 SER Chi-restraints excluded: chain A residue 1783 PHE Chi-restraints excluded: chain A residue 1789 LEU Chi-restraints excluded: chain A residue 1807 LEU Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 106 LYS Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 257 ARG Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 306 CYS Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 550 TYR Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 639 GLU Chi-restraints excluded: chain C residue 643 GLU Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 771 THR Chi-restraints excluded: chain C residue 789 TRP Chi-restraints excluded: chain C residue 810 ASP Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 820 ARG Chi-restraints excluded: chain C residue 874 VAL Chi-restraints excluded: chain C residue 892 LEU Chi-restraints excluded: chain C residue 902 THR Chi-restraints excluded: chain E residue 79 CYS Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 200 PHE Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 306 CYS Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain E residue 333 SER Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 342 LYS Chi-restraints excluded: chain E residue 354 THR Chi-restraints excluded: chain q residue 46 SER Chi-restraints excluded: chain r residue 2 PHE Chi-restraints excluded: chain r residue 9 VAL Chi-restraints excluded: chain r residue 18 LYS Chi-restraints excluded: chain r residue 41 THR Chi-restraints excluded: chain r residue 55 VAL Chi-restraints excluded: chain r residue 95 HIS Chi-restraints excluded: chain r residue 113 ARG Chi-restraints excluded: chain s residue 85 LEU Chi-restraints excluded: chain t residue 105 LEU Chi-restraints excluded: chain a residue 19 GLU Chi-restraints excluded: chain a residue 44 MET Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 68 ILE Chi-restraints excluded: chain g residue 38 MET Chi-restraints excluded: chain e residue 9 MET Chi-restraints excluded: chain e residue 10 THR Chi-restraints excluded: chain e residue 55 GLU Chi-restraints excluded: chain e residue 58 GLU Chi-restraints excluded: chain e residue 72 ILE Chi-restraints excluded: chain f residue 22 ILE Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 48 SER Chi-restraints excluded: chain d residue 42 CYS Chi-restraints excluded: chain d residue 68 GLU Chi-restraints excluded: chain d residue 80 GLN Chi-restraints excluded: chain c residue 2 VAL Chi-restraints excluded: chain c residue 10 LYS Chi-restraints excluded: chain c residue 75 LEU Chi-restraints excluded: chain c residue 79 THR Chi-restraints excluded: chain b residue 36 ARG Chi-restraints excluded: chain b residue 40 LEU Chi-restraints excluded: chain b residue 45 SER Chi-restraints excluded: chain b residue 105 ILE Chi-restraints excluded: chain I residue 356 LEU Chi-restraints excluded: chain I residue 366 SER Chi-restraints excluded: chain I residue 367 VAL Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain I residue 412 LYS Chi-restraints excluded: chain I residue 438 GLN Chi-restraints excluded: chain I residue 456 CYS Chi-restraints excluded: chain I residue 473 ASP Chi-restraints excluded: chain I residue 574 HIS Chi-restraints excluded: chain I residue 599 ARG Chi-restraints excluded: chain I residue 625 GLU Chi-restraints excluded: chain I residue 650 ARG Chi-restraints excluded: chain I residue 670 VAL Chi-restraints excluded: chain I residue 687 SER Chi-restraints excluded: chain I residue 697 ARG Chi-restraints excluded: chain I residue 702 GLU Chi-restraints excluded: chain I residue 746 THR Chi-restraints excluded: chain I residue 747 PHE Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 71 ARG Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain J residue 144 ARG Chi-restraints excluded: chain J residue 202 PHE Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain J residue 318 GLU Chi-restraints excluded: chain P residue 13 ILE Chi-restraints excluded: chain M residue 476 PHE Chi-restraints excluded: chain M residue 496 VAL Chi-restraints excluded: chain M residue 510 LYS Chi-restraints excluded: chain T residue 190 ARG Chi-restraints excluded: chain T residue 212 CYS Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 286 SER Chi-restraints excluded: chain T residue 314 VAL Chi-restraints excluded: chain T residue 324 VAL Chi-restraints excluded: chain T residue 388 PHE Chi-restraints excluded: chain T residue 396 GLU Chi-restraints excluded: chain T residue 446 ARG Chi-restraints excluded: chain T residue 465 SER Chi-restraints excluded: chain O residue 38 ILE Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 120 MET Chi-restraints excluded: chain O residue 165 VAL Chi-restraints excluded: chain O residue 184 HIS Chi-restraints excluded: chain O residue 224 THR Chi-restraints excluded: chain O residue 239 VAL Chi-restraints excluded: chain O residue 248 VAL Chi-restraints excluded: chain O residue 264 MET Chi-restraints excluded: chain O residue 266 VAL Chi-restraints excluded: chain O residue 267 LYS Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 19 ILE Chi-restraints excluded: chain N residue 21 GLU Chi-restraints excluded: chain N residue 52 ARG Chi-restraints excluded: chain N residue 82 GLU Chi-restraints excluded: chain N residue 170 GLU Chi-restraints excluded: chain R residue 83 ILE Chi-restraints excluded: chain R residue 88 LYS Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 118 VAL Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 191 ILE Chi-restraints excluded: chain R residue 195 ASP Chi-restraints excluded: chain R residue 205 LYS Chi-restraints excluded: chain R residue 211 VAL Chi-restraints excluded: chain R residue 220 VAL Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 231 THR Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 255 ILE Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain S residue 23 HIS Chi-restraints excluded: chain S residue 28 CYS Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain S residue 146 VAL Chi-restraints excluded: chain S residue 152 ILE Chi-restraints excluded: chain W residue 87 LEU Chi-restraints excluded: chain W residue 91 HIS Chi-restraints excluded: chain W residue 107 VAL Chi-restraints excluded: chain W residue 112 ASP Chi-restraints excluded: chain W residue 118 ILE Chi-restraints excluded: chain W residue 121 GLU Chi-restraints excluded: chain W residue 167 THR Chi-restraints excluded: chain W residue 168 THR Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 188 ARG Chi-restraints excluded: chain L residue 241 ARG Chi-restraints excluded: chain L residue 545 ARG Chi-restraints excluded: chain L residue 557 GLU Chi-restraints excluded: chain L residue 566 GLN Chi-restraints excluded: chain L residue 601 GLU Chi-restraints excluded: chain L residue 614 HIS Chi-restraints excluded: chain L residue 618 LYS Chi-restraints excluded: chain L residue 646 GLU Chi-restraints excluded: chain L residue 650 GLU Chi-restraints excluded: chain L residue 696 SER Chi-restraints excluded: chain L residue 744 LEU Chi-restraints excluded: chain L residue 798 ASP Chi-restraints excluded: chain L residue 800 THR Chi-restraints excluded: chain K residue 28 HIS Chi-restraints excluded: chain K residue 66 LEU Chi-restraints excluded: chain K residue 87 TYR Chi-restraints excluded: chain K residue 104 TYR Chi-restraints excluded: chain K residue 113 ARG Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 2 TYR Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain V residue 668 ASP Chi-restraints excluded: chain V residue 678 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 956 random chunks: chunk 64 optimal weight: 0.9980 chunk 545 optimal weight: 8.9990 chunk 563 optimal weight: 3.9990 chunk 389 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 527 optimal weight: 20.0000 chunk 751 optimal weight: 3.9990 chunk 856 optimal weight: 9.9990 chunk 566 optimal weight: 3.9990 chunk 748 optimal weight: 4.9990 chunk 498 optimal weight: 0.6980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 HIS ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 GLN A 587 ASN A 939 HIS ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1246 ASN C 68 HIS ** C 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 915 GLN ** E 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 96 GLN r 99 GLN ** s 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 21 HIS a 47 GLN ** e 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 45 GLN R 80 GLN ** R 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 141 GLN ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4983 r_free = 0.4983 target = 0.279227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.248946 restraints weight = 84829.714| |-----------------------------------------------------------------------------| r_work (start): 0.4729 rms_B_bonded: 1.78 r_work: 0.4450 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.4410 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.4410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6193 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 75153 Z= 0.372 Angle : 0.721 13.260 103334 Z= 0.369 Chirality : 0.047 0.289 11959 Planarity : 0.005 0.088 12679 Dihedral : 16.991 179.953 14326 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.33 % Favored : 94.62 % Rotamer: Outliers : 6.34 % Allowed : 32.87 % Favored : 60.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.09), residues: 9287 helix: 0.86 (0.08), residues: 4353 sheet: -0.93 (0.15), residues: 1146 loop : -1.25 (0.10), residues: 3788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRP A1701 HIS 0.009 0.002 HIS A 269 PHE 0.029 0.002 PHE J 175 TYR 0.030 0.002 TYR A1433 ARG 0.015 0.001 ARG C 957 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18574 Ramachandran restraints generated. 9287 Oldfield, 0 Emsley, 9287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18574 Ramachandran restraints generated. 9287 Oldfield, 0 Emsley, 9287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 970 residues out of total 8096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 372 poor density : 598 time to evaluate : 5.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.7982 (ptt90) cc_final: 0.7770 (ptm160) REVERT: A 276 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7880 (ptmt) REVERT: A 331 ILE cc_start: 0.4430 (OUTLIER) cc_final: 0.4099 (pp) REVERT: A 589 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.7555 (pttm) REVERT: A 1046 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6903 (mm-30) REVERT: A 1233 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7346 (tp30) REVERT: A 1273 ASN cc_start: 0.2175 (OUTLIER) cc_final: 0.1868 (p0) REVERT: A 1299 GLU cc_start: 0.7669 (tp30) cc_final: 0.7442 (tp30) REVERT: A 1362 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.6527 (tpt90) REVERT: A 1417 PHE cc_start: 0.4698 (OUTLIER) cc_final: 0.4353 (p90) REVERT: A 1465 ARG cc_start: 0.4506 (OUTLIER) cc_final: 0.4109 (tmm-80) REVERT: A 1480 ILE cc_start: 0.7024 (OUTLIER) cc_final: 0.6619 (tp) REVERT: A 1630 ILE cc_start: 0.7798 (OUTLIER) cc_final: 0.7384 (mt) REVERT: A 1742 ARG cc_start: 0.7196 (OUTLIER) cc_final: 0.6967 (ttp-170) REVERT: A 1748 PHE cc_start: 0.7763 (t80) cc_final: 0.7507 (t80) REVERT: A 1783 PHE cc_start: 0.2829 (OUTLIER) cc_final: 0.1694 (p90) REVERT: C 69 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.6342 (tp30) REVERT: C 177 GLN cc_start: 0.4315 (OUTLIER) cc_final: 0.3823 (tt0) REVERT: C 227 GLU cc_start: 0.6626 (OUTLIER) cc_final: 0.5919 (mm-30) REVERT: C 257 ARG cc_start: 0.5503 (OUTLIER) cc_final: 0.4076 (mpt-90) REVERT: C 527 LEU cc_start: 0.3921 (OUTLIER) cc_final: 0.3214 (mp) REVERT: C 550 TYR cc_start: 0.4319 (OUTLIER) cc_final: 0.3655 (t80) REVERT: C 639 GLU cc_start: 0.1032 (OUTLIER) cc_final: 0.0679 (pm20) REVERT: C 643 GLU cc_start: 0.3322 (OUTLIER) cc_final: 0.3036 (tm-30) REVERT: C 690 LYS cc_start: 0.4483 (OUTLIER) cc_final: 0.4041 (pptt) REVERT: C 789 TRP cc_start: 0.2982 (OUTLIER) cc_final: 0.2513 (t60) REVERT: C 892 LEU cc_start: 0.5740 (OUTLIER) cc_final: 0.5434 (tt) REVERT: E 228 ASP cc_start: 0.5592 (OUTLIER) cc_final: 0.5058 (t0) REVERT: E 311 ARG cc_start: 0.7239 (OUTLIER) cc_final: 0.6771 (mtm180) REVERT: E 337 VAL cc_start: 0.4352 (OUTLIER) cc_final: 0.4054 (t) REVERT: E 342 LYS cc_start: 0.6511 (OUTLIER) cc_final: 0.5765 (mmtt) REVERT: r 18 LYS cc_start: 0.2789 (OUTLIER) cc_final: 0.1467 (mttt) REVERT: r 84 MET cc_start: 0.2135 (tpt) cc_final: 0.1483 (mpp) REVERT: r 95 HIS cc_start: 0.1724 (OUTLIER) cc_final: 0.1261 (m170) REVERT: t 105 LEU cc_start: 0.1190 (OUTLIER) cc_final: 0.0644 (tt) REVERT: a 44 MET cc_start: 0.5679 (OUTLIER) cc_final: 0.5179 (tmm) REVERT: g 48 GLU cc_start: 0.4277 (OUTLIER) cc_final: 0.3141 (tm-30) REVERT: e 9 MET cc_start: 0.3299 (tpt) cc_final: 0.1315 (pmm) REVERT: e 49 MET cc_start: 0.0389 (mmp) cc_final: -0.0180 (mtt) REVERT: d 68 GLU cc_start: 0.2524 (OUTLIER) cc_final: 0.1193 (pp20) REVERT: c 1 MET cc_start: 0.3263 (mtt) cc_final: 0.2363 (tmm) REVERT: c 10 LYS cc_start: 0.3744 (OUTLIER) cc_final: 0.2414 (tptp) REVERT: c 37 MET cc_start: 0.3574 (mpp) cc_final: 0.3199 (mtm) REVERT: c 75 LEU cc_start: 0.1208 (OUTLIER) cc_final: 0.0481 (mt) REVERT: b 32 MET cc_start: 0.3415 (mmm) cc_final: 0.3050 (mmm) REVERT: b 42 LEU cc_start: 0.3811 (OUTLIER) cc_final: 0.3491 (tp) REVERT: b 45 SER cc_start: 0.3019 (OUTLIER) cc_final: 0.2711 (t) REVERT: I 356 LEU cc_start: 0.1422 (OUTLIER) cc_final: 0.0803 (mt) REVERT: I 366 SER cc_start: 0.1415 (OUTLIER) cc_final: 0.0951 (t) REVERT: I 367 VAL cc_start: 0.3422 (OUTLIER) cc_final: 0.2965 (t) REVERT: I 412 LYS cc_start: 0.2007 (OUTLIER) cc_final: 0.1498 (mtpp) REVERT: I 417 TRP cc_start: 0.0864 (m100) cc_final: 0.0374 (m-90) REVERT: I 456 CYS cc_start: 0.3235 (OUTLIER) cc_final: 0.2850 (m) REVERT: I 461 MET cc_start: 0.0578 (tmm) cc_final: 0.0181 (ptm) REVERT: I 492 GLU cc_start: 0.4593 (mm-30) cc_final: 0.3701 (pp20) REVERT: I 574 HIS cc_start: 0.2761 (OUTLIER) cc_final: 0.1737 (m-70) REVERT: I 625 GLU cc_start: 0.2741 (OUTLIER) cc_final: 0.1530 (pt0) REVERT: I 650 ARG cc_start: 0.2240 (OUTLIER) cc_final: 0.1788 (mmm160) REVERT: I 672 GLU cc_start: 0.2879 (mt-10) cc_final: 0.2248 (tt0) REVERT: I 747 PHE cc_start: 0.1243 (OUTLIER) cc_final: 0.0883 (m-80) REVERT: I 748 LYS cc_start: 0.4984 (mmmt) cc_final: 0.4610 (ptpp) REVERT: I 750 MET cc_start: 0.1879 (mtp) cc_final: 0.0392 (mmp) REVERT: J 71 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.7179 (ptp90) REVERT: P 62 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7838 (mt-10) REVERT: M 510 LYS cc_start: 0.4042 (OUTLIER) cc_final: 0.3274 (tmmt) REVERT: T 190 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7608 (mtp-110) REVERT: O 264 MET cc_start: 0.1077 (pmm) cc_final: 0.0574 (pmt) REVERT: N 6 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.8095 (pttt) REVERT: N 10 LYS cc_start: 0.6302 (OUTLIER) cc_final: 0.4318 (pmmt) REVERT: N 21 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6591 (tm-30) REVERT: N 52 ARG cc_start: 0.9083 (OUTLIER) cc_final: 0.8139 (ttp-170) REVERT: N 82 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7294 (mp0) REVERT: N 170 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7019 (mt-10) REVERT: R 205 LYS cc_start: 0.7522 (OUTLIER) cc_final: 0.6885 (mptt) REVERT: R 259 LYS cc_start: 0.6882 (ttmm) cc_final: 0.6516 (tttm) REVERT: S 67 GLU cc_start: 0.6567 (mp0) cc_final: 0.5971 (mm-30) REVERT: L 150 MET cc_start: 0.6380 (ttm) cc_final: 0.5987 (tmm) REVERT: L 188 ARG cc_start: 0.4092 (OUTLIER) cc_final: 0.3014 (ttp80) REVERT: L 220 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8322 (pt0) REVERT: L 236 MET cc_start: 0.7919 (mtt) cc_final: 0.7568 (mtt) REVERT: L 241 ARG cc_start: 0.3231 (OUTLIER) cc_final: 0.2522 (pmt170) REVERT: L 545 ARG cc_start: 0.3247 (OUTLIER) cc_final: 0.2199 (mtt90) REVERT: L 601 GLU cc_start: 0.3009 (OUTLIER) cc_final: 0.2578 (mm-30) REVERT: L 608 MET cc_start: 0.2349 (ptp) cc_final: 0.1278 (mmt) REVERT: L 614 HIS cc_start: 0.1480 (OUTLIER) cc_final: 0.0711 (t-90) REVERT: L 618 LYS cc_start: 0.2896 (OUTLIER) cc_final: 0.1636 (tmtt) REVERT: L 646 GLU cc_start: 0.3106 (OUTLIER) cc_final: 0.1883 (mm-30) REVERT: L 650 GLU cc_start: 0.2640 (OUTLIER) cc_final: 0.1753 (tt0) REVERT: L 744 LEU cc_start: -0.0201 (OUTLIER) cc_final: -0.0674 (pp) REVERT: L 776 LYS cc_start: 0.5724 (ttpp) cc_final: 0.5196 (tptm) REVERT: L 798 ASP cc_start: 0.3407 (OUTLIER) cc_final: 0.2221 (t70) REVERT: K 28 HIS cc_start: 0.3843 (OUTLIER) cc_final: 0.3079 (p-80) REVERT: K 87 TYR cc_start: 0.2088 (OUTLIER) cc_final: 0.0542 (t80) REVERT: K 104 TYR cc_start: 0.0053 (OUTLIER) cc_final: -0.0536 (t80) REVERT: K 113 ARG cc_start: 0.3470 (OUTLIER) cc_final: 0.2974 (ttm-80) REVERT: K 144 LEU cc_start: 0.3568 (OUTLIER) cc_final: 0.2954 (mm) REVERT: K 146 LYS cc_start: 0.2253 (OUTLIER) cc_final: 0.1941 (ptpt) REVERT: V 678 LYS cc_start: 0.5324 (OUTLIER) cc_final: 0.3508 (ptpt) outliers start: 372 outliers final: 216 residues processed: 914 average time/residue: 1.4332 time to fit residues: 1755.5259 Evaluate side-chains 874 residues out of total 8096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 291 poor density : 583 time to evaluate : 5.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 493 CYS Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 544 LYS Chi-restraints excluded: chain A residue 589 LYS Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 909 ARG Chi-restraints excluded: chain A residue 912 GLU Chi-restraints excluded: chain A residue 978 LEU Chi-restraints excluded: chain A residue 995 ASP Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1026 VAL Chi-restraints excluded: chain A residue 1046 GLU Chi-restraints excluded: chain A residue 1059 ARG Chi-restraints excluded: chain A residue 1087 SER Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1131 CYS Chi-restraints excluded: chain A residue 1231 THR Chi-restraints excluded: chain A residue 1233 GLU Chi-restraints excluded: chain A residue 1240 SER Chi-restraints excluded: chain A residue 1273 ASN Chi-restraints excluded: chain A residue 1285 THR Chi-restraints excluded: chain A residue 1289 THR Chi-restraints excluded: chain A residue 1307 ARG Chi-restraints excluded: chain A residue 1319 THR Chi-restraints excluded: chain A residue 1351 LEU Chi-restraints excluded: chain A residue 1362 ARG Chi-restraints excluded: chain A residue 1365 ILE Chi-restraints excluded: chain A residue 1385 GLU Chi-restraints excluded: chain A residue 1402 SER Chi-restraints excluded: chain A residue 1417 PHE Chi-restraints excluded: chain A residue 1428 LEU Chi-restraints excluded: chain A residue 1465 ARG Chi-restraints excluded: chain A residue 1472 LEU Chi-restraints excluded: chain A residue 1480 ILE Chi-restraints excluded: chain A residue 1493 THR Chi-restraints excluded: chain A residue 1502 VAL Chi-restraints excluded: chain A residue 1512 THR Chi-restraints excluded: chain A residue 1538 VAL Chi-restraints excluded: chain A residue 1557 THR Chi-restraints excluded: chain A residue 1593 ILE Chi-restraints excluded: chain A residue 1605 THR Chi-restraints excluded: chain A residue 1626 MET Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1635 ILE Chi-restraints excluded: chain A residue 1638 ILE Chi-restraints excluded: chain A residue 1658 CYS Chi-restraints excluded: chain A residue 1671 GLU Chi-restraints excluded: chain A residue 1688 SER Chi-restraints excluded: chain A residue 1712 THR Chi-restraints excluded: chain A residue 1719 LYS Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1728 VAL Chi-restraints excluded: chain A residue 1742 ARG Chi-restraints excluded: chain A residue 1747 LYS Chi-restraints excluded: chain A residue 1783 PHE Chi-restraints excluded: chain A residue 1807 LEU Chi-restraints excluded: chain A residue 1820 SER Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 257 ARG Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 306 CYS Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 550 TYR Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 639 GLU Chi-restraints excluded: chain C residue 643 GLU Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 690 LYS Chi-restraints excluded: chain C residue 771 THR Chi-restraints excluded: chain C residue 789 TRP Chi-restraints excluded: chain C residue 810 ASP Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 820 ARG Chi-restraints excluded: chain C residue 874 VAL Chi-restraints excluded: chain C residue 892 LEU Chi-restraints excluded: chain C residue 902 THR Chi-restraints excluded: chain E residue 79 CYS Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 200 PHE Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 306 CYS Chi-restraints excluded: chain E residue 311 ARG Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 333 SER Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 342 LYS Chi-restraints excluded: chain E residue 354 THR Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain q residue 46 SER Chi-restraints excluded: chain q residue 78 ASP Chi-restraints excluded: chain r residue 2 PHE Chi-restraints excluded: chain r residue 9 VAL Chi-restraints excluded: chain r residue 18 LYS Chi-restraints excluded: chain r residue 41 THR Chi-restraints excluded: chain r residue 55 VAL Chi-restraints excluded: chain r residue 63 THR Chi-restraints excluded: chain r residue 95 HIS Chi-restraints excluded: chain r residue 113 ARG Chi-restraints excluded: chain s residue 85 LEU Chi-restraints excluded: chain t residue 105 LEU Chi-restraints excluded: chain a residue 19 GLU Chi-restraints excluded: chain a residue 44 MET Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 68 ILE Chi-restraints excluded: chain g residue 38 MET Chi-restraints excluded: chain g residue 48 GLU Chi-restraints excluded: chain e residue 10 THR Chi-restraints excluded: chain e residue 72 ILE Chi-restraints excluded: chain f residue 22 ILE Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 44 LEU Chi-restraints excluded: chain f residue 48 SER Chi-restraints excluded: chain d residue 42 CYS Chi-restraints excluded: chain d residue 68 GLU Chi-restraints excluded: chain d residue 80 GLN Chi-restraints excluded: chain c residue 2 VAL Chi-restraints excluded: chain c residue 10 LYS Chi-restraints excluded: chain c residue 75 LEU Chi-restraints excluded: chain c residue 79 THR Chi-restraints excluded: chain b residue 36 ARG Chi-restraints excluded: chain b residue 40 LEU Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 45 SER Chi-restraints excluded: chain b residue 105 ILE Chi-restraints excluded: chain I residue 356 LEU Chi-restraints excluded: chain I residue 366 SER Chi-restraints excluded: chain I residue 367 VAL Chi-restraints excluded: chain I residue 380 HIS Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain I residue 412 LYS Chi-restraints excluded: chain I residue 456 CYS Chi-restraints excluded: chain I residue 574 HIS Chi-restraints excluded: chain I residue 599 ARG Chi-restraints excluded: chain I residue 625 GLU Chi-restraints excluded: chain I residue 650 ARG Chi-restraints excluded: chain I residue 670 VAL Chi-restraints excluded: chain I residue 687 SER Chi-restraints excluded: chain I residue 702 GLU Chi-restraints excluded: chain I residue 746 THR Chi-restraints excluded: chain I residue 747 PHE Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 71 ARG Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain J residue 144 ARG Chi-restraints excluded: chain J residue 195 VAL Chi-restraints excluded: chain J residue 228 VAL Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain P residue 13 ILE Chi-restraints excluded: chain M residue 496 VAL Chi-restraints excluded: chain M residue 510 LYS Chi-restraints excluded: chain T residue 190 ARG Chi-restraints excluded: chain T residue 212 CYS Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 286 SER Chi-restraints excluded: chain T residue 292 SER Chi-restraints excluded: chain T residue 314 VAL Chi-restraints excluded: chain T residue 324 VAL Chi-restraints excluded: chain T residue 388 PHE Chi-restraints excluded: chain T residue 396 GLU Chi-restraints excluded: chain T residue 422 SER Chi-restraints excluded: chain T residue 446 ARG Chi-restraints excluded: chain T residue 465 SER Chi-restraints excluded: chain O residue 38 ILE Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 120 MET Chi-restraints excluded: chain O residue 165 VAL Chi-restraints excluded: chain O residue 184 HIS Chi-restraints excluded: chain O residue 224 THR Chi-restraints excluded: chain O residue 239 VAL Chi-restraints excluded: chain O residue 248 VAL Chi-restraints excluded: chain O residue 266 VAL Chi-restraints excluded: chain O residue 267 LYS Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 10 LYS Chi-restraints excluded: chain N residue 19 ILE Chi-restraints excluded: chain N residue 21 GLU Chi-restraints excluded: chain N residue 52 ARG Chi-restraints excluded: chain N residue 82 GLU Chi-restraints excluded: chain N residue 170 GLU Chi-restraints excluded: chain R residue 83 ILE Chi-restraints excluded: chain R residue 88 LYS Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 118 VAL Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 195 ASP Chi-restraints excluded: chain R residue 205 LYS Chi-restraints excluded: chain R residue 211 VAL Chi-restraints excluded: chain R residue 220 VAL Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 231 THR Chi-restraints excluded: chain R residue 236 GLN Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 255 ILE Chi-restraints excluded: chain S residue 23 HIS Chi-restraints excluded: chain S residue 28 CYS Chi-restraints excluded: chain S residue 76 ASP Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain S residue 146 VAL Chi-restraints excluded: chain S residue 152 ILE Chi-restraints excluded: chain W residue 87 LEU Chi-restraints excluded: chain W residue 91 HIS Chi-restraints excluded: chain W residue 107 VAL Chi-restraints excluded: chain W residue 112 ASP Chi-restraints excluded: chain W residue 118 ILE Chi-restraints excluded: chain W residue 121 GLU Chi-restraints excluded: chain W residue 168 THR Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 188 ARG Chi-restraints excluded: chain L residue 207 VAL Chi-restraints excluded: chain L residue 220 GLN Chi-restraints excluded: chain L residue 241 ARG Chi-restraints excluded: chain L residue 545 ARG Chi-restraints excluded: chain L residue 601 GLU Chi-restraints excluded: chain L residue 614 HIS Chi-restraints excluded: chain L residue 618 LYS Chi-restraints excluded: chain L residue 646 GLU Chi-restraints excluded: chain L residue 650 GLU Chi-restraints excluded: chain L residue 696 SER Chi-restraints excluded: chain L residue 744 LEU Chi-restraints excluded: chain L residue 798 ASP Chi-restraints excluded: chain L residue 800 THR Chi-restraints excluded: chain K residue 28 HIS Chi-restraints excluded: chain K residue 31 ASP Chi-restraints excluded: chain K residue 87 TYR Chi-restraints excluded: chain K residue 104 TYR Chi-restraints excluded: chain K residue 113 ARG Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain K residue 146 LYS Chi-restraints excluded: chain U residue 2 TYR Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain V residue 655 LEU Chi-restraints excluded: chain V residue 661 LEU Chi-restraints excluded: chain V residue 668 ASP Chi-restraints excluded: chain V residue 678 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 956 random chunks: chunk 47 optimal weight: 0.7980 chunk 939 optimal weight: 30.0000 chunk 416 optimal weight: 8.9990 chunk 119 optimal weight: 0.9980 chunk 481 optimal weight: 0.9990 chunk 718 optimal weight: 6.9990 chunk 714 optimal weight: 6.9990 chunk 499 optimal weight: 0.9990 chunk 574 optimal weight: 0.9990 chunk 792 optimal weight: 7.9990 chunk 252 optimal weight: 7.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 HIS A 512 GLN A 587 ASN A 939 HIS ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1246 ASN A1616 GLN C 68 HIS ** C 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 96 GLN r 99 GLN ** s 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 47 GLN ** e 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 28 GLN P 45 GLN R 80 GLN ** R 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 198 GLN K 141 GLN ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4999 r_free = 0.4999 target = 0.281169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4765 r_free = 0.4765 target = 0.251802 restraints weight = 85100.455| |-----------------------------------------------------------------------------| r_work (start): 0.4755 rms_B_bonded: 1.70 r_work: 0.4502 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.4469 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.4469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6073 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 75153 Z= 0.217 Angle : 0.656 11.815 103334 Z= 0.335 Chirality : 0.043 0.267 11959 Planarity : 0.005 0.086 12679 Dihedral : 16.694 178.869 14319 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.19 % Favored : 95.76 % Rotamer: Outliers : 4.89 % Allowed : 34.36 % Favored : 60.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.09), residues: 9287 helix: 1.12 (0.08), residues: 4362 sheet: -0.86 (0.15), residues: 1157 loop : -1.13 (0.10), residues: 3768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP A1701 HIS 0.009 0.001 HIS C 145 PHE 0.027 0.002 PHE W 217 TYR 0.023 0.002 TYR A1779 ARG 0.021 0.001 ARG C 957 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18574 Ramachandran restraints generated. 9287 Oldfield, 0 Emsley, 9287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18574 Ramachandran restraints generated. 9287 Oldfield, 0 Emsley, 9287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 903 residues out of total 8096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 287 poor density : 616 time to evaluate : 5.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7856 (ptmt) REVERT: A 329 MET cc_start: 0.3183 (ptt) cc_final: 0.2849 (ptm) REVERT: A 331 ILE cc_start: 0.4639 (OUTLIER) cc_final: 0.4182 (pp) REVERT: A 833 LYS cc_start: 0.7647 (tptp) cc_final: 0.7380 (tptm) REVERT: A 1046 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6767 (mm-30) REVERT: A 1215 ARG cc_start: 0.7856 (mtt-85) cc_final: 0.7629 (mtp180) REVERT: A 1233 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7315 (tp30) REVERT: A 1235 ASP cc_start: 0.8076 (m-30) cc_final: 0.7842 (m-30) REVERT: A 1266 MET cc_start: 0.6996 (ttm) cc_final: 0.6572 (ttp) REVERT: A 1273 ASN cc_start: 0.2269 (OUTLIER) cc_final: 0.1651 (p0) REVERT: A 1630 ILE cc_start: 0.7815 (OUTLIER) cc_final: 0.7401 (mt) REVERT: A 1742 ARG cc_start: 0.7186 (ttp-170) cc_final: 0.6949 (ttp-170) REVERT: A 1748 PHE cc_start: 0.7524 (t80) cc_final: 0.7302 (t80) REVERT: C 69 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6259 (tp30) REVERT: C 106 LYS cc_start: 0.4872 (OUTLIER) cc_final: 0.4574 (mtpm) REVERT: C 177 GLN cc_start: 0.4213 (OUTLIER) cc_final: 0.3674 (tt0) REVERT: C 527 LEU cc_start: 0.3588 (OUTLIER) cc_final: 0.2946 (mp) REVERT: C 550 TYR cc_start: 0.4220 (OUTLIER) cc_final: 0.3564 (t80) REVERT: C 643 GLU cc_start: 0.3200 (OUTLIER) cc_final: 0.2287 (pm20) REVERT: C 690 LYS cc_start: 0.4626 (OUTLIER) cc_final: 0.4058 (pptt) REVERT: C 789 TRP cc_start: 0.3051 (OUTLIER) cc_final: 0.2416 (t60) REVERT: C 892 LEU cc_start: 0.5637 (OUTLIER) cc_final: 0.5370 (tt) REVERT: E 139 THR cc_start: 0.5110 (p) cc_final: 0.4669 (t) REVERT: E 200 PHE cc_start: 0.4690 (OUTLIER) cc_final: 0.3631 (t80) REVERT: E 219 TRP cc_start: 0.3594 (m100) cc_final: 0.3234 (m-90) REVERT: E 311 ARG cc_start: 0.7149 (OUTLIER) cc_final: 0.6729 (mtm110) REVERT: E 337 VAL cc_start: 0.4238 (OUTLIER) cc_final: 0.3957 (t) REVERT: E 342 LYS cc_start: 0.6541 (OUTLIER) cc_final: 0.5771 (mmtt) REVERT: r 18 LYS cc_start: 0.2733 (OUTLIER) cc_final: 0.1480 (mttp) REVERT: r 84 MET cc_start: 0.1780 (tpt) cc_final: 0.1318 (mpp) REVERT: r 95 HIS cc_start: 0.1528 (OUTLIER) cc_final: 0.1101 (m170) REVERT: s 84 MET cc_start: 0.1866 (tpt) cc_final: 0.1384 (ppp) REVERT: t 105 LEU cc_start: 0.0892 (OUTLIER) cc_final: 0.0352 (tt) REVERT: a 44 MET cc_start: 0.5637 (OUTLIER) cc_final: 0.5036 (tmm) REVERT: e 9 MET cc_start: 0.3206 (tpt) cc_final: 0.1318 (pmm) REVERT: e 49 MET cc_start: 0.0787 (mmp) cc_final: 0.0163 (mtt) REVERT: e 67 LYS cc_start: 0.1164 (OUTLIER) cc_final: 0.0902 (ttpp) REVERT: d 68 GLU cc_start: 0.2385 (OUTLIER) cc_final: 0.1101 (pp20) REVERT: c 1 MET cc_start: 0.3291 (mtt) cc_final: 0.2438 (tmm) REVERT: c 37 MET cc_start: 0.3520 (mpp) cc_final: 0.2527 (ptp) REVERT: b 32 MET cc_start: 0.3369 (mmm) cc_final: 0.3164 (mmm) REVERT: I 356 LEU cc_start: 0.1113 (OUTLIER) cc_final: 0.0732 (mt) REVERT: I 366 SER cc_start: 0.1419 (OUTLIER) cc_final: 0.0955 (t) REVERT: I 367 VAL cc_start: 0.3227 (OUTLIER) cc_final: 0.2865 (t) REVERT: I 412 LYS cc_start: 0.1859 (OUTLIER) cc_final: 0.1295 (mtpp) REVERT: I 417 TRP cc_start: 0.0861 (m100) cc_final: 0.0361 (m-90) REVERT: I 456 CYS cc_start: 0.3063 (OUTLIER) cc_final: 0.2771 (m) REVERT: I 461 MET cc_start: 0.0504 (tmm) cc_final: 0.0196 (ptp) REVERT: I 492 GLU cc_start: 0.4467 (mm-30) cc_final: 0.3673 (pp20) REVERT: I 574 HIS cc_start: 0.2667 (OUTLIER) cc_final: 0.1484 (m-70) REVERT: I 625 GLU cc_start: 0.2636 (OUTLIER) cc_final: 0.1584 (pt0) REVERT: I 672 GLU cc_start: 0.2761 (mt-10) cc_final: 0.2264 (tt0) REVERT: I 697 ARG cc_start: 0.2562 (OUTLIER) cc_final: 0.1659 (mmt-90) REVERT: I 747 PHE cc_start: 0.1136 (OUTLIER) cc_final: 0.0871 (m-80) REVERT: I 748 LYS cc_start: 0.4911 (mmmt) cc_final: 0.4601 (ptpp) REVERT: I 750 MET cc_start: 0.1750 (mtp) cc_final: 0.0351 (mmp) REVERT: J 144 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.7635 (tpt90) REVERT: J 254 LYS cc_start: 0.6879 (mptp) cc_final: 0.6525 (tppp) REVERT: P 62 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7802 (mt-10) REVERT: M 510 LYS cc_start: 0.3991 (ttpt) cc_final: 0.3392 (pptt) REVERT: T 190 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7586 (mtp-110) REVERT: O 264 MET cc_start: 0.1015 (OUTLIER) cc_final: 0.0599 (pmt) REVERT: O 267 LYS cc_start: 0.2310 (OUTLIER) cc_final: 0.1352 (ptmt) REVERT: N 6 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.8041 (pttt) REVERT: N 10 LYS cc_start: 0.6246 (OUTLIER) cc_final: 0.4315 (pmmt) REVERT: N 21 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6527 (tt0) REVERT: N 52 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.8131 (ttp-170) REVERT: N 170 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7040 (mt-10) REVERT: R 205 LYS cc_start: 0.7493 (OUTLIER) cc_final: 0.6909 (mptt) REVERT: S 37 LYS cc_start: 0.6505 (mttp) cc_final: 0.6304 (mttp) REVERT: S 67 GLU cc_start: 0.6482 (mp0) cc_final: 0.5896 (mm-30) REVERT: L 236 MET cc_start: 0.7874 (mtt) cc_final: 0.7639 (mtt) REVERT: L 241 ARG cc_start: 0.3221 (OUTLIER) cc_final: 0.2634 (pmt170) REVERT: L 545 ARG cc_start: 0.3253 (OUTLIER) cc_final: 0.2287 (mtt90) REVERT: L 601 GLU cc_start: 0.3016 (OUTLIER) cc_final: 0.2588 (mm-30) REVERT: L 608 MET cc_start: 0.2344 (ptp) cc_final: 0.1252 (mmt) REVERT: L 614 HIS cc_start: 0.1190 (OUTLIER) cc_final: 0.0535 (t-90) REVERT: L 618 LYS cc_start: 0.2812 (OUTLIER) cc_final: 0.1570 (tmtt) REVERT: L 646 GLU cc_start: 0.3106 (OUTLIER) cc_final: 0.1829 (mm-30) REVERT: L 650 GLU cc_start: 0.2793 (OUTLIER) cc_final: 0.1883 (tt0) REVERT: L 744 LEU cc_start: 0.0008 (OUTLIER) cc_final: -0.0452 (pp) REVERT: L 765 VAL cc_start: 0.2112 (m) cc_final: 0.1889 (t) REVERT: L 776 LYS cc_start: 0.5661 (ttpp) cc_final: 0.5215 (tptm) REVERT: L 798 ASP cc_start: 0.3295 (OUTLIER) cc_final: 0.2289 (t70) REVERT: K 36 VAL cc_start: 0.2550 (m) cc_final: 0.2073 (p) REVERT: K 69 MET cc_start: 0.1767 (tpp) cc_final: 0.1314 (mpt) REVERT: K 104 TYR cc_start: 0.0260 (OUTLIER) cc_final: -0.0412 (t80) REVERT: K 113 ARG cc_start: 0.3436 (OUTLIER) cc_final: 0.3049 (ttm-80) REVERT: K 144 LEU cc_start: 0.3371 (OUTLIER) cc_final: 0.2913 (mm) REVERT: K 146 LYS cc_start: 0.2268 (OUTLIER) cc_final: 0.2010 (ptpt) outliers start: 287 outliers final: 164 residues processed: 858 average time/residue: 1.4979 time to fit residues: 1722.1677 Evaluate side-chains 807 residues out of total 8096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 221 poor density : 586 time to evaluate : 5.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 493 CYS Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain A residue 544 LYS Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 912 GLU Chi-restraints excluded: chain A residue 978 LEU Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1026 VAL Chi-restraints excluded: chain A residue 1038 VAL Chi-restraints excluded: chain A residue 1046 GLU Chi-restraints excluded: chain A residue 1059 ARG Chi-restraints excluded: chain A residue 1087 SER Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1131 CYS Chi-restraints excluded: chain A residue 1231 THR Chi-restraints excluded: chain A residue 1233 GLU Chi-restraints excluded: chain A residue 1273 ASN Chi-restraints excluded: chain A residue 1285 THR Chi-restraints excluded: chain A residue 1289 THR Chi-restraints excluded: chain A residue 1307 ARG Chi-restraints excluded: chain A residue 1319 THR Chi-restraints excluded: chain A residue 1351 LEU Chi-restraints excluded: chain A residue 1365 ILE Chi-restraints excluded: chain A residue 1402 SER Chi-restraints excluded: chain A residue 1417 PHE Chi-restraints excluded: chain A residue 1428 LEU Chi-restraints excluded: chain A residue 1480 ILE Chi-restraints excluded: chain A residue 1493 THR Chi-restraints excluded: chain A residue 1502 VAL Chi-restraints excluded: chain A residue 1512 THR Chi-restraints excluded: chain A residue 1557 THR Chi-restraints excluded: chain A residue 1605 THR Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1635 ILE Chi-restraints excluded: chain A residue 1658 CYS Chi-restraints excluded: chain A residue 1671 GLU Chi-restraints excluded: chain A residue 1688 SER Chi-restraints excluded: chain A residue 1712 THR Chi-restraints excluded: chain A residue 1719 LYS Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1728 VAL Chi-restraints excluded: chain A residue 1783 PHE Chi-restraints excluded: chain A residue 1807 LEU Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 106 LYS Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 550 TYR Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 643 GLU Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 690 LYS Chi-restraints excluded: chain C residue 771 THR Chi-restraints excluded: chain C residue 789 TRP Chi-restraints excluded: chain C residue 810 ASP Chi-restraints excluded: chain C residue 820 ARG Chi-restraints excluded: chain C residue 874 VAL Chi-restraints excluded: chain C residue 892 LEU Chi-restraints excluded: chain C residue 902 THR Chi-restraints excluded: chain E residue 79 CYS Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 200 PHE Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 306 CYS Chi-restraints excluded: chain E residue 311 ARG Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain E residue 333 SER Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 342 LYS Chi-restraints excluded: chain q residue 46 SER Chi-restraints excluded: chain q residue 78 ASP Chi-restraints excluded: chain r residue 2 PHE Chi-restraints excluded: chain r residue 9 VAL Chi-restraints excluded: chain r residue 18 LYS Chi-restraints excluded: chain r residue 41 THR Chi-restraints excluded: chain r residue 55 VAL Chi-restraints excluded: chain r residue 63 THR Chi-restraints excluded: chain r residue 95 HIS Chi-restraints excluded: chain r residue 113 ARG Chi-restraints excluded: chain t residue 105 LEU Chi-restraints excluded: chain a residue 44 MET Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain e residue 10 THR Chi-restraints excluded: chain e residue 67 LYS Chi-restraints excluded: chain e residue 72 ILE Chi-restraints excluded: chain f residue 22 ILE Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain d residue 42 CYS Chi-restraints excluded: chain d residue 68 GLU Chi-restraints excluded: chain d residue 80 GLN Chi-restraints excluded: chain c residue 2 VAL Chi-restraints excluded: chain c residue 10 LYS Chi-restraints excluded: chain c residue 79 THR Chi-restraints excluded: chain b residue 36 ARG Chi-restraints excluded: chain b residue 105 ILE Chi-restraints excluded: chain I residue 356 LEU Chi-restraints excluded: chain I residue 366 SER Chi-restraints excluded: chain I residue 367 VAL Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain I residue 412 LYS Chi-restraints excluded: chain I residue 456 CYS Chi-restraints excluded: chain I residue 574 HIS Chi-restraints excluded: chain I residue 613 GLU Chi-restraints excluded: chain I residue 625 GLU Chi-restraints excluded: chain I residue 670 VAL Chi-restraints excluded: chain I residue 687 SER Chi-restraints excluded: chain I residue 697 ARG Chi-restraints excluded: chain I residue 702 GLU Chi-restraints excluded: chain I residue 746 THR Chi-restraints excluded: chain I residue 747 PHE Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain J residue 144 ARG Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain T residue 190 ARG Chi-restraints excluded: chain T residue 212 CYS Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 292 SER Chi-restraints excluded: chain T residue 324 VAL Chi-restraints excluded: chain T residue 388 PHE Chi-restraints excluded: chain T residue 396 GLU Chi-restraints excluded: chain O residue 38 ILE Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 120 MET Chi-restraints excluded: chain O residue 165 VAL Chi-restraints excluded: chain O residue 184 HIS Chi-restraints excluded: chain O residue 224 THR Chi-restraints excluded: chain O residue 239 VAL Chi-restraints excluded: chain O residue 248 VAL Chi-restraints excluded: chain O residue 264 MET Chi-restraints excluded: chain O residue 266 VAL Chi-restraints excluded: chain O residue 267 LYS Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 10 LYS Chi-restraints excluded: chain N residue 19 ILE Chi-restraints excluded: chain N residue 21 GLU Chi-restraints excluded: chain N residue 52 ARG Chi-restraints excluded: chain N residue 82 GLU Chi-restraints excluded: chain N residue 170 GLU Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 118 VAL Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 195 ASP Chi-restraints excluded: chain R residue 205 LYS Chi-restraints excluded: chain R residue 211 VAL Chi-restraints excluded: chain R residue 220 VAL Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 255 ILE Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain S residue 152 ILE Chi-restraints excluded: chain W residue 87 LEU Chi-restraints excluded: chain W residue 91 HIS Chi-restraints excluded: chain W residue 112 ASP Chi-restraints excluded: chain W residue 118 ILE Chi-restraints excluded: chain W residue 121 GLU Chi-restraints excluded: chain W residue 168 THR Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 241 ARG Chi-restraints excluded: chain L residue 545 ARG Chi-restraints excluded: chain L residue 601 GLU Chi-restraints excluded: chain L residue 614 HIS Chi-restraints excluded: chain L residue 618 LYS Chi-restraints excluded: chain L residue 646 GLU Chi-restraints excluded: chain L residue 650 GLU Chi-restraints excluded: chain L residue 696 SER Chi-restraints excluded: chain L residue 744 LEU Chi-restraints excluded: chain L residue 798 ASP Chi-restraints excluded: chain L residue 800 THR Chi-restraints excluded: chain K residue 28 HIS Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 104 TYR Chi-restraints excluded: chain K residue 113 ARG Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain K residue 146 LYS Chi-restraints excluded: chain U residue 2 TYR Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain V residue 655 LEU Chi-restraints excluded: chain V residue 661 LEU Chi-restraints excluded: chain V residue 668 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 956 random chunks: chunk 778 optimal weight: 6.9990 chunk 249 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 791 optimal weight: 0.3980 chunk 462 optimal weight: 0.9990 chunk 807 optimal weight: 0.6980 chunk 157 optimal weight: 6.9990 chunk 171 optimal weight: 20.0000 chunk 745 optimal weight: 0.7980 chunk 821 optimal weight: 6.9990 chunk 45 optimal weight: 0.4980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 HIS A 496 GLN A 512 GLN A 587 ASN ** A 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 939 HIS ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1246 ASN C 68 HIS ** C 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 600 GLN ** C 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 96 GLN r 99 GLN ** s 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 47 GLN ** e 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 20 GLN ** I 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 449 HIS O 30 ASN R 80 GLN ** R 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 83 HIS K 141 GLN ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5008 r_free = 0.5008 target = 0.282313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4778 r_free = 0.4778 target = 0.253159 restraints weight = 85562.168| |-----------------------------------------------------------------------------| r_work (start): 0.4763 rms_B_bonded: 1.68 r_work: 0.4516 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.4486 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.4486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6026 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 75153 Z= 0.190 Angle : 0.632 11.519 103334 Z= 0.323 Chirality : 0.042 0.269 11959 Planarity : 0.005 0.084 12679 Dihedral : 16.380 179.163 14273 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.12 % Favored : 95.83 % Rotamer: Outliers : 3.90 % Allowed : 35.17 % Favored : 60.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.09), residues: 9287 helix: 1.36 (0.08), residues: 4356 sheet: -0.78 (0.15), residues: 1174 loop : -1.00 (0.10), residues: 3757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A1701 HIS 0.008 0.001 HIS C 145 PHE 0.025 0.001 PHE W 106 TYR 0.031 0.001 TYR I 618 ARG 0.023 0.001 ARG C 957 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 56685.61 seconds wall clock time: 966 minutes 46.69 seconds (58006.69 seconds total)