Starting phenix.real_space_refine on Tue Aug 26 10:19:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xmc_38471/08_2025/8xmc_38471.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xmc_38471/08_2025/8xmc_38471.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xmc_38471/08_2025/8xmc_38471.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xmc_38471/08_2025/8xmc_38471.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xmc_38471/08_2025/8xmc_38471.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xmc_38471/08_2025/8xmc_38471.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.052 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 9 6.06 5 P 58 5.49 5 Mg 1 5.21 5 S 220 5.16 5 C 22509 2.51 5 N 6234 2.21 5 O 6599 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35630 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 8651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1167, 8651 Classifications: {'peptide': 1167} Incomplete info: {'truncation_to_alanine': 141} Link IDs: {'PCIS': 2, 'PTRANS': 52, 'TRANS': 1112} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 493 Unresolved non-hydrogen angles: 606 Unresolved non-hydrogen dihedrals: 395 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLU:plan': 25, 'ASN:plan1': 7, 'ASP:plan': 26, 'ARG:plan': 10, 'PHE:plan': 2, 'GLN:plan1': 6, 'TYR:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 309 Chain: "B" Number of atoms: 8178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1082, 8178 Classifications: {'peptide': 1082} Incomplete info: {'truncation_to_alanine': 120} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 1040} Chain breaks: 5 Unresolved non-hydrogen bonds: 416 Unresolved non-hydrogen angles: 503 Unresolved non-hydrogen dihedrals: 337 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASN:plan1': 5, 'GLU:plan': 36, 'ASP:plan': 22, 'GLN:plan1': 5, 'TYR:plan': 2, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 269 Chain: "C" Number of atoms: 2140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2140 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 12, 'TRANS': 274} Chain breaks: 1 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 90 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 14, 'ASN:plan1': 1, 'PHE:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 101 Chain: "D" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 869 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "E" Number of atoms: 1511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1511 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 6, 'TRANS': 191} Chain breaks: 1 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 181 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 7, 'GLN:plan1': 3, 'ARG:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 104 Chain: "F" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 568 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 4, 'TRANS': 71} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "G" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1096 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 9, 'TRANS': 164} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 318 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 278 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'PHE:plan': 7, 'ASP:plan': 8, 'GLU:plan': 9, 'ARG:plan': 6, 'GLN:plan1': 2, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 187 Chain: "H" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 953 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 7, 'HIS:plan': 3, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 48 Chain: "I" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 823 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 4, 'TRANS': 108} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ASP:plan': 3, 'GLN:plan1': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 67 Chain: "J" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 476 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 60} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'ASP:plan': 5, 'GLN:plan1': 1, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "K" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 791 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 1, 'GLU:plan': 5, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 41 Chain: "L" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 312 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 41} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "M" Number of atoms: 8043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1052, 8043 Classifications: {'peptide': 1052} Incomplete info: {'truncation_to_alanine': 114} Link IDs: {'PTRANS': 40, 'TRANS': 1011} Chain breaks: 3 Unresolved non-hydrogen bonds: 423 Unresolved non-hydrogen angles: 526 Unresolved non-hydrogen dihedrals: 343 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLU:plan': 19, 'ASP:plan': 12, 'ARG:plan': 11, 'ASN:plan1': 5, 'GLN:plan1': 8, 'PHE:plan': 3, 'TYR:plan': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 272 Chain: "N" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 390 Classifications: {'DNA': 19} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 18} Chain: "O" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 218 Classifications: {'RNA': 10} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 7, 'rna3p_pyr': 2} Link IDs: {'rna2p': 1, 'rna3p': 8} Chain: "Q" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 601 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 1, ' ZN': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" 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: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" 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 334 SG CYS A 56 48.742 65.647 120.535 1.00193.41 S ATOM 352 SG CYS A 59 48.986 69.409 121.342 1.00187.66 S ATOM 399 SG CYS A 67 49.727 68.173 117.816 1.00185.01 S ATOM 7039 SG CYS A1044 141.725 71.693 87.687 1.00139.86 S ATOM 621 SG CYS A 97 98.948 62.150 141.353 1.00263.88 S ATOM 638 SG CYS A 100 99.387 63.279 144.991 1.00268.74 S ATOM 669 SG CYS A 118 100.515 59.718 143.909 1.00288.58 S ATOM 698 SG CYS A 121 102.243 62.858 142.459 1.00292.80 S ATOM 16451 SG CYS B1108 57.341 80.144 132.233 1.00148.05 S ATOM 16473 SG CYS B1111 60.621 78.628 133.376 1.00150.14 S ATOM 16543 SG CYS B1133 57.769 76.548 131.798 1.00207.80 S ATOM 16567 SG CYS B1136 57.319 77.817 135.312 1.00191.08 S ATOM 17496 SG CYS C 90 22.507 84.340 60.344 1.00157.24 S ATOM 17512 SG CYS C 93 22.183 80.823 61.715 1.00178.71 S ATOM 17545 SG CYS C 99 21.635 81.217 58.065 1.00149.65 S ATOM 17567 SG CYS C 102 25.063 81.769 59.236 1.00154.84 S ATOM 24500 SG CYS I 76 116.138 105.359 67.701 1.00137.51 S ATOM 24521 SG CYS I 79 112.501 105.220 66.518 1.00137.25 S ATOM 24699 SG CYS I 103 113.985 102.286 68.432 1.00134.53 S ATOM 24734 SG CYS I 108 115.054 103.114 64.830 1.00132.23 S ATOM 24013 SG CYS I 7 137.282 40.375 86.399 1.00146.00 S ATOM 24039 SG CYS I 10 134.679 38.181 87.777 1.00166.91 S ATOM 24166 SG CYS I 29 136.243 40.946 90.041 1.00171.03 S ATOM 24191 SG CYS I 32 138.070 37.776 89.257 1.00173.25 S ATOM 24841 SG CYS J 7 53.878 79.199 47.765 1.00129.77 S ATOM 25122 SG CYS J 44 56.833 82.425 46.980 1.00114.68 S ATOM 25128 SG CYS J 45 54.296 79.999 44.855 1.00128.48 S ATOM 26088 SG CYS L 12 45.037 40.304 69.102 1.00150.45 S ATOM 26190 SG CYS L 29 42.963 37.892 70.373 1.00154.34 S ATOM 26206 SG CYS L 32 46.598 36.886 68.744 1.00168.78 S Time building chain proxies: 7.65, per 1000 atoms: 0.21 Number of scatterers: 35630 At special positions: 0 Unit cell: (184.8, 171.6, 188.1, 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 9 29.99 S 220 16.00 P 58 15.00 Mg 1 11.99 O 6599 8.00 N 6234 7.00 C 22509 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=0, symmetry=0 Time building additional restraints: 2.94 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 1.2 microseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1501 " pdb="ZN ZN A1501 " - pdb=" NE2 HIS A 70 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 59 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 56 " pdb=" ZN A1503 " pdb="ZN ZN A1503 " - pdb=" SG CYS A1044 " pdb="ZN ZN A1503 " - pdb=" ND1 HIS A 983 " pdb="ZN ZN A1503 " - pdb=" NE2 HIS A 985 " pdb=" ZN A1504 " pdb="ZN ZN A1504 " - pdb=" SG CYS A 121 " pdb="ZN ZN A1504 " - pdb=" SG CYS A 97 " pdb="ZN ZN A1504 " - pdb=" SG CYS A 118 " pdb="ZN ZN A1504 " - pdb=" SG CYS A 100 " pdb=" ZN B2001 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1111 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1108 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1133 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1136 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 102 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 99 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 93 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 90 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 108 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 79 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 76 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 103 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 29 " pdb=" ZN J 200 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 45 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 12 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 29 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 32 " Number of angles added : 33 9070 Ramachandran restraints generated. 4535 Oldfield, 0 Emsley, 4535 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8666 Finding SS restraints... Secondary structure from input PDB file: 166 helices and 53 sheets defined 38.1% alpha, 18.6% beta 26 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 5.21 Creating SS restraints... Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 38 through 42 removed outlier: 4.084A pdb=" N VAL A 42 " --> pdb=" O PRO A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 96 Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.584A pdb=" N THR A 125 " --> pdb=" O THR A 122 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY A 126 " --> pdb=" O LEU A 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 122 through 126' Processing helix chain 'A' and resid 150 through 160 Processing helix chain 'A' and resid 166 through 171 removed outlier: 4.386A pdb=" N TRP A 170 " --> pdb=" O PRO A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 201 Processing helix chain 'A' and resid 204 through 212 Processing helix chain 'A' and resid 214 through 217 Processing helix chain 'A' and resid 249 through 256 Processing helix chain 'A' and resid 262 through 275 removed outlier: 3.630A pdb=" N LEU A 266 " --> pdb=" O ASN A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 313 Processing helix chain 'A' and resid 341 through 347 removed outlier: 3.686A pdb=" N ARG A 346 " --> pdb=" O SER A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 420 Processing helix chain 'A' and resid 437 through 439 No H-bonds generated for 'chain 'A' and resid 437 through 439' Processing helix chain 'A' and resid 440 through 445 removed outlier: 3.813A pdb=" N PHE A 444 " --> pdb=" O CYS A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 471 removed outlier: 3.562A pdb=" N GLU A 469 " --> pdb=" O VAL A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 503 Processing helix chain 'A' and resid 509 through 518 removed outlier: 3.636A pdb=" N MET A 518 " --> pdb=" O GLN A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 549 removed outlier: 3.604A pdb=" N LEU A 546 " --> pdb=" O THR A 542 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET A 549 " --> pdb=" O GLN A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 596 Processing helix chain 'A' and resid 599 through 619 Processing helix chain 'A' and resid 623 through 629 removed outlier: 3.585A pdb=" N LEU A 627 " --> pdb=" O SER A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 659 removed outlier: 3.770A pdb=" N LEU A 659 " --> pdb=" O ASN A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 663 removed outlier: 7.053A pdb=" N SER A 663 " --> pdb=" O MET A 660 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 660 through 663' Processing helix chain 'A' and resid 664 through 669 Processing helix chain 'A' and resid 675 through 682 removed outlier: 3.782A pdb=" N VAL A 680 " --> pdb=" O GLU A 676 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP A 682 " --> pdb=" O ASP A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 693 removed outlier: 4.223A pdb=" N CYS A 687 " --> pdb=" O LEU A 683 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR A 688 " --> pdb=" O ALA A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 713 removed outlier: 4.412A pdb=" N ASP A 710 " --> pdb=" O ASP A 706 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL A 711 " --> pdb=" O ALA A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 719 removed outlier: 4.158A pdb=" N ARG A 717 " --> pdb=" O ALA A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 732 Processing helix chain 'A' and resid 736 through 745 Processing helix chain 'A' and resid 765 through 770 removed outlier: 3.503A pdb=" N ASN A 770 " --> pdb=" O CYS A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 817 Processing helix chain 'A' and resid 826 through 840 Processing helix chain 'A' and resid 876 through 892 Processing helix chain 'A' and resid 893 through 895 No H-bonds generated for 'chain 'A' and resid 893 through 895' Processing helix chain 'A' and resid 903 through 913 Processing helix chain 'A' and resid 930 through 935 removed outlier: 3.809A pdb=" N LEU A 933 " --> pdb=" O SER A 930 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS A 935 " --> pdb=" O TYR A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 952 Processing helix chain 'A' and resid 956 through 960 Processing helix chain 'A' and resid 988 through 995 Processing helix chain 'A' and resid 997 through 1012 removed outlier: 3.705A pdb=" N ARG A1012 " --> pdb=" O GLN A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1060 through 1074 removed outlier: 4.282A pdb=" N ILE A1068 " --> pdb=" O ARG A1064 " (cutoff:3.500A) Proline residue: A1069 - end of helix Processing helix chain 'A' and resid 1121 through 1130 Processing helix chain 'A' and resid 1131 through 1134 Processing helix chain 'A' and resid 1149 through 1155 Processing helix chain 'A' and resid 1155 through 1175 Processing helix chain 'A' and resid 1179 through 1191 removed outlier: 3.831A pdb=" N LEU A1183 " --> pdb=" O LEU A1179 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1212 Processing helix chain 'A' and resid 1215 through 1223 Processing helix chain 'A' and resid 1224 through 1236 Processing helix chain 'A' and resid 1243 through 1250 Processing helix chain 'B' and resid 27 through 46 Processing helix chain 'B' and resid 50 through 62 Processing helix chain 'B' and resid 62 through 71 Processing helix chain 'B' and resid 117 through 125 Processing helix chain 'B' and resid 192 through 197 removed outlier: 3.762A pdb=" N LYS B 197 " --> pdb=" O GLU B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 286 Processing helix chain 'B' and resid 290 through 298 Processing helix chain 'B' and resid 304 through 322 Processing helix chain 'B' and resid 329 through 341 Processing helix chain 'B' and resid 349 through 357 removed outlier: 4.655A pdb=" N HIS B 355 " --> pdb=" O ASP B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 384 removed outlier: 3.703A pdb=" N LYS B 368 " --> pdb=" O SER B 364 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA B 369 " --> pdb=" O LEU B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 396 No H-bonds generated for 'chain 'B' and resid 394 through 396' Processing helix chain 'B' and resid 405 through 431 removed outlier: 3.946A pdb=" N GLU B 410 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER B 431 " --> pdb=" O GLN B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 445 through 459 removed outlier: 3.930A pdb=" N THR B 449 " --> pdb=" O ALA B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 491 removed outlier: 3.584A pdb=" N THR B 486 " --> pdb=" O ASN B 482 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG B 491 " --> pdb=" O LEU B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 508 removed outlier: 4.336A pdb=" N ARG B 507 " --> pdb=" O GLY B 504 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR B 508 " --> pdb=" O ASP B 505 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 504 through 508' Processing helix chain 'B' and resid 510 through 514 Processing helix chain 'B' and resid 548 through 556 removed outlier: 3.585A pdb=" N PHE B 553 " --> pdb=" O VAL B 549 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA B 554 " --> pdb=" O GLU B 550 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N CYS B 555 " --> pdb=" O LYS B 551 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY B 556 " --> pdb=" O LEU B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 600 Processing helix chain 'B' and resid 636 through 641 Processing helix chain 'B' and resid 649 through 656 Processing helix chain 'B' and resid 664 through 670 removed outlier: 3.777A pdb=" N GLU B 668 " --> pdb=" O ILE B 664 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP B 669 " --> pdb=" O GLU B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 675 through 682 removed outlier: 3.765A pdb=" N GLU B 682 " --> pdb=" O GLN B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 697 Processing helix chain 'B' and resid 698 through 703 removed outlier: 3.892A pdb=" N VAL B 703 " --> pdb=" O VAL B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 710 Processing helix chain 'B' and resid 711 through 721 Processing helix chain 'B' and resid 721 through 726 Processing helix chain 'B' and resid 733 through 737 removed outlier: 3.522A pdb=" N ILE B 736 " --> pdb=" O ASN B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 762 Processing helix chain 'B' and resid 792 through 797 Processing helix chain 'B' and resid 929 through 933 Processing helix chain 'B' and resid 949 through 955 removed outlier: 3.988A pdb=" N SER B 953 " --> pdb=" O HIS B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 971 Processing helix chain 'B' and resid 980 through 984 removed outlier: 4.082A pdb=" N THR B 983 " --> pdb=" O ALA B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 990 through 994 removed outlier: 3.641A pdb=" N THR B 994 " --> pdb=" O PRO B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 996 through 1007 Processing helix chain 'B' and resid 1044 through 1048 removed outlier: 3.511A pdb=" N VAL B1048 " --> pdb=" O GLU B1045 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1087 Processing helix chain 'B' and resid 1088 through 1097 removed outlier: 3.584A pdb=" N LEU B1092 " --> pdb=" O ALA B1088 " (cutoff:3.500A) Processing helix chain 'B' and resid 1149 through 1162 Processing helix chain 'C' and resid 30 through 44 removed outlier: 3.643A pdb=" N ALA C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 73 Processing helix chain 'C' and resid 129 through 133 Processing helix chain 'C' and resid 199 through 204 removed outlier: 3.950A pdb=" N THR C 203 " --> pdb=" O ASP C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 216 removed outlier: 3.889A pdb=" N SER C 216 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 238 removed outlier: 3.545A pdb=" N ALA C 237 " --> pdb=" O ASP C 234 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR C 238 " --> pdb=" O PRO C 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 234 through 238' Processing helix chain 'C' and resid 243 through 252 Processing helix chain 'C' and resid 277 through 297 Processing helix chain 'D' and resid 94 through 109 removed outlier: 3.532A pdb=" N LEU D 101 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 128 removed outlier: 4.414A pdb=" N TYR D 123 " --> pdb=" O ILE D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 152 removed outlier: 3.637A pdb=" N SER D 141 " --> pdb=" O THR D 137 " (cutoff:3.500A) Proline residue: D 148 - end of helix Processing helix chain 'D' and resid 155 through 166 Processing helix chain 'D' and resid 169 through 177 removed outlier: 4.156A pdb=" N VAL D 173 " --> pdb=" O SER D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 181 Processing helix chain 'D' and resid 187 through 202 removed outlier: 3.674A pdb=" N LEU D 191 " --> pdb=" O ILE D 187 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS D 202 " --> pdb=" O LEU D 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 25 Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 45 Processing helix chain 'E' and resid 78 through 93 removed outlier: 3.732A pdb=" N MET E 82 " --> pdb=" O GLY E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 116 Processing helix chain 'E' and resid 128 through 132 removed outlier: 3.935A pdb=" N VAL E 132 " --> pdb=" O GLU E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 159 Processing helix chain 'E' and resid 172 through 179 Processing helix chain 'F' and resid 66 through 83 Processing helix chain 'F' and resid 96 through 107 Processing helix chain 'G' and resid 20 through 23 Processing helix chain 'G' and resid 24 through 40 removed outlier: 3.518A pdb=" N GLU G 39 " --> pdb=" O ALA G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 117 removed outlier: 3.768A pdb=" N LYS G 116 " --> pdb=" O SER G 113 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N MET G 117 " --> pdb=" O HIS G 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 113 through 117' Processing helix chain 'G' and resid 131 through 135 removed outlier: 4.140A pdb=" N TYR G 134 " --> pdb=" O MET G 131 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 16 No H-bonds generated for 'chain 'J' and resid 14 through 16' Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 Processing helix chain 'J' and resid 55 through 62 Processing helix chain 'K' and resid 39 through 53 removed outlier: 3.536A pdb=" N GLY K 43 " --> pdb=" O ASP K 39 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG K 52 " --> pdb=" O MET K 48 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP K 53 " --> pdb=" O GLN K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 110 Processing helix chain 'M' and resid 22 through 34 Processing helix chain 'M' and resid 63 through 76 Processing helix chain 'M' and resid 229 through 234 Processing helix chain 'M' and resid 246 through 252 removed outlier: 4.083A pdb=" N ILE M 250 " --> pdb=" O THR M 246 " (cutoff:3.500A) Processing helix chain 'M' and resid 292 through 305 Processing helix chain 'M' and resid 309 through 314 Processing helix chain 'M' and resid 315 through 324 removed outlier: 3.619A pdb=" N ILE M 319 " --> pdb=" O ASP M 315 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY M 324 " --> pdb=" O LYS M 320 " (cutoff:3.500A) Processing helix chain 'M' and resid 326 through 340 removed outlier: 3.742A pdb=" N GLN M 340 " --> pdb=" O LYS M 336 " (cutoff:3.500A) Processing helix chain 'M' and resid 346 through 355 removed outlier: 3.548A pdb=" N MET M 355 " --> pdb=" O VAL M 351 " (cutoff:3.500A) Processing helix chain 'M' and resid 368 through 377 Processing helix chain 'M' and resid 403 through 408 removed outlier: 3.809A pdb=" N ASN M 407 " --> pdb=" O TYR M 403 " (cutoff:3.500A) Processing helix chain 'M' and resid 429 through 433 Processing helix chain 'M' and resid 448 through 461 Processing helix chain 'M' and resid 475 through 481 removed outlier: 3.764A pdb=" N ARG M 480 " --> pdb=" O ALA M 476 " (cutoff:3.500A) Processing helix chain 'M' and resid 494 through 503 Processing helix chain 'M' and resid 510 through 521 removed outlier: 4.316A pdb=" N LEU M 521 " --> pdb=" O ARG M 517 " (cutoff:3.500A) Processing helix chain 'M' and resid 561 through 573 removed outlier: 4.188A pdb=" N LYS M 571 " --> pdb=" O GLN M 567 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N CYS M 572 " --> pdb=" O VAL M 568 " (cutoff:3.500A) Processing helix chain 'M' and resid 632 through 640 Processing helix chain 'M' and resid 645 through 662 removed outlier: 4.291A pdb=" N PHE M 649 " --> pdb=" O GLU M 645 " (cutoff:3.500A) Processing helix chain 'M' and resid 666 through 675 removed outlier: 3.531A pdb=" N ALA M 670 " --> pdb=" O ASP M 666 " (cutoff:3.500A) Processing helix chain 'M' and resid 684 through 692 removed outlier: 3.669A pdb=" N LEU M 691 " --> pdb=" O VAL M 687 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN M 692 " --> pdb=" O LYS M 688 " (cutoff:3.500A) Processing helix chain 'M' and resid 699 through 720 removed outlier: 3.588A pdb=" N MET M 705 " --> pdb=" O TYR M 701 " (cutoff:3.500A) Processing helix chain 'M' and resid 753 through 759 Processing helix chain 'M' and resid 788 through 792 removed outlier: 3.538A pdb=" N ILE M 792 " --> pdb=" O PRO M 789 " (cutoff:3.500A) Processing helix chain 'M' and resid 800 through 807 removed outlier: 3.655A pdb=" N LYS M 806 " --> pdb=" O HIS M 802 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY M 807 " --> pdb=" O PHE M 803 " (cutoff:3.500A) Processing helix chain 'M' and resid 821 through 826 Processing helix chain 'M' and resid 870 through 879 Processing helix chain 'M' and resid 884 through 899 removed outlier: 4.120A pdb=" N SER M 889 " --> pdb=" O LEU M 885 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR M 890 " --> pdb=" O GLY M 886 " (cutoff:3.500A) Processing helix chain 'M' and resid 905 through 920 Processing helix chain 'M' and resid 955 through 969 Processing helix chain 'M' and resid 999 through 1018 Processing helix chain 'M' and resid 1021 through 1027 removed outlier: 3.528A pdb=" N ILE M1025 " --> pdb=" O ASN M1021 " (cutoff:3.500A) Processing helix chain 'M' and resid 1040 through 1071 removed outlier: 4.175A pdb=" N TYR M1044 " --> pdb=" O ASP M1040 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS M1070 " --> pdb=" O PHE M1066 " (cutoff:3.500A) Processing helix chain 'M' and resid 1072 through 1089 Processing helix chain 'M' and resid 1090 through 1093 removed outlier: 3.582A pdb=" N ARG M1093 " --> pdb=" O PRO M1090 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 1090 through 1093' Processing sheet with id=AA1, first strand: chain 'A' and resid 1238 through 1239 removed outlier: 4.845A pdb=" N SER A 17 " --> pdb=" O ASP B1168 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP B1168 " --> pdb=" O SER A 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 81 removed outlier: 3.710A pdb=" N GLY A 72 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N THR A 221 " --> pdb=" O PHE A 76 " (cutoff:3.500A) removed outlier: 11.353A pdb=" N TYR A 78 " --> pdb=" O GLY A 219 " (cutoff:3.500A) removed outlier: 9.974A pdb=" N GLY A 219 " --> pdb=" O TYR A 78 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 130 through 135 removed outlier: 3.591A pdb=" N THR A 135 " --> pdb=" O GLY A 144 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY A 144 " --> pdb=" O THR A 135 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ILE A 145 " --> pdb=" O ILE A 191 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 316 through 318 removed outlier: 4.030A pdb=" N ILE B1073 " --> pdb=" O SER A 318 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1049 through 1051 removed outlier: 3.685A pdb=" N THR A 324 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N VAL A 434 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL A 325 " --> pdb=" O VAL A 434 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N LEU A 436 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N VAL A 327 " --> pdb=" O LEU A 436 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 348 through 349 Processing sheet with id=AA7, first strand: chain 'A' and resid 528 through 529 removed outlier: 3.721A pdb=" N ILE A 529 " --> pdb=" O GLN A 540 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 557 through 559 removed outlier: 6.577A pdb=" N VAL A 565 " --> pdb=" O LEU A 572 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 748 through 751 Processing sheet with id=AB1, first strand: chain 'A' and resid 842 through 844 removed outlier: 6.312A pdb=" N ASN A 852 " --> pdb=" O LEU A 858 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LEU A 858 " --> pdb=" O ASN A 852 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 925 through 926 Processing sheet with id=AB3, first strand: chain 'A' and resid 954 through 955 removed outlier: 6.643A pdb=" N LEU A 954 " --> pdb=" O VAL A1076 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1022 through 1028 removed outlier: 4.069A pdb=" N ASP A1022 " --> pdb=" O VAL A1050 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP A1024 " --> pdb=" O THR A1048 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR I 44 " --> pdb=" O ILE A 965 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1082 through 1090 removed outlier: 6.910A pdb=" N THR A1112 " --> pdb=" O LYS A1083 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N VAL A1085 " --> pdb=" O LYS A1110 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LYS A1110 " --> pdb=" O VAL A1085 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ILE A1087 " --> pdb=" O TYR A1108 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N TYR A1108 " --> pdb=" O ILE A1087 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N TRP A1089 " --> pdb=" O GLU A1106 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLU A1106 " --> pdb=" O TRP A1089 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1261 through 1264 Processing sheet with id=AB7, first strand: chain 'B' and resid 94 through 102 removed outlier: 6.122A pdb=" N VAL B 95 " --> pdb=" O GLU B 139 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N GLU B 139 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N PHE B 97 " --> pdb=" O GLN B 137 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLN B 137 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N GLU B 99 " --> pdb=" O ASN B 135 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASN B 135 " --> pdb=" O GLU B 99 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ALA B 130 " --> pdb=" O SER B 175 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N SER B 175 " --> pdb=" O ALA B 130 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ILE B 132 " --> pdb=" O ILE B 173 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 107 through 108 Processing sheet with id=AB9, first strand: chain 'B' and resid 208 through 209 Processing sheet with id=AC1, first strand: chain 'B' and resid 398 through 401 removed outlier: 6.285A pdb=" N ALA B 219 " --> pdb=" O ARG B 494 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 229 through 231 removed outlier: 4.035A pdb=" N TRP B 235 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 539 through 540 Processing sheet with id=AC4, first strand: chain 'B' and resid 539 through 540 Processing sheet with id=AC5, first strand: chain 'B' and resid 558 through 559 removed outlier: 7.260A pdb=" N VAL B 574 " --> pdb=" O VAL B 581 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU B 583 " --> pdb=" O HIS B 572 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N HIS B 572 " --> pdb=" O LEU B 583 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LYS B 573 " --> pdb=" O VAL B 618 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE B 620 " --> pdb=" O LYS B 573 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU B 575 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU B 617 " --> pdb=" O ASP B 612 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP B 612 " --> pdb=" O GLU B 617 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 742 through 745 removed outlier: 3.982A pdb=" N LYS B 885 " --> pdb=" O SER B 901 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ARG B 903 " --> pdb=" O VAL B 883 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N VAL B 883 " --> pdb=" O ARG B 903 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N VAL B 905 " --> pdb=" O GLY B 881 " (cutoff:3.500A) removed outlier: 9.519A pdb=" N GLY B 881 " --> pdb=" O VAL B 905 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 742 through 745 removed outlier: 3.982A pdb=" N LYS B 885 " --> pdb=" O SER B 901 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ARG B 903 " --> pdb=" O VAL B 883 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N VAL B 883 " --> pdb=" O ARG B 903 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N VAL B 905 " --> pdb=" O GLY B 881 " (cutoff:3.500A) removed outlier: 9.519A pdb=" N GLY B 881 " --> pdb=" O VAL B 905 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N VAL B 886 " --> pdb=" O LYS L 39 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1014 through 1015 removed outlier: 7.741A pdb=" N MET B 790 " --> pdb=" O GLY B 925 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LEU B 927 " --> pdb=" O MET B 790 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N ILE B 944 " --> pdb=" O ASN B 771 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE B 773 " --> pdb=" O ILE B 944 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ILE B 946 " --> pdb=" O ILE B 773 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ALA B 775 " --> pdb=" O ILE B 946 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N PHE B1031 " --> pdb=" O VAL B 776 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 828 through 829 Processing sheet with id=AD1, first strand: chain 'B' and resid 859 through 861 Processing sheet with id=AD2, first strand: chain 'B' and resid 1113 through 1114 removed outlier: 4.088A pdb=" N THR B1113 " --> pdb=" O CYS B1108 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 11 through 17 removed outlier: 6.832A pdb=" N LYS C 23 " --> pdb=" O ARG C 15 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LEU C 17 " --> pdb=" O TYR C 21 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N TYR C 21 " --> pdb=" O LEU C 17 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 126 through 127 removed outlier: 5.150A pdb=" N CYS C 112 " --> pdb=" O GLN C 161 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N GLN C 161 " --> pdb=" O CYS C 112 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N GLU C 162 " --> pdb=" O ASN C 58 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ASN C 58 " --> pdb=" O GLU C 162 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LYS C 164 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ARG C 170 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ILE C 50 " --> pdb=" O ARG C 170 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLY C 172 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N VAL C 48 " --> pdb=" O GLY C 172 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 118 through 120 Processing sheet with id=AD6, first strand: chain 'C' and resid 193 through 196 removed outlier: 3.698A pdb=" N ASP C 193 " --> pdb=" O SER C 260 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER C 260 " --> pdb=" O ASP C 193 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 221 through 224 removed outlier: 3.567A pdb=" N GLN C 229 " --> pdb=" O ASP C 224 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 56 through 58 removed outlier: 3.941A pdb=" N ARG E 96 " --> pdb=" O GLN E 66 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 142 through 145 removed outlier: 3.774A pdb=" N GLU E 142 " --> pdb=" O ILE E 189 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG E 202 " --> pdb=" O VAL E 186 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 6 through 14 removed outlier: 3.890A pdb=" N PHE G 75 " --> pdb=" O LEU G 7 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL G 11 " --> pdb=" O PHE G 71 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ASN G 76 " --> pdb=" O LEU G 54 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N LEU G 54 " --> pdb=" O ASN G 76 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 6 through 14 removed outlier: 3.890A pdb=" N PHE G 75 " --> pdb=" O LEU G 7 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL G 11 " --> pdb=" O PHE G 71 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU G 68 " --> pdb=" O LYS G 63 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 110 through 112 removed outlier: 3.767A pdb=" N SER G 165 " --> pdb=" O VAL G 147 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 8 through 17 removed outlier: 3.576A pdb=" N VAL H 13 " --> pdb=" O ARG H 33 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N GLU H 31 " --> pdb=" O ASP H 15 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LEU H 17 " --> pdb=" O ARG H 29 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ARG H 29 " --> pdb=" O LEU H 17 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP H 44 " --> pdb=" O LEU H 120 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU H 120 " --> pdb=" O ASP H 44 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N TYR H 113 " --> pdb=" O TYR H 98 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLN H 137 " --> pdb=" O LEU H 97 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE H 8 " --> pdb=" O MET H 62 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 15 through 19 removed outlier: 3.708A pdb=" N TYR I 15 " --> pdb=" O ALA I 28 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP I 19 " --> pdb=" O ILE I 24 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ILE I 24 " --> pdb=" O ASP I 19 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 70 through 71 Processing sheet with id=AE7, first strand: chain 'K' and resid 19 through 23 removed outlier: 6.798A pdb=" N ILE K 72 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N TYR K 61 " --> pdb=" O ILE K 72 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ARG K 74 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ALA K 59 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N HIS K 76 " --> pdb=" O LEU K 57 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 39 through 43 Processing sheet with id=AE9, first strand: chain 'M' and resid 218 through 221 removed outlier: 3.916A pdb=" N MET M 218 " --> pdb=" O VAL M 195 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N CYS M 153 " --> pdb=" O ARG M 194 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N TRP M 148 " --> pdb=" O GLY M 131 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N GLY M 131 " --> pdb=" O TRP M 148 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ALA M 125 " --> pdb=" O PHE M 115 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N PHE M 115 " --> pdb=" O ALA M 125 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLU M 127 " --> pdb=" O VAL M 113 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ILE M 109 " --> pdb=" O GLY M 131 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ARG M 133 " --> pdb=" O ASP M 107 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ASP M 107 " --> pdb=" O ARG M 133 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL M 110 " --> pdb=" O GLU M 240 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS M 184 " --> pdb=" O GLU M 165 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU M 165 " --> pdb=" O LYS M 184 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ARG M 258 " --> pdb=" O ILE M 164 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N THR M 166 " --> pdb=" O ARG M 258 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ASP M 260 " --> pdb=" O THR M 166 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N SER M 168 " --> pdb=" O ASP M 260 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 218 through 221 removed outlier: 3.916A pdb=" N MET M 218 " --> pdb=" O VAL M 195 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N CYS M 153 " --> pdb=" O ARG M 194 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N TRP M 148 " --> pdb=" O GLY M 131 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N GLY M 131 " --> pdb=" O TRP M 148 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA M 125 " --> pdb=" O VAL M 267 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 391 through 400 removed outlier: 6.545A pdb=" N ARG M 383 " --> pdb=" O LEU M 394 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N CYS M 381 " --> pdb=" O PRO M 396 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LEU M 398 " --> pdb=" O MET M 379 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N MET M 379 " --> pdb=" O LEU M 398 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N PHE M 415 " --> pdb=" O SER M 380 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN M 382 " --> pdb=" O PHE M 415 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N TRP M 485 " --> pdb=" O LEU M 472 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 438 through 439 removed outlier: 3.636A pdb=" N GLU M 439 " --> pdb=" O PHE M 442 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE M 442 " --> pdb=" O GLU M 439 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'M' and resid 526 through 527 removed outlier: 3.531A pdb=" N VAL M 620 " --> pdb=" O ARG M 526 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASN M 619 " --> pdb=" O ARG M 584 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG M 584 " --> pdb=" O ASN M 619 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLY M 558 " --> pdb=" O ALA M 593 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 543 through 546 Processing sheet with id=AF6, first strand: chain 'M' and resid 627 through 631 removed outlier: 4.223A pdb=" N MET M 627 " --> pdb=" O ILE M 730 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLY M 728 " --> pdb=" O CYS M 629 " (cutoff:3.500A) removed outlier: 11.587A pdb=" N LEU M 631 " --> pdb=" O PRO M 726 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N SER M 839 " --> pdb=" O VAL M 780 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N VAL M 780 " --> pdb=" O SER M 839 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL M 746 " --> pdb=" O ASP M 796 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 733 through 735 removed outlier: 6.725A pdb=" N CYS M 734 " --> pdb=" O PHE M 814 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'M' and resid 749 through 751 removed outlier: 3.749A pdb=" N VAL M 750 " --> pdb=" O SER M 773 " (cutoff:3.500A) 1495 hydrogen bonds defined for protein. 4191 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 63 hydrogen bonds 126 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 11.28 Time building geometry restraints manager: 4.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11462 1.34 - 1.46: 7459 1.46 - 1.58: 17050 1.58 - 1.70: 114 1.70 - 1.82: 335 Bond restraints: 36420 Sorted by residual: bond pdb=" C3' DG N 43 " pdb=" O3' DG N 43 " ideal model delta sigma weight residual 1.422 1.460 -0.038 3.00e-02 1.11e+03 1.58e+00 bond pdb=" C3' DC Q 1 " pdb=" O3' DC Q 1 " ideal model delta sigma weight residual 1.422 1.459 -0.037 3.00e-02 1.11e+03 1.50e+00 bond pdb=" CB PRO B 645 " pdb=" CG PRO B 645 " ideal model delta sigma weight residual 1.492 1.540 -0.048 5.00e-02 4.00e+02 9.25e-01 bond pdb=" C GLU B 682 " pdb=" O GLU B 682 " ideal model delta sigma weight residual 1.238 1.249 -0.011 1.28e-02 6.10e+03 7.81e-01 bond pdb=" C3' DC Q 25 " pdb=" C2' DC Q 25 " ideal model delta sigma weight residual 1.525 1.542 -0.017 2.00e-02 2.50e+03 7.28e-01 ... (remaining 36415 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 49122 1.56 - 3.13: 448 3.13 - 4.69: 51 4.69 - 6.26: 13 6.26 - 7.82: 1 Bond angle restraints: 49635 Sorted by residual: angle pdb=" C GLN B 642 " pdb=" N GLU B 643 " pdb=" CA GLU B 643 " ideal model delta sigma weight residual 121.54 127.58 -6.04 1.91e+00 2.74e-01 1.00e+01 angle pdb=" C HIS A1102 " pdb=" N LEU A1103 " pdb=" CA LEU A1103 " ideal model delta sigma weight residual 121.54 126.90 -5.36 1.91e+00 2.74e-01 7.86e+00 angle pdb=" C LYS M 82 " pdb=" N THR M 83 " pdb=" CA THR M 83 " ideal model delta sigma weight residual 121.54 126.19 -4.65 1.91e+00 2.74e-01 5.94e+00 angle pdb=" N TYR D 129 " pdb=" CA TYR D 129 " pdb=" C TYR D 129 " ideal model delta sigma weight residual 114.04 111.08 2.96 1.24e+00 6.50e-01 5.69e+00 angle pdb=" N ASP C 51 " pdb=" CA ASP C 51 " pdb=" C ASP C 51 " ideal model delta sigma weight residual 114.04 111.21 2.83 1.24e+00 6.50e-01 5.20e+00 ... (remaining 49630 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.77: 21547 35.77 - 71.54: 262 71.54 - 107.31: 9 107.31 - 143.07: 1 143.07 - 178.84: 2 Dihedral angle restraints: 21821 sinusoidal: 8454 harmonic: 13367 Sorted by residual: dihedral pdb=" C4' DG N 43 " pdb=" C3' DG N 43 " pdb=" O3' DG N 43 " pdb=" P DT N 44 " ideal model delta sinusoidal sigma weight residual 220.00 41.16 178.84 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC Q 1 " pdb=" C3' DC Q 1 " pdb=" O3' DC Q 1 " pdb=" P DT Q 2 " ideal model delta sinusoidal sigma weight residual 220.00 42.07 177.93 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT Q 24 " pdb=" C3' DT Q 24 " pdb=" O3' DT Q 24 " pdb=" P DC Q 25 " ideal model delta sinusoidal sigma weight residual 220.00 78.74 141.26 1 3.50e+01 8.16e-04 1.39e+01 ... (remaining 21818 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 3790 0.028 - 0.056: 1275 0.056 - 0.084: 293 0.084 - 0.111: 350 0.111 - 0.139: 59 Chirality restraints: 5767 Sorted by residual: chirality pdb=" CA ILE A 529 " pdb=" N ILE A 529 " pdb=" C ILE A 529 " pdb=" CB ILE A 529 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA ILE J 3 " pdb=" N ILE J 3 " pdb=" C ILE J 3 " pdb=" CB ILE J 3 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" CA VAL K 12 " pdb=" N VAL K 12 " pdb=" C VAL K 12 " pdb=" CB VAL K 12 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.51e-01 ... (remaining 5764 not shown) Planarity restraints: 6146 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE M 939 " -0.022 5.00e-02 4.00e+02 3.36e-02 1.81e+00 pdb=" N PRO M 940 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO M 940 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO M 940 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A O 4 " -0.017 2.00e-02 2.50e+03 7.68e-03 1.62e+00 pdb=" N9 A O 4 " 0.018 2.00e-02 2.50e+03 pdb=" C8 A O 4 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A O 4 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A O 4 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A O 4 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A O 4 " -0.004 2.00e-02 2.50e+03 pdb=" N1 A O 4 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A O 4 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A O 4 " 0.002 2.00e-02 2.50e+03 pdb=" C4 A O 4 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 525 " -0.020 5.00e-02 4.00e+02 3.00e-02 1.44e+00 pdb=" N PRO A 526 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 526 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 526 " -0.017 5.00e-02 4.00e+02 ... (remaining 6143 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 435 2.66 - 3.22: 31940 3.22 - 3.78: 52843 3.78 - 4.34: 70992 4.34 - 4.90: 118225 Nonbonded interactions: 274435 Sorted by model distance: nonbonded pdb=" OD2 ASP A 449 " pdb="MG MG A1502 " model vdw 2.104 2.170 nonbonded pdb=" OD2 ASP B 845 " pdb=" OH TYR L 10 " model vdw 2.232 3.040 nonbonded pdb=" OD2 ASP H 10 " pdb=" OG SER H 34 " model vdw 2.238 3.040 nonbonded pdb=" OG SER M 326 " pdb=" OG1 THR M 329 " model vdw 2.249 3.040 nonbonded pdb=" OG1 THR M 387 " pdb=" O LYS M 390 " model vdw 2.267 3.040 ... (remaining 274430 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: 2.210 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: 0.030 Extract box with map and model: 0.590 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 43.360 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 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 : 0.002 0.048 36453 Z= 0.076 Angle : 0.410 10.037 49668 Z= 0.209 Chirality : 0.038 0.139 5767 Planarity : 0.003 0.034 6146 Dihedral : 10.872 178.843 13155 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.43 % Allowed : 4.34 % Favored : 95.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.12), residues: 4535 helix: 1.61 (0.14), residues: 1533 sheet: 0.31 (0.19), residues: 773 loop : -1.19 (0.12), residues: 2229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 499 TYR 0.011 0.001 TYR K 87 PHE 0.007 0.001 PHE B 729 TRP 0.007 0.001 TRP B 119 HIS 0.003 0.000 HIS B 414 Details of bonding type rmsd covalent geometry : bond 0.00150 (36420) covalent geometry : angle 0.39881 (49635) hydrogen bonds : bond 0.20103 ( 1509) hydrogen bonds : angle 6.71039 ( 4317) metal coordination : bond 0.00643 ( 33) metal coordination : angle 3.67722 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9070 Ramachandran restraints generated. 4535 Oldfield, 0 Emsley, 4535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9070 Ramachandran restraints generated. 4535 Oldfield, 0 Emsley, 4535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 395 time to evaluate : 1.232 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: A 271 MET cc_start: 0.8711 (tpp) cc_final: 0.8216 (ttp) REVERT: A 706 ASP cc_start: 0.9144 (t0) cc_final: 0.8744 (t0) REVERT: A 1136 MET cc_start: 0.9032 (mtp) cc_final: 0.8765 (mtt) REVERT: B 422 MET cc_start: 0.9106 (ttt) cc_final: 0.8690 (tmm) REVERT: B 505 ASP cc_start: 0.9138 (p0) cc_final: 0.8829 (p0) REVERT: C 201 MET cc_start: 0.8164 (mmm) cc_final: 0.7704 (mmm) REVERT: E 14 GLN cc_start: 0.9243 (tm-30) cc_final: 0.8979 (tm-30) REVERT: E 18 MET cc_start: 0.9453 (mmt) cc_final: 0.9129 (mmm) REVERT: E 104 ASN cc_start: 0.8833 (t0) cc_final: 0.8625 (t0) REVERT: E 187 LYS cc_start: 0.8802 (tttm) cc_final: 0.8557 (tttm) REVERT: F 62 SER cc_start: 0.8987 (m) cc_final: 0.8493 (t) REVERT: F 130 GLU cc_start: 0.9155 (mt-10) cc_final: 0.8888 (mp0) REVERT: G 48 LEU cc_start: 0.8808 (pt) cc_final: 0.8341 (tp) REVERT: G 75 PHE cc_start: 0.8022 (p90) cc_final: 0.7431 (p90) REVERT: G 78 ILE cc_start: 0.8306 (OUTLIER) cc_final: 0.7953 (tp) REVERT: G 149 LEU cc_start: 0.3591 (mm) cc_final: 0.3331 (mp) REVERT: H 39 MET cc_start: 0.8245 (mtp) cc_final: 0.7979 (mtt) REVERT: I 97 MET cc_start: 0.9292 (mmt) cc_final: 0.8997 (mmm) REVERT: I 98 THR cc_start: 0.9206 (m) cc_final: 0.8801 (p) REVERT: L 40 LYS cc_start: 0.9258 (tttp) cc_final: 0.9040 (ttmm) REVERT: M 946 PHE cc_start: 0.8649 (m-80) cc_final: 0.8442 (m-80) outliers start: 15 outliers final: 4 residues processed: 407 average time/residue: 0.2334 time to fit residues: 145.7068 Evaluate side-chains 256 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 251 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain M residue 59 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 432 optimal weight: 3.9990 chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 5.9990 chunk 455 optimal weight: 10.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 8.9990 chunk 401 optimal weight: 40.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 GLN A 476 GLN A 545 GLN A 562 ASN A 634 GLN A 658 GLN A 742 GLN A 805 ASN A 857 GLN A1008 GLN ** A1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1219 GLN A1227 GLN B 220 GLN B 222 GLN B 316 HIS B 355 HIS B 477 ASN B 513 HIS B 543 GLN B 600 GLN B 711 HIS B 724 GLN B 749 GLN B 768 ASN B 779 HIS B 804 GLN B 949 HIS B1003 GLN D 140 GLN E 126 GLN H 124 GLN I 80 GLN K 89 GLN K 104 GLN L 17 GLN L 28 GLN L 47 GLN M 84 HIS M 85 ASN M 277 GLN M 298 GLN M 300 ASN M 304 HIS M 306 GLN M 377 ASN M 478 GLN M 482 ASN M 567 GLN M 822 HIS M 873 HIS M1059 HIS M1092 HIS Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.061976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.041867 restraints weight = 183912.306| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 4.06 r_work: 0.2748 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 36453 Z= 0.299 Angle : 0.654 10.997 49668 Z= 0.336 Chirality : 0.044 0.180 5767 Planarity : 0.004 0.065 6146 Dihedral : 12.057 178.066 5623 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.53 % Allowed : 7.46 % Favored : 91.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.12), residues: 4535 helix: 1.57 (0.14), residues: 1575 sheet: 0.19 (0.19), residues: 757 loop : -1.16 (0.12), residues: 2203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 142 TYR 0.030 0.002 TYR K 87 PHE 0.022 0.002 PHE B 43 TRP 0.016 0.002 TRP A1250 HIS 0.007 0.001 HIS B 414 Details of bonding type rmsd covalent geometry : bond 0.00667 (36420) covalent geometry : angle 0.64584 (49635) hydrogen bonds : bond 0.04701 ( 1509) hydrogen bonds : angle 4.92972 ( 4317) metal coordination : bond 0.01201 ( 33) metal coordination : angle 4.10678 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9070 Ramachandran restraints generated. 4535 Oldfield, 0 Emsley, 4535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9070 Ramachandran restraints generated. 4535 Oldfield, 0 Emsley, 4535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 247 time to evaluate : 1.158 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 271 MET cc_start: 0.8868 (tpp) cc_final: 0.8163 (ptt) REVERT: A 423 MET cc_start: 0.9235 (mtp) cc_final: 0.9024 (mmm) REVERT: A 946 GLU cc_start: 0.9023 (tm-30) cc_final: 0.8769 (tm-30) REVERT: B 257 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.7887 (pptt) REVERT: B 422 MET cc_start: 0.9051 (ttt) cc_final: 0.8770 (tmm) REVERT: B 557 MET cc_start: 0.9075 (ttp) cc_final: 0.8798 (ttt) REVERT: B 799 MET cc_start: 0.9540 (ttm) cc_final: 0.9307 (ttp) REVERT: B 973 ILE cc_start: 0.9502 (OUTLIER) cc_final: 0.9240 (pt) REVERT: C 200 MET cc_start: 0.7822 (mtp) cc_final: 0.7600 (mtp) REVERT: C 201 MET cc_start: 0.8402 (mmm) cc_final: 0.7921 (mmm) REVERT: C 223 MET cc_start: 0.9401 (tpt) cc_final: 0.9079 (tpt) REVERT: D 93 MET cc_start: 0.3772 (mmt) cc_final: 0.3229 (mmt) REVERT: E 14 GLN cc_start: 0.9401 (tm-30) cc_final: 0.9137 (tm-30) REVERT: E 18 MET cc_start: 0.9567 (mmt) cc_final: 0.9305 (mmm) REVERT: E 103 GLN cc_start: 0.8950 (mt0) cc_final: 0.8495 (pt0) REVERT: E 129 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8759 (pt0) REVERT: E 159 THR cc_start: 0.9440 (OUTLIER) cc_final: 0.9168 (p) REVERT: F 62 SER cc_start: 0.9293 (m) cc_final: 0.8865 (t) REVERT: F 102 MET cc_start: 0.9319 (tmm) cc_final: 0.9025 (tmm) REVERT: G 36 PHE cc_start: 0.8538 (p90) cc_final: 0.8249 (p90) REVERT: G 47 TYR cc_start: 0.7970 (m-80) cc_final: 0.7365 (m-80) REVERT: G 48 LEU cc_start: 0.8381 (pt) cc_final: 0.8165 (tp) REVERT: G 80 PHE cc_start: -0.2058 (OUTLIER) cc_final: -0.2457 (t80) REVERT: H 23 LYS cc_start: 0.9058 (mmmt) cc_final: 0.8835 (tppt) REVERT: H 29 ARG cc_start: 0.9167 (OUTLIER) cc_final: 0.8910 (ttm-80) REVERT: H 39 MET cc_start: 0.8599 (mtp) cc_final: 0.7508 (mtp) REVERT: H 111 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8339 (pm20) REVERT: I 70 ARG cc_start: 0.8982 (mtp85) cc_final: 0.8617 (mtt90) REVERT: I 97 MET cc_start: 0.9461 (mmt) cc_final: 0.9010 (mmm) REVERT: M 486 MET cc_start: 0.9290 (mtt) cc_final: 0.9020 (mmm) REVERT: M 738 MET cc_start: 0.8229 (ttp) cc_final: 0.7062 (ppp) REVERT: M 946 PHE cc_start: 0.8993 (m-80) cc_final: 0.8703 (m-80) REVERT: M 1063 MET cc_start: 0.8723 (mmm) cc_final: 0.8408 (tpp) outliers start: 53 outliers final: 20 residues processed: 287 average time/residue: 0.1806 time to fit residues: 85.7618 Evaluate side-chains 248 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 222 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain B residue 1163 ILE Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 76 ASN Chi-restraints excluded: chain G residue 80 PHE Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain H residue 29 ARG Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain M residue 576 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 97 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 367 optimal weight: 4.9990 chunk 110 optimal weight: 0.0980 chunk 190 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 chunk 378 optimal weight: 20.0000 chunk 210 optimal weight: 1.9990 chunk 332 optimal weight: 0.9980 chunk 349 optimal weight: 9.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 GLN ** A1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1182 HIS B1091 ASN M1002 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.062903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.042764 restraints weight = 184345.509| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 4.25 r_work: 0.2780 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 36453 Z= 0.112 Angle : 0.502 8.677 49668 Z= 0.258 Chirality : 0.040 0.177 5767 Planarity : 0.003 0.051 6146 Dihedral : 11.977 178.696 5620 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.16 % Allowed : 8.42 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.12), residues: 4535 helix: 1.78 (0.14), residues: 1579 sheet: 0.06 (0.18), residues: 783 loop : -1.14 (0.12), residues: 2173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 506 TYR 0.022 0.001 TYR K 87 PHE 0.017 0.001 PHE G 36 TRP 0.012 0.001 TRP F 126 HIS 0.005 0.001 HIS A 454 Details of bonding type rmsd covalent geometry : bond 0.00245 (36420) covalent geometry : angle 0.49463 (49635) hydrogen bonds : bond 0.03524 ( 1509) hydrogen bonds : angle 4.54983 ( 4317) metal coordination : bond 0.00447 ( 33) metal coordination : angle 3.33970 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9070 Ramachandran restraints generated. 4535 Oldfield, 0 Emsley, 4535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9070 Ramachandran restraints generated. 4535 Oldfield, 0 Emsley, 4535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 236 time to evaluate : 1.389 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: A 152 GLU cc_start: 0.9569 (mp0) cc_final: 0.9267 (pp20) REVERT: A 271 MET cc_start: 0.8916 (tpp) cc_final: 0.8286 (ptt) REVERT: A 423 MET cc_start: 0.9285 (mtp) cc_final: 0.9056 (mtp) REVERT: A 946 GLU cc_start: 0.9188 (tm-30) cc_final: 0.8855 (tm-30) REVERT: A 1113 MET cc_start: 0.8929 (mtp) cc_final: 0.8654 (mtm) REVERT: B 257 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8037 (pptt) REVERT: B 422 MET cc_start: 0.9028 (ttt) cc_final: 0.8721 (tmm) REVERT: B 557 MET cc_start: 0.9097 (ttp) cc_final: 0.8770 (ttt) REVERT: B 973 ILE cc_start: 0.9467 (OUTLIER) cc_final: 0.9184 (pt) REVERT: C 201 MET cc_start: 0.8236 (mmm) cc_final: 0.7711 (mmm) REVERT: C 223 MET cc_start: 0.9379 (tpt) cc_final: 0.9021 (tpt) REVERT: D 93 MET cc_start: 0.3777 (mmt) cc_final: 0.3061 (mmt) REVERT: E 14 GLN cc_start: 0.9394 (tm-30) cc_final: 0.9118 (tm-30) REVERT: E 18 MET cc_start: 0.9562 (mmt) cc_final: 0.9262 (mmm) REVERT: E 48 MET cc_start: 0.8706 (mpp) cc_final: 0.8473 (mpp) REVERT: E 129 GLU cc_start: 0.9036 (mt-10) cc_final: 0.8831 (pt0) REVERT: E 142 GLU cc_start: 0.8371 (tm-30) cc_final: 0.7924 (tm-30) REVERT: E 159 THR cc_start: 0.9423 (OUTLIER) cc_final: 0.9171 (p) REVERT: F 62 SER cc_start: 0.9290 (m) cc_final: 0.8852 (t) REVERT: F 102 MET cc_start: 0.9315 (tmm) cc_final: 0.9025 (tmm) REVERT: G 47 TYR cc_start: 0.8098 (m-80) cc_final: 0.7623 (m-80) REVERT: G 80 PHE cc_start: -0.2286 (OUTLIER) cc_final: -0.2652 (t80) REVERT: H 39 MET cc_start: 0.8581 (mtp) cc_final: 0.8377 (mtp) REVERT: H 41 MET cc_start: 0.9389 (ttp) cc_final: 0.9095 (ttt) REVERT: H 62 MET cc_start: 0.9394 (mtp) cc_final: 0.9181 (mtt) REVERT: H 111 GLU cc_start: 0.8631 (pt0) cc_final: 0.8283 (pm20) REVERT: I 70 ARG cc_start: 0.8999 (mtp85) cc_final: 0.8724 (mtt90) REVERT: I 97 MET cc_start: 0.9441 (mmt) cc_final: 0.9107 (mmm) REVERT: M 946 PHE cc_start: 0.9025 (m-80) cc_final: 0.8713 (m-80) REVERT: M 1063 MET cc_start: 0.8797 (mmm) cc_final: 0.8513 (tpp) outliers start: 40 outliers final: 22 residues processed: 269 average time/residue: 0.1866 time to fit residues: 83.5662 Evaluate side-chains 246 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 220 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 746 PHE Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1035 THR Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain B residue 1163 ILE Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 80 PHE Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain H residue 29 ARG Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 163 ILE Chi-restraints excluded: chain M residue 299 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 195 optimal weight: 6.9990 chunk 12 optimal weight: 20.0000 chunk 374 optimal weight: 30.0000 chunk 447 optimal weight: 20.0000 chunk 425 optimal weight: 9.9990 chunk 137 optimal weight: 1.9990 chunk 452 optimal weight: 30.0000 chunk 184 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 chunk 414 optimal weight: 30.0000 chunk 282 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 GLN A 985 HIS A1006 ASN ** A1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 771 ASN B1042 HIS C 197 ASN E 143 HIS ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 50 HIS K 76 HIS M 243 ASN ** M 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 407 ASN M 478 GLN M 824 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.060037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.040017 restraints weight = 185541.049| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 3.83 r_work: 0.2667 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.254 36453 Z= 0.360 Angle : 0.697 10.610 49668 Z= 0.354 Chirality : 0.045 0.205 5767 Planarity : 0.005 0.057 6146 Dihedral : 12.161 178.727 5620 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.17 % Allowed : 8.47 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.12), residues: 4535 helix: 1.58 (0.13), residues: 1563 sheet: -0.23 (0.18), residues: 791 loop : -1.11 (0.13), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 859 TYR 0.022 0.002 TYR K 87 PHE 0.019 0.002 PHE B 43 TRP 0.015 0.002 TRP F 126 HIS 0.009 0.002 HIS C 177 Details of bonding type rmsd covalent geometry : bond 0.00797 (36420) covalent geometry : angle 0.68760 (49635) hydrogen bonds : bond 0.05078 ( 1509) hydrogen bonds : angle 4.84285 ( 4317) metal coordination : bond 0.04597 ( 33) metal coordination : angle 4.50919 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9070 Ramachandran restraints generated. 4535 Oldfield, 0 Emsley, 4535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9070 Ramachandran restraints generated. 4535 Oldfield, 0 Emsley, 4535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 221 time to evaluate : 1.064 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: A 152 GLU cc_start: 0.9604 (mp0) cc_final: 0.9293 (pp20) REVERT: A 271 MET cc_start: 0.8972 (tpp) cc_final: 0.8207 (ttp) REVERT: A 839 MET cc_start: 0.9263 (mmm) cc_final: 0.8890 (mmm) REVERT: B 257 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.7925 (pptt) REVERT: B 422 MET cc_start: 0.9015 (ttt) cc_final: 0.8802 (tmm) REVERT: B 557 MET cc_start: 0.9122 (ttp) cc_final: 0.8818 (ttt) REVERT: B 799 MET cc_start: 0.9590 (ttm) cc_final: 0.9336 (ttp) REVERT: B 973 ILE cc_start: 0.9619 (OUTLIER) cc_final: 0.9370 (pt) REVERT: C 84 MET cc_start: 0.9241 (mtp) cc_final: 0.8966 (ttp) REVERT: C 223 MET cc_start: 0.9322 (tpt) cc_final: 0.9043 (tpp) REVERT: D 92 MET cc_start: 0.4653 (pmm) cc_final: 0.3875 (tpt) REVERT: D 93 MET cc_start: 0.3624 (mmt) cc_final: 0.1966 (mmt) REVERT: E 14 GLN cc_start: 0.9370 (tm-30) cc_final: 0.9091 (tm-30) REVERT: E 18 MET cc_start: 0.9579 (mmt) cc_final: 0.9278 (mmm) REVERT: E 101 VAL cc_start: 0.9549 (OUTLIER) cc_final: 0.9311 (m) REVERT: E 103 GLN cc_start: 0.8892 (mt0) cc_final: 0.8516 (pm20) REVERT: E 129 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8823 (pt0) REVERT: E 142 GLU cc_start: 0.8400 (tm-30) cc_final: 0.7943 (tm-30) REVERT: E 159 THR cc_start: 0.9449 (OUTLIER) cc_final: 0.9169 (p) REVERT: F 62 SER cc_start: 0.9510 (m) cc_final: 0.9115 (t) REVERT: F 102 MET cc_start: 0.9298 (tmm) cc_final: 0.9022 (tmm) REVERT: G 61 LYS cc_start: 0.8055 (ttpt) cc_final: 0.7849 (ttpp) REVERT: G 64 GLU cc_start: 0.8425 (mp0) cc_final: 0.8221 (mp0) REVERT: G 80 PHE cc_start: -0.2074 (OUTLIER) cc_final: -0.2637 (t80) REVERT: H 41 MET cc_start: 0.9425 (ttp) cc_final: 0.9172 (ttt) REVERT: H 111 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8399 (pm20) REVERT: I 70 ARG cc_start: 0.9121 (mtp85) cc_final: 0.8916 (mtt90) REVERT: I 75 ARG cc_start: 0.8880 (ttm-80) cc_final: 0.8673 (tpp80) REVERT: I 97 MET cc_start: 0.9403 (mmt) cc_final: 0.8913 (mmm) REVERT: K 9 ARG cc_start: 0.8628 (ttp-170) cc_final: 0.8128 (ptm160) REVERT: M 379 MET cc_start: 0.9292 (ppp) cc_final: 0.8644 (ppp) REVERT: M 486 MET cc_start: 0.9062 (mmm) cc_final: 0.8743 (mmm) REVERT: M 1063 MET cc_start: 0.8888 (mmm) cc_final: 0.8686 (tpp) outliers start: 75 outliers final: 36 residues processed: 280 average time/residue: 0.1808 time to fit residues: 84.5122 Evaluate side-chains 256 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 214 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 454 HIS Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 771 ASN Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1035 THR Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 76 ASN Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 80 PHE Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain M residue 163 ILE Chi-restraints excluded: chain M residue 279 VAL Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain M residue 319 ILE Chi-restraints excluded: chain M residue 599 PHE Chi-restraints excluded: chain M residue 738 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 433 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 320 optimal weight: 7.9990 chunk 324 optimal weight: 4.9990 chunk 368 optimal weight: 4.9990 chunk 252 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 274 optimal weight: 8.9990 chunk 110 optimal weight: 0.8980 chunk 339 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 12 ASN I 31 ASN I 50 HIS K 76 HIS ** M 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.061089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.040673 restraints weight = 182616.789| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 4.15 r_work: 0.2727 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 36453 Z= 0.140 Angle : 0.528 8.828 49668 Z= 0.271 Chirality : 0.041 0.185 5767 Planarity : 0.003 0.043 6146 Dihedral : 12.028 176.785 5620 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.36 % Allowed : 9.75 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.13), residues: 4535 helix: 1.81 (0.14), residues: 1572 sheet: -0.17 (0.18), residues: 775 loop : -1.08 (0.13), residues: 2188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 859 TYR 0.019 0.001 TYR K 87 PHE 0.027 0.001 PHE G 36 TRP 0.008 0.001 TRP A 980 HIS 0.007 0.001 HIS A 454 Details of bonding type rmsd covalent geometry : bond 0.00310 (36420) covalent geometry : angle 0.52022 (49635) hydrogen bonds : bond 0.03525 ( 1509) hydrogen bonds : angle 4.49676 ( 4317) metal coordination : bond 0.00585 ( 33) metal coordination : angle 3.49767 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9070 Ramachandran restraints generated. 4535 Oldfield, 0 Emsley, 4535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9070 Ramachandran restraints generated. 4535 Oldfield, 0 Emsley, 4535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 218 time to evaluate : 1.160 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: A 271 MET cc_start: 0.8933 (tpp) cc_final: 0.8261 (ptt) REVERT: A 839 MET cc_start: 0.9245 (mmm) cc_final: 0.8922 (mmm) REVERT: A 946 GLU cc_start: 0.9302 (tm-30) cc_final: 0.8982 (tm-30) REVERT: B 257 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.8007 (pptt) REVERT: B 422 MET cc_start: 0.8944 (ttt) cc_final: 0.8707 (tmm) REVERT: B 557 MET cc_start: 0.9114 (ttp) cc_final: 0.8744 (ttt) REVERT: B 973 ILE cc_start: 0.9578 (OUTLIER) cc_final: 0.9377 (pt) REVERT: D 93 MET cc_start: 0.3462 (mmt) cc_final: 0.2584 (mmt) REVERT: E 14 GLN cc_start: 0.9351 (tm-30) cc_final: 0.9070 (tm-30) REVERT: E 18 MET cc_start: 0.9559 (mmt) cc_final: 0.9244 (mmm) REVERT: E 103 GLN cc_start: 0.8857 (mt0) cc_final: 0.8523 (pm20) REVERT: E 129 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8815 (pt0) REVERT: E 142 GLU cc_start: 0.8393 (tm-30) cc_final: 0.7890 (tm-30) REVERT: E 159 THR cc_start: 0.9413 (OUTLIER) cc_final: 0.9170 (p) REVERT: F 62 SER cc_start: 0.9444 (m) cc_final: 0.9043 (t) REVERT: F 102 MET cc_start: 0.9248 (tmm) cc_final: 0.8959 (tmm) REVERT: G 39 GLU cc_start: 0.8445 (pp20) cc_final: 0.8181 (pp20) REVERT: G 47 TYR cc_start: 0.8026 (m-80) cc_final: 0.7767 (m-80) REVERT: G 61 LYS cc_start: 0.7963 (ttpt) cc_final: 0.7633 (ttpp) REVERT: G 80 PHE cc_start: -0.2364 (OUTLIER) cc_final: -0.2594 (t80) REVERT: H 41 MET cc_start: 0.9410 (ttp) cc_final: 0.9171 (ttp) REVERT: H 111 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8474 (pm20) REVERT: I 70 ARG cc_start: 0.9068 (mtp85) cc_final: 0.8850 (mtt90) REVERT: I 83 GLU cc_start: 0.8456 (tp30) cc_final: 0.7999 (tp30) REVERT: I 97 MET cc_start: 0.9372 (mmt) cc_final: 0.8894 (mmm) REVERT: M 486 MET cc_start: 0.8993 (mmm) cc_final: 0.8699 (mmm) REVERT: M 705 MET cc_start: 0.9009 (mmp) cc_final: 0.8780 (mmp) REVERT: M 1063 MET cc_start: 0.8968 (mmm) cc_final: 0.8756 (tpp) outliers start: 47 outliers final: 30 residues processed: 255 average time/residue: 0.1783 time to fit residues: 76.1075 Evaluate side-chains 250 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 215 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 454 HIS Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 746 PHE Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain B residue 1163 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 79 CYS Chi-restraints excluded: chain G residue 80 PHE Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 163 ILE Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain M residue 319 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 176 optimal weight: 6.9990 chunk 269 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 chunk 223 optimal weight: 5.9990 chunk 415 optimal weight: 50.0000 chunk 387 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 chunk 430 optimal weight: 5.9990 chunk 414 optimal weight: 30.0000 chunk 236 optimal weight: 0.5980 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 771 ASN I 50 HIS ** M 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.060288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.040015 restraints weight = 185992.240| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 4.05 r_work: 0.2694 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 36453 Z= 0.235 Angle : 0.592 14.175 49668 Z= 0.298 Chirality : 0.042 0.177 5767 Planarity : 0.004 0.042 6146 Dihedral : 12.057 175.735 5620 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.82 % Allowed : 9.51 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.13), residues: 4535 helix: 1.80 (0.14), residues: 1567 sheet: -0.19 (0.19), residues: 763 loop : -1.07 (0.13), residues: 2205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 898 TYR 0.047 0.001 TYR A 102 PHE 0.012 0.001 PHE B 284 TRP 0.008 0.001 TRP B 280 HIS 0.007 0.001 HIS A 454 Details of bonding type rmsd covalent geometry : bond 0.00528 (36420) covalent geometry : angle 0.58159 (49635) hydrogen bonds : bond 0.03922 ( 1509) hydrogen bonds : angle 4.55008 ( 4317) metal coordination : bond 0.00864 ( 33) metal coordination : angle 4.26364 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9070 Ramachandran restraints generated. 4535 Oldfield, 0 Emsley, 4535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9070 Ramachandran restraints generated. 4535 Oldfield, 0 Emsley, 4535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 215 time to evaluate : 0.951 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: A 141 ARG cc_start: 0.6973 (tpt90) cc_final: 0.6514 (tpt90) REVERT: A 839 MET cc_start: 0.9275 (mmm) cc_final: 0.8876 (mmm) REVERT: B 257 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8071 (pptt) REVERT: B 557 MET cc_start: 0.9102 (ttp) cc_final: 0.8727 (ttt) REVERT: B 799 MET cc_start: 0.9543 (ttm) cc_final: 0.9231 (ttp) REVERT: B 973 ILE cc_start: 0.9589 (OUTLIER) cc_final: 0.9387 (pt) REVERT: D 92 MET cc_start: 0.6716 (pmm) cc_final: 0.6073 (tpt) REVERT: D 93 MET cc_start: 0.3474 (mmt) cc_final: 0.1963 (mmt) REVERT: E 14 GLN cc_start: 0.9351 (tm-30) cc_final: 0.9058 (tm-30) REVERT: E 18 MET cc_start: 0.9558 (mmt) cc_final: 0.9222 (mmm) REVERT: E 103 GLN cc_start: 0.8943 (mt0) cc_final: 0.8731 (pt0) REVERT: E 129 GLU cc_start: 0.9060 (mt-10) cc_final: 0.8834 (pt0) REVERT: E 142 GLU cc_start: 0.8458 (tm-30) cc_final: 0.7916 (tm-30) REVERT: E 159 THR cc_start: 0.9413 (OUTLIER) cc_final: 0.9164 (p) REVERT: F 62 SER cc_start: 0.9460 (m) cc_final: 0.9071 (t) REVERT: F 102 MET cc_start: 0.9262 (tmm) cc_final: 0.8988 (tmm) REVERT: G 39 GLU cc_start: 0.8465 (pp20) cc_final: 0.8236 (pp20) REVERT: G 47 TYR cc_start: 0.8129 (m-80) cc_final: 0.7775 (m-80) REVERT: G 80 PHE cc_start: -0.2365 (OUTLIER) cc_final: -0.3183 (t80) REVERT: H 41 MET cc_start: 0.9403 (ttp) cc_final: 0.9173 (ttt) REVERT: H 111 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8468 (pm20) REVERT: I 70 ARG cc_start: 0.9096 (mtp85) cc_final: 0.8889 (mtt90) REVERT: I 75 ARG cc_start: 0.9018 (ttm-80) cc_final: 0.8696 (ttm-80) REVERT: I 83 GLU cc_start: 0.8474 (tp30) cc_final: 0.8000 (tp30) REVERT: I 95 GLU cc_start: 0.8850 (pm20) cc_final: 0.8646 (pm20) REVERT: I 97 MET cc_start: 0.9388 (mmt) cc_final: 0.8877 (mmm) REVERT: K 9 ARG cc_start: 0.8636 (ttp-170) cc_final: 0.7827 (ttp-110) REVERT: M 486 MET cc_start: 0.8982 (mmm) cc_final: 0.8668 (mmm) REVERT: M 663 MET cc_start: 0.7336 (ptp) cc_final: 0.6875 (mpp) REVERT: M 1063 MET cc_start: 0.8958 (mmm) cc_final: 0.8736 (tpp) outliers start: 63 outliers final: 42 residues processed: 264 average time/residue: 0.1769 time to fit residues: 78.3805 Evaluate side-chains 258 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 211 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 454 HIS Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 607 MET Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 746 PHE Chi-restraints excluded: chain B residue 771 ASN Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1035 THR Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain B residue 1163 ILE Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 80 PHE Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain M residue 163 ILE Chi-restraints excluded: chain M residue 279 VAL Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain M residue 319 ILE Chi-restraints excluded: chain M residue 599 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 353 optimal weight: 0.0070 chunk 279 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 296 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 191 optimal weight: 0.9980 chunk 408 optimal weight: 6.9990 chunk 177 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 233 optimal weight: 7.9990 chunk 403 optimal weight: 20.0000 overall best weight: 2.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 771 ASN I 50 HIS ** M 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1092 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.060802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.040529 restraints weight = 185321.236| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 4.01 r_work: 0.2716 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 36453 Z= 0.152 Angle : 0.543 13.312 49668 Z= 0.274 Chirality : 0.041 0.239 5767 Planarity : 0.003 0.042 6146 Dihedral : 12.017 175.393 5620 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.68 % Allowed : 9.86 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.13), residues: 4535 helix: 1.91 (0.14), residues: 1562 sheet: -0.15 (0.19), residues: 763 loop : -1.04 (0.13), residues: 2210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 399 TYR 0.022 0.001 TYR A 102 PHE 0.012 0.001 PHE B 108 TRP 0.008 0.001 TRP B 280 HIS 0.007 0.001 HIS A 454 Details of bonding type rmsd covalent geometry : bond 0.00342 (36420) covalent geometry : angle 0.53242 (49635) hydrogen bonds : bond 0.03416 ( 1509) hydrogen bonds : angle 4.43017 ( 4317) metal coordination : bond 0.00628 ( 33) metal coordination : angle 4.15174 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9070 Ramachandran restraints generated. 4535 Oldfield, 0 Emsley, 4535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9070 Ramachandran restraints generated. 4535 Oldfield, 0 Emsley, 4535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 216 time to evaluate : 1.038 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: A 271 MET cc_start: 0.8973 (tpp) cc_final: 0.8300 (ptt) REVERT: A 839 MET cc_start: 0.9266 (mmm) cc_final: 0.8905 (mmm) REVERT: A 946 GLU cc_start: 0.9294 (tm-30) cc_final: 0.8980 (tm-30) REVERT: B 257 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8123 (pptt) REVERT: B 557 MET cc_start: 0.9079 (ttp) cc_final: 0.8703 (ttt) REVERT: D 92 MET cc_start: 0.6712 (pmm) cc_final: 0.6059 (tpt) REVERT: D 93 MET cc_start: 0.3474 (mmt) cc_final: 0.1640 (mmt) REVERT: E 14 GLN cc_start: 0.9335 (tm-30) cc_final: 0.9037 (tm-30) REVERT: E 18 MET cc_start: 0.9560 (mmt) cc_final: 0.9223 (mmm) REVERT: E 129 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8844 (pt0) REVERT: E 142 GLU cc_start: 0.8473 (tm-30) cc_final: 0.7938 (tm-30) REVERT: E 144 GLN cc_start: 0.9176 (tt0) cc_final: 0.8820 (tm-30) REVERT: E 159 THR cc_start: 0.9419 (OUTLIER) cc_final: 0.9179 (p) REVERT: F 62 SER cc_start: 0.9440 (m) cc_final: 0.9051 (t) REVERT: F 83 MET cc_start: 0.9402 (mmm) cc_final: 0.9168 (tpp) REVERT: F 102 MET cc_start: 0.9234 (tmm) cc_final: 0.8955 (tmm) REVERT: G 47 TYR cc_start: 0.8062 (m-80) cc_final: 0.7737 (m-80) REVERT: G 80 PHE cc_start: -0.2516 (OUTLIER) cc_final: -0.3258 (t80) REVERT: H 41 MET cc_start: 0.9370 (ttp) cc_final: 0.9136 (ttp) REVERT: H 111 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8538 (pm20) REVERT: I 75 ARG cc_start: 0.9028 (ttm-80) cc_final: 0.8672 (ttm-80) REVERT: I 83 GLU cc_start: 0.8478 (tp30) cc_final: 0.7996 (tp30) REVERT: I 97 MET cc_start: 0.9388 (mmt) cc_final: 0.8874 (mmm) REVERT: K 9 ARG cc_start: 0.8634 (ttp-170) cc_final: 0.7856 (ttp-110) REVERT: M 486 MET cc_start: 0.8970 (mmm) cc_final: 0.8625 (mmm) REVERT: M 608 MET cc_start: 0.7867 (tpp) cc_final: 0.7463 (mmm) REVERT: M 1063 MET cc_start: 0.8957 (mmm) cc_final: 0.8738 (tpp) outliers start: 58 outliers final: 45 residues processed: 261 average time/residue: 0.1796 time to fit residues: 78.0285 Evaluate side-chains 259 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 210 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 454 HIS Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 607 MET Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 746 PHE Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 1035 THR Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain B residue 1163 ILE Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 79 CYS Chi-restraints excluded: chain G residue 80 PHE Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain H residue 29 ARG Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 163 ILE Chi-restraints excluded: chain M residue 279 VAL Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain M residue 599 PHE Chi-restraints excluded: chain M residue 641 THR Chi-restraints excluded: chain M residue 738 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 271 optimal weight: 10.0000 chunk 162 optimal weight: 0.9990 chunk 202 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 316 optimal weight: 5.9990 chunk 238 optimal weight: 4.9990 chunk 390 optimal weight: 1.9990 chunk 200 optimal weight: 10.0000 chunk 289 optimal weight: 50.0000 chunk 259 optimal weight: 30.0000 chunk 443 optimal weight: 40.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 771 ASN E 103 GLN I 50 HIS ** M 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.060534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.040367 restraints weight = 184954.605| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 4.13 r_work: 0.2695 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 36453 Z= 0.185 Angle : 0.567 12.566 49668 Z= 0.285 Chirality : 0.041 0.212 5767 Planarity : 0.003 0.042 6146 Dihedral : 12.009 174.473 5620 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.82 % Allowed : 9.95 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.13), residues: 4535 helix: 1.88 (0.14), residues: 1571 sheet: -0.25 (0.18), residues: 773 loop : -1.06 (0.13), residues: 2191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 141 TYR 0.024 0.001 TYR A 102 PHE 0.015 0.001 PHE G 36 TRP 0.008 0.001 TRP B 280 HIS 0.007 0.001 HIS A 454 Details of bonding type rmsd covalent geometry : bond 0.00417 (36420) covalent geometry : angle 0.55854 (49635) hydrogen bonds : bond 0.03498 ( 1509) hydrogen bonds : angle 4.43006 ( 4317) metal coordination : bond 0.00727 ( 33) metal coordination : angle 3.91611 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9070 Ramachandran restraints generated. 4535 Oldfield, 0 Emsley, 4535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9070 Ramachandran restraints generated. 4535 Oldfield, 0 Emsley, 4535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 209 time to evaluate : 1.175 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: A 839 MET cc_start: 0.9263 (mmm) cc_final: 0.8890 (mmm) REVERT: A 946 GLU cc_start: 0.9268 (tm-30) cc_final: 0.8936 (tm-30) REVERT: B 257 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8162 (pptt) REVERT: B 295 MET cc_start: 0.9512 (mmm) cc_final: 0.9290 (mmm) REVERT: B 557 MET cc_start: 0.9088 (ttp) cc_final: 0.8707 (ttt) REVERT: B 799 MET cc_start: 0.9545 (ttm) cc_final: 0.9231 (ttp) REVERT: C 197 ASN cc_start: 0.9467 (OUTLIER) cc_final: 0.9072 (t0) REVERT: D 92 MET cc_start: 0.5854 (pmm) cc_final: 0.4910 (tpt) REVERT: D 93 MET cc_start: 0.3576 (mmt) cc_final: 0.1769 (mmt) REVERT: E 14 GLN cc_start: 0.9334 (tm-30) cc_final: 0.9074 (tm-30) REVERT: E 18 MET cc_start: 0.9548 (mmt) cc_final: 0.9199 (mmp) REVERT: E 103 GLN cc_start: 0.9152 (OUTLIER) cc_final: 0.8741 (pm20) REVERT: E 129 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8807 (pt0) REVERT: E 142 GLU cc_start: 0.8539 (tm-30) cc_final: 0.7962 (tm-30) REVERT: E 144 GLN cc_start: 0.9195 (tt0) cc_final: 0.8826 (tm-30) REVERT: E 159 THR cc_start: 0.9419 (OUTLIER) cc_final: 0.9179 (p) REVERT: F 62 SER cc_start: 0.9461 (m) cc_final: 0.9077 (t) REVERT: F 83 MET cc_start: 0.9401 (mmm) cc_final: 0.9193 (tpp) REVERT: F 102 MET cc_start: 0.9261 (tmm) cc_final: 0.8987 (tmm) REVERT: G 47 TYR cc_start: 0.7675 (m-80) cc_final: 0.7424 (m-80) REVERT: G 68 GLU cc_start: 0.5212 (pp20) cc_final: 0.4927 (pp20) REVERT: G 75 PHE cc_start: 0.7918 (p90) cc_final: 0.7412 (p90) REVERT: G 80 PHE cc_start: -0.2101 (OUTLIER) cc_final: -0.2751 (t80) REVERT: H 111 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8498 (pm20) REVERT: I 72 LYS cc_start: 0.9499 (mmmm) cc_final: 0.9247 (mmtp) REVERT: I 75 ARG cc_start: 0.9054 (ttm-80) cc_final: 0.8675 (ttm-80) REVERT: I 83 GLU cc_start: 0.8600 (tp30) cc_final: 0.8241 (tp30) REVERT: I 95 GLU cc_start: 0.8718 (pm20) cc_final: 0.8507 (pm20) REVERT: I 97 MET cc_start: 0.9407 (mmt) cc_final: 0.8904 (mmm) REVERT: K 9 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8099 (ptm160) REVERT: M 486 MET cc_start: 0.8952 (mmm) cc_final: 0.8586 (mmm) REVERT: M 663 MET cc_start: 0.7116 (mpp) cc_final: 0.6316 (mpp) REVERT: M 1063 MET cc_start: 0.8898 (mmm) cc_final: 0.8690 (tpp) outliers start: 63 outliers final: 47 residues processed: 259 average time/residue: 0.1903 time to fit residues: 82.6856 Evaluate side-chains 261 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 207 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 454 HIS Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 607 MET Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 746 PHE Chi-restraints excluded: chain B residue 771 ASN Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 1035 THR Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain B residue 1163 ILE Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 79 CYS Chi-restraints excluded: chain G residue 80 PHE Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain H residue 29 ARG Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain K residue 9 ARG Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 279 VAL Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain M residue 319 ILE Chi-restraints excluded: chain M residue 599 PHE Chi-restraints excluded: chain M residue 641 THR Chi-restraints excluded: chain M residue 738 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 439 optimal weight: 7.9990 chunk 208 optimal weight: 0.5980 chunk 203 optimal weight: 0.8980 chunk 138 optimal weight: 6.9990 chunk 109 optimal weight: 0.8980 chunk 147 optimal weight: 5.9990 chunk 320 optimal weight: 5.9990 chunk 4 optimal weight: 0.5980 chunk 116 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 280 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN ** A1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 50 HIS ** M 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.061450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.042462 restraints weight = 181629.930| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 4.15 r_work: 0.2727 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 36453 Z= 0.097 Angle : 0.534 11.675 49668 Z= 0.267 Chirality : 0.040 0.185 5767 Planarity : 0.003 0.040 6146 Dihedral : 11.946 177.403 5620 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.56 % Allowed : 10.18 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.13), residues: 4535 helix: 1.92 (0.14), residues: 1569 sheet: -0.13 (0.19), residues: 776 loop : -1.05 (0.13), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 141 TYR 0.022 0.001 TYR A 102 PHE 0.012 0.001 PHE G 36 TRP 0.009 0.001 TRP M 129 HIS 0.007 0.001 HIS A 454 Details of bonding type rmsd covalent geometry : bond 0.00206 (36420) covalent geometry : angle 0.52545 (49635) hydrogen bonds : bond 0.02917 ( 1509) hydrogen bonds : angle 4.26896 ( 4317) metal coordination : bond 0.00377 ( 33) metal coordination : angle 3.62149 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9070 Ramachandran restraints generated. 4535 Oldfield, 0 Emsley, 4535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9070 Ramachandran restraints generated. 4535 Oldfield, 0 Emsley, 4535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 213 time to evaluate : 0.982 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: A 839 MET cc_start: 0.9255 (mmm) cc_final: 0.8977 (mmm) REVERT: A 946 GLU cc_start: 0.9332 (tm-30) cc_final: 0.8962 (tm-30) REVERT: A 1134 MET cc_start: 0.9460 (mmm) cc_final: 0.9122 (mmm) REVERT: B 257 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8256 (pptt) REVERT: B 557 MET cc_start: 0.9085 (ttp) cc_final: 0.8653 (ttt) REVERT: B 756 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9039 (tt) REVERT: C 197 ASN cc_start: 0.9473 (OUTLIER) cc_final: 0.9055 (t0) REVERT: D 92 MET cc_start: 0.5623 (pmm) cc_final: 0.4714 (tpt) REVERT: D 93 MET cc_start: 0.3298 (mmt) cc_final: 0.1594 (mmt) REVERT: E 14 GLN cc_start: 0.9357 (tm-30) cc_final: 0.9075 (tm-30) REVERT: E 18 MET cc_start: 0.9562 (mmt) cc_final: 0.9205 (mmp) REVERT: E 103 GLN cc_start: 0.9206 (OUTLIER) cc_final: 0.8851 (pm20) REVERT: E 129 GLU cc_start: 0.9077 (mt-10) cc_final: 0.8841 (pt0) REVERT: E 142 GLU cc_start: 0.8559 (tm-30) cc_final: 0.7961 (tm-30) REVERT: E 144 GLN cc_start: 0.9229 (tt0) cc_final: 0.8867 (tm-30) REVERT: E 159 THR cc_start: 0.9414 (OUTLIER) cc_final: 0.9176 (p) REVERT: F 62 SER cc_start: 0.9415 (m) cc_final: 0.9018 (t) REVERT: F 83 MET cc_start: 0.9377 (mmm) cc_final: 0.9158 (tpp) REVERT: F 102 MET cc_start: 0.9212 (tmm) cc_final: 0.8960 (tmm) REVERT: G 47 TYR cc_start: 0.7435 (m-80) cc_final: 0.7199 (m-80) REVERT: G 68 GLU cc_start: 0.5232 (pp20) cc_final: 0.4968 (pp20) REVERT: G 75 PHE cc_start: 0.7974 (p90) cc_final: 0.7510 (p90) REVERT: G 80 PHE cc_start: -0.2148 (OUTLIER) cc_final: -0.2728 (t80) REVERT: H 111 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8523 (pm20) REVERT: I 72 LYS cc_start: 0.9426 (mmmm) cc_final: 0.9027 (mmtp) REVERT: I 83 GLU cc_start: 0.8671 (tp30) cc_final: 0.7715 (tp30) REVERT: I 97 MET cc_start: 0.9379 (mmt) cc_final: 0.8916 (mmm) REVERT: K 9 ARG cc_start: 0.8582 (ttp-170) cc_final: 0.7828 (ttp-110) REVERT: M 486 MET cc_start: 0.8959 (mmm) cc_final: 0.8601 (mmm) REVERT: M 663 MET cc_start: 0.7409 (mpp) cc_final: 0.6637 (mpp) REVERT: M 1063 MET cc_start: 0.8928 (mmm) cc_final: 0.8717 (tpp) outliers start: 54 outliers final: 41 residues processed: 254 average time/residue: 0.1773 time to fit residues: 75.6694 Evaluate side-chains 255 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 207 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 454 HIS Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 746 PHE Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 771 ASN Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1035 THR Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain B residue 1163 ILE Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 79 CYS Chi-restraints excluded: chain G residue 80 PHE Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain H residue 29 ARG Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain M residue 641 THR Chi-restraints excluded: chain M residue 738 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 26 optimal weight: 10.0000 chunk 233 optimal weight: 8.9990 chunk 368 optimal weight: 0.0020 chunk 116 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 244 optimal weight: 4.9990 chunk 424 optimal weight: 30.0000 chunk 149 optimal weight: 7.9990 chunk 409 optimal weight: 8.9990 overall best weight: 3.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 657 GLN ** A1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 718 GLN B 771 ASN D 138 ASN E 103 GLN I 50 HIS ** M 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.060519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.040176 restraints weight = 185557.641| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 4.21 r_work: 0.2705 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 36453 Z= 0.179 Angle : 0.567 14.125 49668 Z= 0.283 Chirality : 0.041 0.174 5767 Planarity : 0.003 0.042 6146 Dihedral : 11.970 175.650 5620 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.50 % Allowed : 10.35 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.13), residues: 4535 helix: 1.96 (0.14), residues: 1575 sheet: -0.15 (0.19), residues: 774 loop : -1.06 (0.13), residues: 2186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 141 TYR 0.021 0.001 TYR A 102 PHE 0.022 0.001 PHE J 8 TRP 0.008 0.001 TRP B 119 HIS 0.007 0.001 HIS A 454 Details of bonding type rmsd covalent geometry : bond 0.00402 (36420) covalent geometry : angle 0.55914 (49635) hydrogen bonds : bond 0.03410 ( 1509) hydrogen bonds : angle 4.34222 ( 4317) metal coordination : bond 0.00675 ( 33) metal coordination : angle 3.64564 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9070 Ramachandran restraints generated. 4535 Oldfield, 0 Emsley, 4535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9070 Ramachandran restraints generated. 4535 Oldfield, 0 Emsley, 4535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 208 time to evaluate : 1.197 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: A 423 MET cc_start: 0.9208 (mtp) cc_final: 0.9001 (mmm) REVERT: A 839 MET cc_start: 0.9283 (mmm) cc_final: 0.8895 (mmm) REVERT: A 946 GLU cc_start: 0.9295 (tm-30) cc_final: 0.8976 (tm-30) REVERT: B 557 MET cc_start: 0.9111 (ttp) cc_final: 0.8741 (ttt) REVERT: C 197 ASN cc_start: 0.9468 (OUTLIER) cc_final: 0.9068 (t0) REVERT: D 92 MET cc_start: 0.6504 (pmm) cc_final: 0.5957 (tpt) REVERT: D 93 MET cc_start: 0.2816 (mmt) cc_final: 0.1529 (mmt) REVERT: E 14 GLN cc_start: 0.9335 (tm-30) cc_final: 0.9123 (tm-30) REVERT: E 103 GLN cc_start: 0.9173 (OUTLIER) cc_final: 0.8866 (pm20) REVERT: E 129 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8844 (pt0) REVERT: E 142 GLU cc_start: 0.8518 (tm-30) cc_final: 0.7936 (tm-30) REVERT: E 144 GLN cc_start: 0.9172 (tt0) cc_final: 0.8820 (tm-30) REVERT: E 159 THR cc_start: 0.9413 (OUTLIER) cc_final: 0.9178 (p) REVERT: F 62 SER cc_start: 0.9446 (m) cc_final: 0.9064 (t) REVERT: F 83 MET cc_start: 0.9395 (mmm) cc_final: 0.9177 (tpp) REVERT: F 102 MET cc_start: 0.9247 (tmm) cc_final: 0.8974 (tmm) REVERT: G 47 TYR cc_start: 0.8289 (m-80) cc_final: 0.8015 (m-80) REVERT: G 68 GLU cc_start: 0.5133 (pp20) cc_final: 0.4882 (pp20) REVERT: G 75 PHE cc_start: 0.8044 (p90) cc_final: 0.7655 (p90) REVERT: G 80 PHE cc_start: -0.2174 (OUTLIER) cc_final: -0.2888 (t80) REVERT: G 163 LEU cc_start: 0.8075 (tt) cc_final: 0.7832 (mp) REVERT: H 16 LYS cc_start: 0.9380 (ptmm) cc_final: 0.9150 (ptmm) REVERT: H 111 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8505 (pm20) REVERT: I 75 ARG cc_start: 0.9031 (ttm-80) cc_final: 0.8764 (ttm-80) REVERT: I 97 MET cc_start: 0.9247 (mmt) cc_final: 0.8465 (mmm) REVERT: K 9 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.7932 (ttp-110) REVERT: M 325 MET cc_start: 0.7682 (ptt) cc_final: 0.7289 (ppp) REVERT: M 486 MET cc_start: 0.8939 (mmm) cc_final: 0.8591 (mmm) REVERT: M 663 MET cc_start: 0.7606 (mpp) cc_final: 0.6801 (mpp) outliers start: 52 outliers final: 45 residues processed: 247 average time/residue: 0.1742 time to fit residues: 72.7613 Evaluate side-chains 255 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 204 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 454 HIS Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 607 MET Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 746 PHE Chi-restraints excluded: chain B residue 771 ASN Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1035 THR Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain B residue 1163 ILE Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 79 CYS Chi-restraints excluded: chain G residue 80 PHE Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain H residue 29 ARG Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain K residue 9 ARG Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain M residue 599 PHE Chi-restraints excluded: chain M residue 738 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 422 optimal weight: 30.0000 chunk 350 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 238 optimal weight: 5.9990 chunk 29 optimal weight: 0.0970 chunk 301 optimal weight: 40.0000 chunk 316 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 253 optimal weight: 5.9990 chunk 222 optimal weight: 1.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 50 HIS ** M 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.060997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.041097 restraints weight = 183699.010| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 3.91 r_work: 0.2722 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 36453 Z= 0.117 Angle : 0.556 14.095 49668 Z= 0.275 Chirality : 0.040 0.173 5767 Planarity : 0.003 0.048 6146 Dihedral : 11.951 176.231 5620 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.39 % Allowed : 10.58 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.13), residues: 4535 helix: 1.94 (0.14), residues: 1575 sheet: -0.07 (0.19), residues: 765 loop : -1.04 (0.13), residues: 2195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 141 TYR 0.021 0.001 TYR A 102 PHE 0.022 0.001 PHE J 8 TRP 0.008 0.001 TRP B 280 HIS 0.007 0.001 HIS A 454 Details of bonding type rmsd covalent geometry : bond 0.00263 (36420) covalent geometry : angle 0.54857 (49635) hydrogen bonds : bond 0.03042 ( 1509) hydrogen bonds : angle 4.27572 ( 4317) metal coordination : bond 0.00465 ( 33) metal coordination : angle 3.44416 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9295.36 seconds wall clock time: 159 minutes 6.34 seconds (9546.34 seconds total)