Starting phenix.real_space_refine on Mon Sep 14 19:22:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7eu0_31305/09_2026/7eu0_31305.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eu0_31305/09_2026/7eu0_31305.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7eu0_31305/09_2026/7eu0_31305.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7eu0_31305/09_2026/7eu0_31305.cif" model { file = "/net/cci-nas-00/data/ceres_data/7eu0_31305/09_2026/7eu0_31305.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eu0_31305/09_2026/7eu0_31305.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7eu0_31305/09_2026/7eu0_31305.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eu0_31305/09_2026/7eu0_31305.map" } resolution = 3.16 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= 0.000 sd= 0.005 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 8 6.06 5 P 80 5.49 5 Mg 2 5.21 5 S 195 5.16 5 C 20549 2.51 5 N 5716 2.21 5 O 6136 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 117 residue(s): 0.22s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32686 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 7722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 7722 Classifications: {'peptide': 1060} Incomplete info: {'truncation_to_alanine': 161} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 1012} Chain breaks: 8 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 567 Unresolved non-hydrogen angles: 694 Unresolved non-hydrogen dihedrals: 457 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLU:plan': 30, 'ASN:plan1': 8, 'ASP:plan': 27, 'ARG:plan': 11, 'PHE:plan': 3, 'GLN:plan1': 6, 'TYR:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 346 Chain: "B" Number of atoms: 7861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1054, 7861 Classifications: {'peptide': 1054} Incomplete info: {'truncation_to_alanine': 151} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 1013} Chain breaks: 10 Unresolved non-hydrogen bonds: 540 Unresolved non-hydrogen angles: 656 Unresolved non-hydrogen dihedrals: 434 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASN:plan1': 6, 'GLU:plan': 42, 'ASP:plan': 26, 'GLN:plan1': 9, 'TYR:plan': 2, 'ARG:plan': 8, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 364 Chain: "C" Number of atoms: 2148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2148 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 12, 'TRANS': 278} Chain breaks: 1 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 11, 'ASP:plan': 17, 'ASN:plan1': 1, 'PHE:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 114 Chain: "E" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1458 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 6, 'TRANS': 191} Chain breaks: 1 Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 250 Unresolved non-hydrogen dihedrals: 173 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 12, 'ASP:plan': 7, 'GLN:plan1': 4, 'ARG:plan': 3, 'HIS:plan': 2, 'ASN:plan1': 3, 'TYR:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 138 Chain: "F" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 554 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 71} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 7, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "H" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 923 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 7, 'ARG:plan': 2, 'HIS:plan': 3, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 58 Chain: "I" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 819 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 4, 'TRANS': 108} Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 78 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: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 472 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 1, 'TRANS': 60} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'ASP:plan': 5, 'GLN:plan1': 2, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "K" Number of atoms: 711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 711 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 3, 'TRANS': 90} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 1, 'GLU:plan': 5, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 45 Chain: "L" Number of atoms: 293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 293 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'TRANS': 41} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 4, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "M" Number of atoms: 8055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1052, 8055 Classifications: {'peptide': 1052} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PTRANS': 40, 'TRANS': 1011} Chain breaks: 3 Unresolved non-hydrogen bonds: 411 Unresolved non-hydrogen angles: 512 Unresolved non-hydrogen dihedrals: 333 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLU:plan': 19, 'ASP:plan': 12, 'ARG:plan': 9, 'ASN:plan1': 5, 'GLN:plan1': 8, 'PHE:plan': 3, 'TYR:plan': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 262 Chain: "N" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 353 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "O" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 664 Classifications: {'RNAv2': 32} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 6, 'rna3p_pur': 8, 'rna3p_pyr': 17} Link IDs: {'rna2p': 6, 'rna3p': 25} Chain: "Q" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 561 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "R" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 82 Classifications: {'RNAv2': 4} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 1, 'rna3p_pyr': 2} Link IDs: {'rna3p': 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 329 SG CYS A 56 40.465 71.937 132.111 1.00 44.12 S ATOM 394 SG CYS A 67 41.325 74.870 129.408 1.00 36.96 S ATOM 6117 SG CYS A1031 130.908 59.988 87.955 1.00 43.17 S ATOM 6186 SG CYS A1044 129.169 61.814 90.521 1.00 21.45 S ATOM 15211 SG CYS B1108 51.869 86.840 141.400 1.00 42.54 S ATOM 15233 SG CYS B1111 55.162 83.832 141.966 1.00 49.31 S ATOM 15303 SG CYS B1133 51.477 83.351 142.231 1.00 51.21 S ATOM 15327 SG CYS B1136 51.962 85.702 144.216 1.00 50.56 S ATOM 16250 SG CYS C 90 10.597 88.609 73.299 1.00 33.61 S ATOM 16266 SG CYS C 93 7.780 85.951 73.146 1.00 48.83 S ATOM 16321 SG CYS C 102 12.517 85.276 72.448 1.00 30.81 S ATOM 21196 SG CYS I 76 106.607 96.137 69.380 1.00 21.63 S ATOM 21217 SG CYS I 79 102.526 96.334 68.713 1.00 24.95 S ATOM 21395 SG CYS I 103 103.676 93.926 71.177 1.00 11.99 S ATOM 21430 SG CYS I 108 104.608 94.243 67.606 1.00 13.46 S ATOM 20713 SG CYS I 7 120.977 30.961 93.195 1.00 36.75 S ATOM 20739 SG CYS I 10 117.375 29.064 95.516 1.00 46.88 S ATOM 20866 SG CYS I 29 119.609 32.031 96.440 1.00 42.76 S ATOM 20891 SG CYS I 32 120.947 29.279 95.969 1.00 48.26 S ATOM 21537 SG CYS J 7 40.262 78.526 59.346 1.00 12.08 S ATOM 21561 SG CYS J 10 39.038 81.661 56.305 1.00 8.91 S ATOM 21814 SG CYS J 44 42.457 80.900 56.825 1.00 10.37 S ATOM 21820 SG CYS J 45 39.715 78.793 55.634 1.00 7.44 S ATOM 22700 SG CYS L 12 28.818 43.442 85.970 1.00 25.02 S ATOM 22718 SG CYS L 15 27.839 40.756 82.462 1.00 32.97 S ATOM 22801 SG CYS L 29 27.772 40.860 87.122 1.00 32.08 S ATOM 22817 SG CYS L 32 29.316 39.178 85.014 1.00 35.00 S Time building chain proxies: 6.45, per 1000 atoms: 0.20 Number of scatterers: 32686 At special positions: 0 Unit cell: (178.08, 155.82, 162.18, 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 8 29.99 S 195 16.00 P 80 15.00 Mg 2 11.99 O 6136 8.00 N 5716 7.00 C 20549 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: 2.59 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1601 " pdb="ZN ZN A1601 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1601 " - pdb=" NE2 HIS A 70 " pdb="ZN ZN A1601 " - pdb=" SG CYS A 56 " pdb=" ZN A1603 " pdb="ZN ZN A1603 " - pdb=" NE2 HIS A 985 " pdb="ZN ZN A1603 " - pdb=" ND1 HIS A 983 " pdb="ZN ZN A1603 " - pdb=" SG CYS A1044 " pdb="ZN ZN A1603 " - pdb=" SG CYS A1031 " pdb=" ZN B2001 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1133 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1136 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1108 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1111 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 102 " 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 79 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 76 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 108 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 10 " pdb=" ZN J 200 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 32 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 15 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 29 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 12 " Number of angles added : 31 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7874 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 49 sheets defined 32.9% alpha, 17.7% beta 24 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 3.59 Creating SS restraints... Processing helix chain 'A' and resid 24 through 31 removed outlier: 3.556A pdb=" N ARG A 28 " --> pdb=" O ASN A 24 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASP A 29 " --> pdb=" O ASN A 25 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS A 30 " --> pdb=" O ASN A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.919A pdb=" N LYS A 210 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 274 removed outlier: 4.333A pdb=" N SER A 267 " --> pdb=" O THR A 263 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N SER A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG A 269 " --> pdb=" O GLU A 265 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 305 through 313 removed outlier: 3.700A pdb=" N MET A 309 " --> pdb=" O GLY A 305 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP A 311 " --> pdb=" O ARG A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 345 removed outlier: 3.542A pdb=" N LYS A 345 " --> pdb=" O GLU A 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 341 through 345' Processing helix chain 'A' and resid 416 through 418 No H-bonds generated for 'chain 'A' and resid 416 through 418' 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: 3.713A pdb=" N PHE A 444 " --> pdb=" O CYS A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 466 removed outlier: 3.804A pdb=" N GLU A 466 " --> pdb=" O GLN A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 471 removed outlier: 3.716A pdb=" N LEU A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 503 removed outlier: 3.688A pdb=" N ASN A 501 " --> pdb=" O ALA A 497 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU A 503 " --> pdb=" O LEU A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 517 Processing helix chain 'A' and resid 543 through 548 removed outlier: 3.528A pdb=" N PHE A 547 " --> pdb=" O GLY A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 596 Processing helix chain 'A' and resid 600 through 619 removed outlier: 3.621A pdb=" N TYR A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 629 removed outlier: 3.720A pdb=" N LEU A 627 " --> pdb=" O SER A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 658 removed outlier: 3.512A pdb=" N ARG A 636 " --> pdb=" O ASP A 632 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG A 648 " --> pdb=" O SER A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 669 Processing helix chain 'A' and resid 682 through 693 removed outlier: 3.746A pdb=" N PHE A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N CYS A 687 " --> pdb=" O LEU A 683 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER A 693 " --> pdb=" O GLU A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 706 removed outlier: 3.834A pdb=" N SER A 702 " --> pdb=" O GLU A 698 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA A 703 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP A 706 " --> pdb=" O SER A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 713 No H-bonds generated for 'chain 'A' and resid 711 through 713' Processing helix chain 'A' and resid 714 through 719 Processing helix chain 'A' and resid 723 through 731 Processing helix chain 'A' and resid 736 through 745 removed outlier: 3.568A pdb=" N LEU A 740 " --> pdb=" O ASN A 736 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN A 742 " --> pdb=" O GLY A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 770 removed outlier: 3.520A pdb=" N TRP A 769 " --> pdb=" O THR A 765 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN A 770 " --> pdb=" O CYS A 766 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 765 through 770' Processing helix chain 'A' and resid 805 through 818 removed outlier: 4.439A pdb=" N ASP A 818 " --> pdb=" O VAL A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 840 removed outlier: 3.646A pdb=" N SER A 832 " --> pdb=" O PRO A 828 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE A 838 " --> pdb=" O ARG A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 891 removed outlier: 3.628A pdb=" N LEU A 885 " --> pdb=" O SER A 881 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA A 888 " --> pdb=" O ALA A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 913 Processing helix chain 'A' and resid 930 through 936 removed outlier: 3.817A pdb=" N LEU A 933 " --> pdb=" O SER A 930 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER A 934 " --> pdb=" O GLU A 931 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS A 935 " --> pdb=" O TYR A 932 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS A 936 " --> pdb=" O LEU A 933 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 930 through 936' Processing helix chain 'A' and resid 938 through 951 Processing helix chain 'A' and resid 988 through 994 removed outlier: 3.861A pdb=" N LYS A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1010 removed outlier: 3.945A pdb=" N VAL A1002 " --> pdb=" O ALA A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1059 through 1066 removed outlier: 3.897A pdb=" N ILE A1063 " --> pdb=" O GLU A1059 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1073 removed outlier: 3.646A pdb=" N LEU A1071 " --> pdb=" O LEU A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1121 through 1127 Processing helix chain 'A' and resid 1146 through 1151 Processing helix chain 'A' and resid 1155 through 1172 removed outlier: 3.862A pdb=" N SER A1161 " --> pdb=" O ASP A1157 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE A1162 " --> pdb=" O ALA A1158 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A1172 " --> pdb=" O GLU A1168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1173 through 1175 No H-bonds generated for 'chain 'A' and resid 1173 through 1175' Processing helix chain 'A' and resid 1179 through 1190 removed outlier: 3.901A pdb=" N LEU A1183 " --> pdb=" O LEU A1179 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A1185 " --> pdb=" O GLU A1181 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A1186 " --> pdb=" O HIS A1182 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1212 removed outlier: 3.651A pdb=" N GLN A1207 " --> pdb=" O GLY A1203 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG A1208 " --> pdb=" O TRP A1204 " (cutoff:3.500A) Processing helix chain 'A' and resid 1215 through 1223 removed outlier: 3.585A pdb=" N GLN A1219 " --> pdb=" O ALA A1215 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER A1223 " --> pdb=" O GLN A1219 " (cutoff:3.500A) Processing helix chain 'A' and resid 1224 through 1236 removed outlier: 3.662A pdb=" N CYS A1228 " --> pdb=" O SER A1224 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS A1231 " --> pdb=" O GLN A1227 " (cutoff:3.500A) Processing helix chain 'A' and resid 1244 through 1249 Processing helix chain 'B' and resid 29 through 46 removed outlier: 3.899A pdb=" N LYS B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE B 43 " --> pdb=" O ALA B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 62 removed outlier: 3.886A pdb=" N SER B 55 " --> pdb=" O HIS B 51 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR B 56 " --> pdb=" O GLN B 52 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE B 59 " --> pdb=" O SER B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 70 removed outlier: 4.104A pdb=" N ASN B 66 " --> pdb=" O HIS B 62 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER B 70 " --> pdb=" O ASN B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 124 Processing helix chain 'B' and resid 278 through 285 removed outlier: 3.523A pdb=" N LEU B 282 " --> pdb=" O PRO B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 298 removed outlier: 3.776A pdb=" N ILE B 298 " --> pdb=" O ALA B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 322 removed outlier: 4.149A pdb=" N THR B 308 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN B 309 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER B 310 " --> pdb=" O SER B 306 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS B 322 " --> pdb=" O ALA B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 341 removed outlier: 3.957A pdb=" N THR B 333 " --> pdb=" O ASN B 329 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR B 334 " --> pdb=" O ASN B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 357 removed outlier: 3.739A pdb=" N LEU B 354 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N HIS B 355 " --> pdb=" O ASP B 351 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 384 Processing helix chain 'B' and resid 407 through 419 removed outlier: 3.880A pdb=" N VAL B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS B 414 " --> pdb=" O GLU B 410 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N HIS B 417 " --> pdb=" O VAL B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 427 removed outlier: 3.925A pdb=" N THR B 423 " --> pdb=" O ARG B 419 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG B 424 " --> pdb=" O ARG B 420 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA B 425 " --> pdb=" O LYS B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 430 No H-bonds generated for 'chain 'B' and resid 428 through 430' Processing helix chain 'B' and resid 445 through 459 removed outlier: 4.207A pdb=" N THR B 449 " --> pdb=" O ALA B 445 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY B 451 " --> pdb=" O VAL B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 490 removed outlier: 3.823A pdb=" N THR B 486 " --> pdb=" O ASN B 482 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 490 " --> pdb=" O THR B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 514 removed outlier: 3.764A pdb=" N TRP B 514 " --> pdb=" O PRO B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 553 Processing helix chain 'B' and resid 587 through 599 removed outlier: 3.867A pdb=" N ALA B 592 " --> pdb=" O GLU B 588 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU B 593 " --> pdb=" O SER B 589 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER B 596 " --> pdb=" O ALA B 592 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG B 597 " --> pdb=" O GLU B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 656 Processing helix chain 'B' and resid 692 through 697 removed outlier: 3.647A pdb=" N PHE B 695 " --> pdb=" O ASP B 692 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU B 696 " --> pdb=" O LEU B 693 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU B 697 " --> pdb=" O SER B 694 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 692 through 697' Processing helix chain 'B' and resid 711 through 721 removed outlier: 3.703A pdb=" N LEU B 716 " --> pdb=" O GLY B 712 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR B 717 " --> pdb=" O ARG B 713 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN B 718 " --> pdb=" O ARG B 714 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN B 720 " --> pdb=" O LEU B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 726 Processing helix chain 'B' and resid 755 through 761 Processing helix chain 'B' and resid 763 through 767 removed outlier: 3.875A pdb=" N LEU B 766 " --> pdb=" O LYS B 763 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N PHE B 767 " --> pdb=" O GLU B 764 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 763 through 767' Processing helix chain 'B' and resid 792 through 796 removed outlier: 3.696A pdb=" N GLU B 796 " --> pdb=" O LYS B 792 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 792 through 796' Processing helix chain 'B' and resid 929 through 933 removed outlier: 3.724A pdb=" N PHE B 933 " --> pdb=" O GLN B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 955 removed outlier: 4.139A 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 990 through 994 removed outlier: 3.769A pdb=" N THR B 994 " --> pdb=" O PRO B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 996 through 1007 removed outlier: 3.524A pdb=" N ILE B1000 " --> pdb=" O GLY B 996 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN B1003 " --> pdb=" O GLU B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1043 through 1047 removed outlier: 3.647A pdb=" N ASP B1046 " --> pdb=" O MET B1043 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1085 removed outlier: 3.625A pdb=" N ALA B1085 " --> pdb=" O ASP B1081 " (cutoff:3.500A) Processing helix chain 'B' and resid 1089 through 1095 Processing helix chain 'B' and resid 1148 through 1159 removed outlier: 3.687A pdb=" N LYS B1152 " --> pdb=" O PRO B1148 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 44 removed outlier: 3.809A pdb=" N ALA C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG C 38 " --> pdb=" O ALA C 34 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER C 43 " --> pdb=" O ARG C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 73 removed outlier: 3.829A pdb=" N ILE C 67 " --> pdb=" O ASN C 63 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA C 68 " --> pdb=" O ASP C 64 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY C 72 " --> pdb=" O ALA C 68 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU C 73 " --> pdb=" O HIS C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 215 Processing helix chain 'C' and resid 243 through 251 Processing helix chain 'C' and resid 277 through 303 removed outlier: 4.025A pdb=" N VAL C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER C 299 " --> pdb=" O ALA C 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 25 removed outlier: 3.628A pdb=" N ARG E 12 " --> pdb=" O LYS E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 42 Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 111 through 116 Processing helix chain 'E' and resid 147 through 159 removed outlier: 3.634A pdb=" N THR E 153 " --> pdb=" O GLU E 149 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR E 158 " --> pdb=" O LEU E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 178 removed outlier: 3.704A pdb=" N PHE E 178 " --> pdb=" O ILE E 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 83 removed outlier: 3.555A pdb=" N ARG F 72 " --> pdb=" O TYR F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 108 removed outlier: 3.534A pdb=" N LYS F 103 " --> pdb=" O GLU F 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 removed outlier: 3.782A pdb=" N LEU J 27 " --> pdb=" O ASP J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 52 removed outlier: 4.118A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET J 50 " --> pdb=" O ARG J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 39 through 51 removed outlier: 3.538A pdb=" N GLY K 43 " --> pdb=" O ASP K 39 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 110 removed outlier: 3.535A pdb=" N LEU K 94 " --> pdb=" O ALA K 90 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS K 96 " --> pdb=" O ASN K 92 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU K 97 " --> pdb=" O ASP K 93 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA K 110 " --> pdb=" O GLU K 106 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 34 removed outlier: 3.515A pdb=" N LEU M 26 " --> pdb=" O VAL M 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 76 removed outlier: 3.627A pdb=" N LYS M 67 " --> pdb=" O THR M 63 " (cutoff:3.500A) Processing helix chain 'M' and resid 230 through 234 Processing helix chain 'M' and resid 247 through 252 Processing helix chain 'M' and resid 283 through 288 removed outlier: 3.589A pdb=" N LEU M 287 " --> pdb=" O ASN M 283 " (cutoff:3.500A) Processing helix chain 'M' and resid 292 through 305 removed outlier: 3.818A pdb=" N GLN M 298 " --> pdb=" O GLU M 294 " (cutoff:3.500A) Processing helix chain 'M' and resid 309 through 314 removed outlier: 3.691A pdb=" N ALA M 313 " --> pdb=" O SER M 309 " (cutoff:3.500A) Processing helix chain 'M' and resid 315 through 320 removed outlier: 3.650A pdb=" N ILE M 319 " --> pdb=" O ASP M 315 " (cutoff:3.500A) Processing helix chain 'M' and resid 328 through 340 removed outlier: 3.727A pdb=" N LEU M 334 " --> pdb=" O ALA M 330 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS M 336 " --> pdb=" O VAL M 332 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU M 337 " --> pdb=" O ILE M 333 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS M 338 " --> pdb=" O LEU M 334 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN M 340 " --> pdb=" O LYS M 336 " (cutoff:3.500A) Processing helix chain 'M' and resid 346 through 355 removed outlier: 3.741A pdb=" N PHE M 350 " --> pdb=" O ASP M 346 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL M 351 " --> pdb=" O PRO M 347 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS M 352 " --> pdb=" O VAL M 348 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET M 355 " --> pdb=" O VAL M 351 " (cutoff:3.500A) Processing helix chain 'M' and resid 368 through 372 Processing helix chain 'M' and resid 372 through 377 removed outlier: 4.148A pdb=" N GLN M 376 " --> pdb=" O ARG M 372 " (cutoff:3.500A) Processing helix chain 'M' and resid 402 through 408 Processing helix chain 'M' and resid 411 through 413 No H-bonds generated for 'chain 'M' and resid 411 through 413' Processing helix chain 'M' and resid 448 through 460 removed outlier: 3.585A pdb=" N ASN M 452 " --> pdb=" O THR M 448 " (cutoff:3.500A) Processing helix chain 'M' and resid 475 through 481 removed outlier: 4.039A pdb=" N ARG M 480 " --> pdb=" O ALA M 476 " (cutoff:3.500A) Processing helix chain 'M' and resid 494 through 503 removed outlier: 3.687A pdb=" N ARG M 499 " --> pdb=" O ALA M 495 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N MET M 502 " --> pdb=" O ILE M 498 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY M 503 " --> pdb=" O ARG M 499 " (cutoff:3.500A) Processing helix chain 'M' and resid 512 through 517 Processing helix chain 'M' and resid 519 through 523 removed outlier: 3.742A pdb=" N PHE M 522 " --> pdb=" O GLY M 519 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N SER M 523 " --> pdb=" O GLN M 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 519 through 523' Processing helix chain 'M' and resid 561 through 570 removed outlier: 3.726A pdb=" N ALA M 565 " --> pdb=" O SER M 561 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS M 566 " --> pdb=" O LEU M 562 " (cutoff:3.500A) Processing helix chain 'M' and resid 632 through 640 Processing helix chain 'M' and resid 647 through 661 removed outlier: 3.917A pdb=" N ALA M 651 " --> pdb=" O ALA M 647 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN M 653 " --> pdb=" O PHE M 649 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N HIS M 656 " --> pdb=" O MET M 652 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N MET M 659 " --> pdb=" O VAL M 655 " (cutoff:3.500A) Processing helix chain 'M' and resid 662 through 664 No H-bonds generated for 'chain 'M' and resid 662 through 664' Processing helix chain 'M' and resid 668 through 673 removed outlier: 3.774A pdb=" N ASN M 672 " --> pdb=" O ASP M 668 " (cutoff:3.500A) Processing helix chain 'M' and resid 684 through 692 removed outlier: 3.907A pdb=" N MET M 689 " --> pdb=" O LEU M 685 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU M 690 " --> pdb=" O LEU M 686 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU M 691 " --> pdb=" O VAL M 687 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN M 692 " --> pdb=" O LYS M 688 " (cutoff:3.500A) Processing helix chain 'M' and resid 699 through 719 removed outlier: 4.075A pdb=" N MET M 705 " --> pdb=" O TYR M 701 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU M 717 " --> pdb=" O GLN M 713 " (cutoff:3.500A) Processing helix chain 'M' and resid 788 through 792 removed outlier: 3.604A pdb=" N ILE M 792 " --> pdb=" O PRO M 789 " (cutoff:3.500A) Processing helix chain 'M' and resid 800 through 805 Processing helix chain 'M' and resid 870 through 878 Processing helix chain 'M' and resid 884 through 899 removed outlier: 3.676A pdb=" N ILE M 888 " --> pdb=" O THR M 884 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N SER M 889 " --> pdb=" O LEU M 885 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N THR M 890 " --> pdb=" O GLY M 886 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP M 897 " --> pdb=" O LEU M 893 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP M 899 " --> pdb=" O HIS M 895 " (cutoff:3.500A) Processing helix chain 'M' and resid 905 through 919 removed outlier: 3.715A pdb=" N LEU M 911 " --> pdb=" O LYS M 907 " (cutoff:3.500A) Processing helix chain 'M' and resid 955 through 966 removed outlier: 3.547A pdb=" N LYS M 959 " --> pdb=" O SER M 955 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL M 964 " --> pdb=" O LEU M 960 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS M 965 " --> pdb=" O TYR M 961 " (cutoff:3.500A) Processing helix chain 'M' and resid 999 through 1011 Processing helix chain 'M' and resid 1011 through 1018 removed outlier: 4.104A pdb=" N ILE M1015 " --> pdb=" O THR M1011 " (cutoff:3.500A) Processing helix chain 'M' and resid 1021 through 1028 removed outlier: 3.827A pdb=" N ILE M1025 " --> pdb=" O ASN M1021 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR M1027 " --> pdb=" O GLU M1023 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY M1028 " --> pdb=" O GLU M1024 " (cutoff:3.500A) Processing helix chain 'M' and resid 1040 through 1070 removed outlier: 3.647A pdb=" N MET M1047 " --> pdb=" O ARG M1043 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR M1052 " --> pdb=" O LYS M1048 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP M1057 " --> pdb=" O LEU M1053 " (cutoff:3.500A) Processing helix chain 'M' and resid 1075 through 1089 removed outlier: 3.759A pdb=" N LEU M1079 " --> pdb=" O GLN M1075 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER M1081 " --> pdb=" O LYS M1077 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ALA M1082 " --> pdb=" O LYS M1078 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TRP M1083 " --> pdb=" O LEU M1079 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR M1087 " --> pdb=" O TRP M1083 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1238 through 1239 Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 81 removed outlier: 10.430A pdb=" N PHE A 76 " --> pdb=" O PRO A 224 " (cutoff:3.500A) removed outlier: 10.076A pdb=" N TYR A 78 " --> pdb=" O SER A 222 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N SER A 222 " --> pdb=" O TYR A 78 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 316 through 318 removed outlier: 3.601A pdb=" N SER A 318 " --> pdb=" O ILE B1073 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ILE B1073 " --> pdb=" O SER A 318 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 321 through 328 removed outlier: 3.520A pdb=" N ILE A 421 " --> pdb=" O MET A 409 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR A 324 " --> pdb=" O LEU A 453 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 350 Processing sheet with id=AA6, first strand: chain 'A' and resid 528 through 529 removed outlier: 3.802A pdb=" N ILE A 529 " --> pdb=" O GLN A 540 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 557 through 559 removed outlier: 6.623A pdb=" N VAL A 565 " --> pdb=" O LEU A 572 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 748 through 751 removed outlier: 3.587A pdb=" N GLY A 748 " --> pdb=" O ILE A 796 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 843 through 844 Processing sheet with id=AB1, first strand: chain 'A' and resid 925 through 926 removed outlier: 3.569A pdb=" N HIS A1143 " --> pdb=" O SER A 926 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 954 through 955 removed outlier: 6.787A pdb=" N LEU A 954 " --> pdb=" O VAL A1076 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1022 through 1028 removed outlier: 4.410A pdb=" N ASP A1022 " --> pdb=" O VAL A1050 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N VAL A1049 " --> pdb=" O TRP A 980 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N TRP A 980 " --> pdb=" O VAL A1049 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR A 962 " --> pdb=" O HIS A 985 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TYR I 44 " --> pdb=" O ILE A 965 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N PHE A 967 " --> pdb=" O CYS I 42 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N CYS I 42 " --> pdb=" O PHE A 967 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1082 through 1090 removed outlier: 3.549A pdb=" N ASN A1086 " --> pdb=" O LYS A1110 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 95 through 102 removed outlier: 5.586A pdb=" N PHE B 97 " --> pdb=" O GLN B 137 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLN B 137 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N GLU B 99 " --> pdb=" O ASN B 135 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY B 174 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL B 134 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N LEU B 172 " --> pdb=" O VAL B 134 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 106 through 108 Processing sheet with id=AB7, first strand: chain 'B' and resid 208 through 209 Processing sheet with id=AB8, first strand: chain 'B' and resid 398 through 401 removed outlier: 5.964A pdb=" N ALA B 219 " --> pdb=" O ARG B 494 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 229 through 231 removed outlier: 3.922A pdb=" N TRP B 235 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 579 through 584 removed outlier: 5.374A pdb=" N TRP B 580 " --> pdb=" O LEU B 576 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU B 576 " --> pdb=" O TRP B 580 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY B 582 " --> pdb=" O VAL B 574 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LYS B 573 " --> pdb=" O VAL B 618 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ILE B 620 " --> pdb=" O LYS B 573 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU B 575 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU B 617 " --> pdb=" O ASP B 612 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP B 612 " --> pdb=" O GLU B 617 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 628 through 632 Processing sheet with id=AC3, first strand: chain 'B' and resid 741 through 745 removed outlier: 3.605A pdb=" N SER B 802 " --> pdb=" O ARG B 906 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA B 898 " --> pdb=" O ALA B 810 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N PHE B 897 " --> pdb=" O LEU B 888 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LEU B 888 " --> pdb=" O PHE B 897 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ALA B 899 " --> pdb=" O VAL B 886 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL B 886 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N SER B 901 " --> pdb=" O GLN B 884 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 741 through 745 removed outlier: 3.605A pdb=" N SER B 802 " --> pdb=" O ARG B 906 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA B 898 " --> pdb=" O ALA B 810 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N PHE B 897 " --> pdb=" O LEU B 888 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LEU B 888 " --> pdb=" O PHE B 897 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ALA B 899 " --> pdb=" O VAL B 886 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL B 886 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N SER B 901 " --> pdb=" O GLN B 884 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N VAL B 886 " --> pdb=" O LYS L 39 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 914 through 916 removed outlier: 8.649A pdb=" N ILE B 944 " --> pdb=" O ASN B 771 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ILE B 773 " --> pdb=" O ILE B 944 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ILE B 946 " --> pdb=" O ILE B 773 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA B 775 " --> pdb=" O ILE B 946 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE B 788 " --> pdb=" O GLY B 925 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU B 927 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N MET B 790 " --> pdb=" O LEU B 927 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 859 through 861 Processing sheet with id=AC7, first strand: chain 'B' and resid 935 through 936 Processing sheet with id=AC8, first strand: chain 'B' and resid 1014 through 1015 Processing sheet with id=AC9, first strand: chain 'B' and resid 1105 through 1108 Processing sheet with id=AD1, first strand: chain 'C' and resid 11 through 17 removed outlier: 3.646A pdb=" N LYS C 13 " --> pdb=" O GLU C 25 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LYS C 23 " --> pdb=" O ARG C 15 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEU C 17 " --> pdb=" O TYR C 21 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N TYR C 21 " --> pdb=" O LEU C 17 " (cutoff:3.500A) removed outlier: 11.345A pdb=" N ILE C 195 " --> pdb=" O PRO C 261 " (cutoff:3.500A) removed outlier: 10.608A pdb=" N ASP C 263 " --> pdb=" O ASP C 193 " (cutoff:3.500A) removed outlier: 12.081A pdb=" N ASP C 193 " --> pdb=" O ASP C 263 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N SER C 265 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 126 through 127 removed outlier: 4.841A pdb=" N CYS C 112 " --> pdb=" O GLN C 161 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N GLN C 161 " --> pdb=" O CYS C 112 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU C 52 " --> pdb=" O ILE C 168 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ARG C 170 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ILE C 50 " --> pdb=" O ARG C 170 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLY C 172 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N VAL C 48 " --> pdb=" O GLY C 172 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL C 53 " --> pdb=" O TYR L 48 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR L 48 " --> pdb=" O VAL C 53 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 118 through 120 Processing sheet with id=AD4, first strand: chain 'C' and resid 221 through 223 Processing sheet with id=AD5, first strand: chain 'E' and resid 55 through 58 removed outlier: 3.711A pdb=" N THR E 55 " --> pdb=" O ILE E 69 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ARG E 96 " --> pdb=" O GLN E 66 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR E 68 " --> pdb=" O ARG E 96 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ALA E 97 " --> pdb=" O GLU E 123 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N PHE E 125 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU E 99 " --> pdb=" O PHE E 125 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 142 through 145 removed outlier: 3.777A pdb=" N GLU E 142 " --> pdb=" O ILE E 189 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N TYR E 198 " --> pdb=" O ARG E 190 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE E 168 " --> pdb=" O VAL E 205 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 113 through 117 Processing sheet with id=AD8, first strand: chain 'H' and resid 9 through 17 removed outlier: 3.578A pdb=" N VAL H 13 " --> pdb=" O ARG H 33 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLU H 31 " --> pdb=" O ASP H 15 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N LEU H 17 " --> pdb=" O ARG H 29 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ARG H 29 " --> pdb=" O LEU H 17 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU H 43 " --> pdb=" O VAL H 30 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP H 44 " --> pdb=" O LEU H 120 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LEU H 120 " --> pdb=" O ASP H 44 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N TYR H 113 " --> pdb=" O TYR H 98 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN H 137 " --> pdb=" O LEU H 97 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 14 through 19 removed outlier: 3.677A pdb=" N ILE I 24 " --> pdb=" O ASP I 19 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 70 through 71 Processing sheet with id=AE2, first strand: chain 'K' and resid 19 through 20 removed outlier: 3.568A pdb=" N ILE K 75 " --> pdb=" O ALA K 31 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY K 60 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE K 58 " --> pdb=" O HIS K 76 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 39 through 43 removed outlier: 3.786A pdb=" N LYS M 13 " --> pdb=" O SER M 89 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 218 through 221 removed outlier: 3.999A pdb=" N MET M 218 " --> pdb=" O VAL M 195 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS M 155 " --> pdb=" O PHE M 192 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N CYS M 153 " --> pdb=" O ARG M 194 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TRP M 146 " --> pdb=" O ARG M 133 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N TRP M 148 " --> pdb=" O GLY M 131 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N GLY M 131 " --> pdb=" O TRP M 148 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ALA M 125 " --> pdb=" O PHE M 115 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N PHE M 115 " --> pdb=" O ALA M 125 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N GLU M 127 " --> pdb=" O VAL M 113 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL M 113 " --> pdb=" O GLU M 127 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ILE M 109 " --> pdb=" O GLY M 131 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ARG M 133 " --> pdb=" O ASP M 107 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ASP M 107 " --> pdb=" O ARG M 133 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N TRP M 135 " --> pdb=" O ARG M 105 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ARG M 105 " --> pdb=" O TRP M 135 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA M 180 " --> pdb=" O SER M 168 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N SER M 168 " --> pdb=" O ALA M 180 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU M 182 " --> pdb=" O THR M 166 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR M 166 " --> pdb=" O LEU M 182 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LYS M 184 " --> pdb=" O ILE M 164 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ARG M 258 " --> pdb=" O ILE M 164 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N THR M 166 " --> pdb=" O ARG M 258 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ASP M 260 " --> pdb=" O THR M 166 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER M 168 " --> pdb=" O ASP M 260 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 218 through 221 removed outlier: 3.999A pdb=" N MET M 218 " --> pdb=" O VAL M 195 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS M 155 " --> pdb=" O PHE M 192 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N CYS M 153 " --> pdb=" O ARG M 194 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TRP M 146 " --> pdb=" O ARG M 133 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N TRP M 148 " --> pdb=" O GLY M 131 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N GLY M 131 " --> pdb=" O TRP M 148 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N PHE M 123 " --> pdb=" O VAL M 267 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 391 through 400 removed outlier: 5.321A pdb=" N LEU M 393 " --> pdb=" O TYR M 385 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N TYR M 385 " --> pdb=" O LEU M 393 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLY M 395 " --> pdb=" O ARG M 383 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG M 383 " --> pdb=" O GLY M 395 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N PHE M 415 " --> pdb=" O SER M 380 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLN M 382 " --> pdb=" O PHE M 415 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR M 419 " --> pdb=" O ALA M 384 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 435 through 438 Processing sheet with id=AE8, first strand: chain 'M' and resid 526 through 530 removed outlier: 4.298A pdb=" N LEU M 618 " --> pdb=" O THR M 528 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE M 581 " --> pdb=" O ILE M 592 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR M 585 " --> pdb=" O TYR M 588 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS M 559 " --> pdb=" O SER M 603 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER M 603 " --> pdb=" O LYS M 559 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 543 through 546 Processing sheet with id=AF1, first strand: chain 'M' and resid 627 through 628 Processing sheet with id=AF2, first strand: chain 'M' and resid 734 through 735 removed outlier: 7.460A pdb=" N CYS M 734 " --> pdb=" O PHE M 814 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'M' and resid 745 through 746 Processing sheet with id=AF4, first strand: chain 'M' and resid 749 through 751 1049 hydrogen bonds defined for protein. 2991 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 57 hydrogen bonds 106 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 6.82 Time building geometry restraints manager: 3.47 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: 9888 1.34 - 1.46: 5634 1.46 - 1.57: 17483 1.57 - 1.69: 157 1.69 - 1.81: 296 Bond restraints: 33458 Sorted by residual: bond pdb=" O3' DA Q 15 " pdb=" P DC Q 16 " ideal model delta sigma weight residual 1.607 1.691 -0.084 1.20e-02 6.94e+03 4.90e+01 bond pdb=" O3' DC Q 7 " pdb=" P DG Q 8 " ideal model delta sigma weight residual 1.607 1.664 -0.057 1.20e-02 6.94e+03 2.28e+01 bond pdb=" C LEU A 442 " pdb=" N PRO A 443 " ideal model delta sigma weight residual 1.336 1.379 -0.043 1.20e-02 6.94e+03 1.27e+01 bond pdb=" N CYS A 59 " pdb=" CA CYS A 59 " ideal model delta sigma weight residual 1.453 1.489 -0.036 1.31e-02 5.83e+03 7.55e+00 bond pdb=" N CYS C 99 " pdb=" CA CYS C 99 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.29e-02 6.01e+03 7.08e+00 ... (remaining 33453 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.68: 45705 6.68 - 13.35: 34 13.35 - 20.03: 1 20.03 - 26.71: 0 26.71 - 33.38: 2 Bond angle restraints: 45742 Sorted by residual: angle pdb=" O3' DA Q 15 " pdb=" P DC Q 16 " pdb=" O5' DC Q 16 " ideal model delta sigma weight residual 104.00 137.38 -33.38 1.90e+00 2.77e-01 3.09e+02 angle pdb=" C3' DA Q 15 " pdb=" O3' DA Q 15 " pdb=" P DC Q 16 " ideal model delta sigma weight residual 119.70 139.40 -19.70 1.20e+00 6.94e-01 2.70e+02 angle pdb=" O3' DA Q 15 " pdb=" P DC Q 16 " pdb=" OP2 DC Q 16 " ideal model delta sigma weight residual 108.00 76.97 31.03 3.00e+00 1.11e-01 1.07e+02 angle pdb=" C3' U O 17 " pdb=" O3' U O 17 " pdb=" P U O 18 " ideal model delta sigma weight residual 119.70 126.11 -6.41 1.20e+00 6.94e-01 2.86e+01 angle pdb=" C ASP C 176 " pdb=" N HIS C 177 " pdb=" CA HIS C 177 " ideal model delta sigma weight residual 121.54 131.06 -9.52 1.91e+00 2.74e-01 2.48e+01 ... (remaining 45737 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.31: 19361 35.31 - 70.62: 498 70.62 - 105.93: 31 105.93 - 141.23: 0 141.23 - 176.54: 2 Dihedral angle restraints: 19892 sinusoidal: 7763 harmonic: 12129 Sorted by residual: dihedral pdb=" C4' G O 33 " pdb=" C3' G O 33 " pdb=" C2' G O 33 " pdb=" C1' G O 33 " ideal model delta sinusoidal sigma weight residual 36.34 -36.07 72.42 1 3.10e+00 1.04e-01 6.97e+02 dihedral pdb=" C4' U O 20 " pdb=" C3' U O 20 " pdb=" C2' U O 20 " pdb=" C1' U O 20 " ideal model delta sinusoidal sigma weight residual 36.35 -35.59 71.94 1 3.10e+00 1.04e-01 6.89e+02 dihedral pdb=" C4' U O 12 " pdb=" C3' U O 12 " pdb=" C2' U O 12 " pdb=" C1' U O 12 " ideal model delta sinusoidal sigma weight residual 36.35 -35.21 71.56 1 3.10e+00 1.04e-01 6.83e+02 ... (remaining 19889 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 4802 0.079 - 0.157: 490 0.157 - 0.236: 26 0.236 - 0.315: 36 0.315 - 0.393: 2 Chirality restraints: 5356 Sorted by residual: chirality pdb=" P U O 18 " pdb=" OP1 U O 18 " pdb=" OP2 U O 18 " pdb=" O5' U O 18 " both_signs ideal model delta sigma weight residual True 2.17 -2.57 -0.39 2.00e-01 2.50e+01 3.87e+00 chirality pdb=" P U O 19 " pdb=" OP1 U O 19 " pdb=" OP2 U O 19 " pdb=" O5' U O 19 " both_signs ideal model delta sigma weight residual True 2.17 -2.54 -0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" C3' U O 17 " pdb=" C4' U O 17 " pdb=" O3' U O 17 " pdb=" C2' U O 17 " both_signs ideal model delta sigma weight residual False -2.50 -2.20 -0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 5353 not shown) Planarity restraints: 5571 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS M 822 " 0.046 5.00e-02 4.00e+02 6.92e-02 7.65e+00 pdb=" N PRO M 823 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO M 823 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO M 823 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR M 387 " 0.043 5.00e-02 4.00e+02 6.44e-02 6.63e+00 pdb=" N PRO M 388 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO M 388 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO M 388 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 525 " -0.035 5.00e-02 4.00e+02 5.25e-02 4.41e+00 pdb=" N PRO A 526 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 526 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 526 " -0.029 5.00e-02 4.00e+02 ... (remaining 5568 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 51 2.42 - 3.04: 16194 3.04 - 3.66: 46902 3.66 - 4.28: 70087 4.28 - 4.90: 117925 Nonbonded interactions: 251159 Sorted by model distance: nonbonded pdb=" O4 DT N 31 " pdb=" N1 DA Q 17 " model vdw 1.797 2.496 nonbonded pdb=" N2 DG N 32 " pdb=" O2 DC Q 16 " model vdw 2.051 2.496 nonbonded pdb=" OD1 ASP M 830 " pdb="MG MG M2001 " model vdw 2.073 2.170 nonbonded pdb=" OD1 ASP M 832 " pdb="MG MG M2001 " model vdw 2.080 2.170 nonbonded pdb=" OD2 ASP M 834 " pdb="MG MG M2001 " model vdw 2.101 2.170 ... (remaining 251154 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: 1.340 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: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 33.880 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.070 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 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 : 0.006 0.639 33488 Z= 0.269 Angle : 0.976 62.857 45773 Z= 0.460 Chirality : 0.052 0.393 5356 Planarity : 0.005 0.069 5571 Dihedral : 15.022 176.543 12018 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.20 % Allowed : 4.98 % Favored : 94.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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 are not related in a simple way. whole: -4.58 (0.10), residues: 4096 helix: -3.71 (0.08), residues: 1291 sheet: -2.10 (0.18), residues: 670 loop : -2.93 (0.10), residues: 2135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 600 TYR 0.012 0.001 TYR M 403 PHE 0.015 0.001 PHE M 581 TRP 0.009 0.001 TRP M 840 HIS 0.012 0.001 HIS M 709 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.20 (33458) covalent geometry : angle 0.75778 / 0.45 (45742) hydrogen bonds : bond 0.23389 / 15.69 ( 1071) hydrogen bonds : angle 8.60673 / 5.99 ( 3097) metal coordination : bond 0.17547 / 10.69 ( 30) metal coordination : angle 23.62299 / 15.98 ( 31) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 3697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 633 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 GLU cc_start: 0.6554 (mm-30) cc_final: 0.5989 (mm-30) REVERT: A 307 ARG cc_start: 0.7863 (tpm170) cc_final: 0.7622 (mmp80) REVERT: A 415 ILE cc_start: 0.7299 (tt) cc_final: 0.7033 (tt) REVERT: A 451 ASP cc_start: 0.6998 (m-30) cc_final: 0.6540 (m-30) REVERT: A 836 MET cc_start: 0.8563 (tpp) cc_final: 0.8354 (tpp) REVERT: A 966 ILE cc_start: 0.8278 (mm) cc_final: 0.7947 (mm) REVERT: B 396 ARG cc_start: 0.8068 (ttp80) cc_final: 0.7779 (ttp80) REVERT: B 465 PHE cc_start: 0.7237 (m-80) cc_final: 0.6762 (m-80) REVERT: C 65 GLU cc_start: 0.7747 (mp0) cc_final: 0.7464 (mp0) REVERT: F 107 GLN cc_start: 0.7483 (mt0) cc_final: 0.7140 (mt0) REVERT: F 117 TYR cc_start: 0.8112 (m-80) cc_final: 0.7902 (m-80) REVERT: K 37 ARG cc_start: 0.8125 (mmt-90) cc_final: 0.7229 (mtm180) REVERT: M 466 PRO cc_start: 0.5586 (Cg_endo) cc_final: 0.5256 (Cg_exo) REVERT: M 605 ARG cc_start: 0.4397 (mmt90) cc_final: 0.4174 (mmm160) REVERT: M 627 MET cc_start: 0.4711 (OUTLIER) cc_final: 0.4220 (mmm) REVERT: M 659 MET cc_start: 0.3171 (ptm) cc_final: 0.2725 (ptm) REVERT: M 735 MET cc_start: 0.4823 (tmm) cc_final: 0.4497 (ttp) REVERT: M 1039 ARG cc_start: 0.4659 (mtt180) cc_final: 0.3166 (tmt-80) outliers start: 6 outliers final: 3 residues processed: 638 average time/residue: 0.2257 time to fit residues: 221.5327 Evaluate side-chains 438 residues out of total 3697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 434 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain M residue 627 MET Chi-restraints excluded: chain M residue 722 ARG Chi-restraints excluded: chain M residue 835 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.0070 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.0170 chunk 401 optimal weight: 10.0000 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 20.0000 overall best weight: 1.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 320 HIS A 459 GLN A 462 GLN A 491 GLN A 634 GLN A 923 GLN A1149 GLN A1166 ASN B 220 GLN B 222 GLN B 577 ASN B 600 GLN B 688 HIS B 711 HIS ** B 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 768 ASN ** B 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 HIS B 877 HIS B 949 HIS B 955 GLN ** B1052 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1091 ASN C 284 ASN ** E 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 GLN L 17 GLN ** L 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 47 GLN M 16 ASN M 84 HIS ** M 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 304 HIS M 339 GLN M 407 ASN M 431 ASN M 478 GLN M 582 GLN M 788 HIS M 824 ASN M 873 HIS M1092 HIS Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.178978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.141251 restraints weight = 39962.822| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.76 r_work: 0.3292 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 33488 Z= 0.160 Angle : 0.716 23.790 45773 Z= 0.319 Chirality : 0.055 1.111 5356 Planarity : 0.004 0.051 5571 Dihedral : 12.650 163.164 5385 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.11 % Allowed : 11.04 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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 are not related in a simple way. whole: -3.42 (0.11), residues: 4096 helix: -2.10 (0.12), residues: 1292 sheet: -1.79 (0.18), residues: 703 loop : -2.55 (0.11), residues: 2101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A1148 TYR 0.027 0.001 TYR M1085 PHE 0.025 0.001 PHE A1222 TRP 0.018 0.001 TRP M 501 HIS 0.011 0.001 HIS A 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (33458) covalent geometry : angle 0.65966 / 0.32 (45742) hydrogen bonds : bond 0.05336 / 3.49 ( 1071) hydrogen bonds : angle 5.30861 / 3.70 ( 3097) metal coordination : bond 0.01215 / 0.89 ( 30) metal coordination : angle 10.72992 / 7.35 ( 31) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 3697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 442 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 PHE cc_start: 0.7319 (t80) cc_final: 0.7063 (t80) REVERT: B 396 ARG cc_start: 0.8330 (ttp80) cc_final: 0.8071 (ttp80) REVERT: B 465 PHE cc_start: 0.7646 (m-80) cc_final: 0.7063 (m-80) REVERT: B 559 GLU cc_start: 0.7688 (tp30) cc_final: 0.7193 (tt0) REVERT: F 107 GLN cc_start: 0.8128 (mt0) cc_final: 0.7880 (mt0) REVERT: H 87 ASP cc_start: 0.7556 (p0) cc_final: 0.7350 (p0) REVERT: K 37 ARG cc_start: 0.8388 (mmt-90) cc_final: 0.7408 (mtm180) REVERT: K 74 ARG cc_start: 0.8284 (ttm-80) cc_final: 0.7475 (ttm170) REVERT: M 466 PRO cc_start: 0.5494 (Cg_endo) cc_final: 0.5253 (Cg_exo) REVERT: M 605 ARG cc_start: 0.4990 (mmt90) cc_final: 0.4131 (mmm160) REVERT: M 618 LEU cc_start: 0.7026 (tp) cc_final: 0.6737 (tp) REVERT: M 817 LYS cc_start: 0.5527 (mppt) cc_final: 0.4470 (pttm) REVERT: M 1039 ARG cc_start: 0.4900 (mtt180) cc_final: 0.3152 (tmm-80) outliers start: 34 outliers final: 27 residues processed: 461 average time/residue: 0.2103 time to fit residues: 153.4859 Evaluate side-chains 418 residues out of total 3697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 391 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 742 SER Chi-restraints excluded: chain B residue 1164 THR Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 116 GLN Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain E residue 112 CYS Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain M residue 144 GLU Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain M residue 287 LEU Chi-restraints excluded: chain M residue 387 THR Chi-restraints excluded: chain M residue 592 ILE Chi-restraints excluded: chain M residue 627 MET Chi-restraints excluded: chain M residue 725 VAL Chi-restraints excluded: chain M residue 835 GLN Chi-restraints excluded: chain M residue 866 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 309 optimal weight: 0.7980 chunk 133 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 chunk 287 optimal weight: 5.9990 chunk 156 optimal weight: 6.9990 chunk 375 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 311 optimal weight: 6.9990 chunk 274 optimal weight: 8.9990 chunk 348 optimal weight: 5.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 658 GLN A 923 GLN A1182 HIS ** A1219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 HIS B 495 GLN B 600 GLN B 718 GLN B 733 ASN B 749 GLN B 771 ASN E 14 GLN ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 HIS ** L 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 300 ASN M 340 GLN M 411 HIS M 582 GLN M 892 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.168643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 105)---------------| | r_work = 0.3418 r_free = 0.3418 target = 0.127921 restraints weight = 39594.267| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.06 r_work: 0.3089 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 33488 Z= 0.305 Angle : 0.805 20.675 45773 Z= 0.386 Chirality : 0.054 0.434 5356 Planarity : 0.006 0.072 5571 Dihedral : 12.846 166.512 5381 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.73 % Allowed : 14.42 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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 are not related in a simple way. whole: -2.91 (0.12), residues: 4096 helix: -1.40 (0.13), residues: 1336 sheet: -1.79 (0.18), residues: 690 loop : -2.34 (0.12), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 801 TYR 0.034 0.003 TYR M 879 PHE 0.027 0.002 PHE B 116 TRP 0.029 0.003 TRP M 501 HIS 0.012 0.002 HIS A 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00730 / 0.30 (33458) covalent geometry : angle 0.76360 / 0.38 (45742) hydrogen bonds : bond 0.05567 / 3.71 ( 1071) hydrogen bonds : angle 5.07046 / 3.53 ( 3097) metal coordination : bond 0.01262 / 0.94 ( 30) metal coordination : angle 9.85860 / 6.86 ( 31) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 388 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 ARG cc_start: 0.7167 (ttm-80) cc_final: 0.6945 (ttm-80) REVERT: A 462 GLN cc_start: 0.8974 (tt0) cc_final: 0.8541 (mp10) REVERT: A 1261 GLN cc_start: 0.9147 (OUTLIER) cc_final: 0.7356 (pm20) REVERT: B 396 ARG cc_start: 0.8350 (ttp80) cc_final: 0.8127 (ttp80) REVERT: B 465 PHE cc_start: 0.7938 (m-80) cc_final: 0.7309 (m-80) REVERT: B 559 GLU cc_start: 0.8163 (tp30) cc_final: 0.7624 (tt0) REVERT: B 597 ARG cc_start: 0.8679 (mmm-85) cc_final: 0.8456 (mtp180) REVERT: B 633 VAL cc_start: 0.9145 (OUTLIER) cc_final: 0.8900 (p) REVERT: B 1105 MET cc_start: 0.8615 (ttp) cc_final: 0.8386 (ttm) REVERT: C 55 ILE cc_start: 0.8781 (pt) cc_final: 0.8390 (mt) REVERT: F 73 ILE cc_start: 0.8632 (mt) cc_final: 0.8414 (mt) REVERT: F 95 THR cc_start: 0.7473 (t) cc_final: 0.7147 (p) REVERT: J 48 MET cc_start: 0.9015 (mmm) cc_final: 0.8611 (mmm) REVERT: K 37 ARG cc_start: 0.8544 (mmt-90) cc_final: 0.7412 (mtm180) REVERT: K 74 ARG cc_start: 0.8648 (ttm-80) cc_final: 0.8062 (ttp-170) REVERT: L 17 GLN cc_start: 0.7369 (tt0) cc_final: 0.6669 (mm110) REVERT: M 316 MET cc_start: 0.7044 (mmm) cc_final: 0.6829 (mmm) REVERT: M 466 PRO cc_start: 0.5630 (Cg_endo) cc_final: 0.5385 (Cg_exo) REVERT: M 627 MET cc_start: 0.5688 (OUTLIER) cc_final: 0.5265 (ptp) REVERT: M 738 MET cc_start: 0.5910 (tpp) cc_final: 0.5665 (tpp) REVERT: M 817 LYS cc_start: 0.5919 (mppt) cc_final: 0.4768 (pttm) REVERT: M 863 MET cc_start: 0.8634 (mmm) cc_final: 0.8291 (mmt) REVERT: M 907 LYS cc_start: 0.8156 (mttt) cc_final: 0.7472 (mmtt) outliers start: 84 outliers final: 50 residues processed: 447 average time/residue: 0.1983 time to fit residues: 142.0170 Evaluate side-chains 414 residues out of total 3697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 361 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 879 SER Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1261 GLN Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 742 SER Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 812 VAL Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 1164 THR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain E residue 112 CYS Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 75 ARG Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain M residue 8 ASN Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 287 LEU Chi-restraints excluded: chain M residue 387 THR Chi-restraints excluded: chain M residue 435 VAL Chi-restraints excluded: chain M residue 592 ILE Chi-restraints excluded: chain M residue 627 MET Chi-restraints excluded: chain M residue 648 MET Chi-restraints excluded: chain M residue 725 VAL Chi-restraints excluded: chain M residue 780 VAL Chi-restraints excluded: chain M residue 835 GLN Chi-restraints excluded: chain M residue 866 ASP Chi-restraints excluded: chain M residue 1015 ILE Chi-restraints excluded: chain M residue 1058 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 16 optimal weight: 3.9990 chunk 333 optimal weight: 0.9990 chunk 156 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 391 optimal weight: 20.0000 chunk 302 optimal weight: 0.6980 chunk 330 optimal weight: 9.9990 chunk 278 optimal weight: 6.9990 chunk 172 optimal weight: 7.9990 chunk 362 optimal weight: 0.0980 chunk 163 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 562 ASN A 923 GLN ** A1219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 600 GLN I 50 HIS ** L 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 582 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.173270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.134032 restraints weight = 39379.900| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.82 r_work: 0.3173 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 33488 Z= 0.109 Angle : 0.598 18.666 45773 Z= 0.280 Chirality : 0.045 0.349 5356 Planarity : 0.004 0.049 5571 Dihedral : 12.602 166.073 5381 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.73 % Allowed : 16.50 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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 are not related in a simple way. whole: -2.28 (0.12), residues: 4096 helix: -0.65 (0.15), residues: 1303 sheet: -1.49 (0.18), residues: 692 loop : -2.09 (0.12), residues: 2101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG M 605 TYR 0.016 0.001 TYR M1016 PHE 0.020 0.001 PHE A 223 TRP 0.025 0.001 TRP M 501 HIS 0.010 0.001 HIS A 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (33458) covalent geometry : angle 0.55564 / 0.28 (45742) hydrogen bonds : bond 0.03858 / 2.53 ( 1071) hydrogen bonds : angle 4.58148 / 3.20 ( 3097) metal coordination : bond 0.00762 / 0.61 ( 30) metal coordination : angle 8.46148 / 5.97 ( 31) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 3697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 391 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1261 GLN cc_start: 0.9018 (OUTLIER) cc_final: 0.7300 (pm20) REVERT: B 396 ARG cc_start: 0.8276 (ttp80) cc_final: 0.8012 (ttp80) REVERT: B 465 PHE cc_start: 0.8033 (m-80) cc_final: 0.7273 (m-80) REVERT: B 559 GLU cc_start: 0.8147 (tp30) cc_final: 0.7684 (tt0) REVERT: B 954 ARG cc_start: 0.8644 (mtt90) cc_final: 0.8303 (mmm-85) REVERT: E 8 LYS cc_start: 0.8206 (ttpp) cc_final: 0.7985 (mtpt) REVERT: F 73 ILE cc_start: 0.8640 (mt) cc_final: 0.8398 (mt) REVERT: F 95 THR cc_start: 0.7486 (t) cc_final: 0.7162 (p) REVERT: K 37 ARG cc_start: 0.8522 (mmt-90) cc_final: 0.7424 (mtm180) REVERT: K 74 ARG cc_start: 0.8594 (ttm-80) cc_final: 0.7834 (ttm170) REVERT: K 96 LYS cc_start: 0.8890 (mtmm) cc_final: 0.8546 (mtpt) REVERT: L 36 ILE cc_start: 0.9378 (mt) cc_final: 0.9111 (mt) REVERT: M 316 MET cc_start: 0.7060 (mmm) cc_final: 0.6815 (mmm) REVERT: M 466 PRO cc_start: 0.5571 (Cg_endo) cc_final: 0.5305 (Cg_exo) REVERT: M 623 TRP cc_start: 0.5480 (p90) cc_final: 0.5152 (p90) REVERT: M 627 MET cc_start: 0.5707 (OUTLIER) cc_final: 0.5399 (ptp) REVERT: M 817 LYS cc_start: 0.5848 (mppt) cc_final: 0.4694 (pttm) REVERT: M 863 MET cc_start: 0.8510 (mmm) cc_final: 0.8153 (mmt) REVERT: M 878 ASP cc_start: 0.8352 (m-30) cc_final: 0.7933 (t0) REVERT: M 907 LYS cc_start: 0.8078 (mttt) cc_final: 0.7368 (mmtt) outliers start: 53 outliers final: 37 residues processed: 426 average time/residue: 0.2181 time to fit residues: 148.9071 Evaluate side-chains 407 residues out of total 3697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 368 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1261 GLN Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 742 SER Chi-restraints excluded: chain C residue 116 GLN Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 107 ASP Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 235 THR Chi-restraints excluded: chain M residue 287 LEU Chi-restraints excluded: chain M residue 464 VAL Chi-restraints excluded: chain M residue 541 ASP Chi-restraints excluded: chain M residue 627 MET Chi-restraints excluded: chain M residue 725 VAL Chi-restraints excluded: chain M residue 835 GLN Chi-restraints excluded: chain M residue 1010 LEU Chi-restraints excluded: chain M residue 1058 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 20 optimal weight: 0.8980 chunk 187 optimal weight: 3.9990 chunk 328 optimal weight: 3.9990 chunk 280 optimal weight: 10.0000 chunk 135 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 400 optimal weight: 0.7980 chunk 371 optimal weight: 7.9990 chunk 10 optimal weight: 0.0770 chunk 341 optimal weight: 20.0000 chunk 291 optimal weight: 2.9990 overall best weight: 1.0940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 600 GLN B1003 GLN H 42 HIS M 892 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.174394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.134251 restraints weight = 39320.519| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.21 r_work: 0.3160 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 33488 Z= 0.121 Angle : 0.580 16.410 45773 Z= 0.273 Chirality : 0.045 0.357 5356 Planarity : 0.003 0.049 5571 Dihedral : 12.520 166.490 5381 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.21 % Allowed : 16.70 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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 are not related in a simple way. whole: -1.97 (0.13), residues: 4096 helix: -0.33 (0.15), residues: 1307 sheet: -1.40 (0.19), residues: 713 loop : -1.92 (0.12), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 22 TYR 0.012 0.001 TYR C 190 PHE 0.013 0.001 PHE M 311 TRP 0.023 0.001 TRP M 501 HIS 0.012 0.001 HIS A 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (33458) covalent geometry : angle 0.54544 / 0.27 (45742) hydrogen bonds : bond 0.03820 / 2.49 ( 1071) hydrogen bonds : angle 4.39697 / 3.08 ( 3097) metal coordination : bond 0.00830 / 0.65 ( 30) metal coordination : angle 7.61540 / 5.33 ( 31) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 374 time to evaluate : 1.271 Fit side-chains revert: symmetry clash REVERT: A 602 ASP cc_start: 0.7660 (p0) cc_final: 0.7363 (t0) REVERT: A 1238 ARG cc_start: 0.7899 (ttm170) cc_final: 0.7680 (ttm170) REVERT: A 1261 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.7230 (pm20) REVERT: B 396 ARG cc_start: 0.8313 (ttp80) cc_final: 0.8062 (ttp80) REVERT: B 465 PHE cc_start: 0.7964 (m-80) cc_final: 0.7199 (m-80) REVERT: B 559 GLU cc_start: 0.8174 (tp30) cc_final: 0.7718 (tt0) REVERT: B 954 ARG cc_start: 0.8707 (mtt90) cc_final: 0.8360 (mmm-85) REVERT: B 1134 ARG cc_start: 0.7555 (mtt90) cc_final: 0.7344 (mtt90) REVERT: E 8 LYS cc_start: 0.8244 (ttpp) cc_final: 0.8021 (mtpt) REVERT: F 73 ILE cc_start: 0.8603 (mt) cc_final: 0.8389 (mt) REVERT: F 95 THR cc_start: 0.7237 (t) cc_final: 0.6836 (p) REVERT: J 48 MET cc_start: 0.8797 (mmm) cc_final: 0.8473 (mmm) REVERT: K 37 ARG cc_start: 0.8563 (mmt-90) cc_final: 0.7439 (mtm180) REVERT: K 96 LYS cc_start: 0.8856 (mtmm) cc_final: 0.8531 (mtpt) REVERT: M 316 MET cc_start: 0.6974 (mmm) cc_final: 0.6651 (mmm) REVERT: M 466 PRO cc_start: 0.5598 (Cg_endo) cc_final: 0.5364 (Cg_exo) REVERT: M 627 MET cc_start: 0.5683 (OUTLIER) cc_final: 0.5361 (ptp) REVERT: M 817 LYS cc_start: 0.5805 (mppt) cc_final: 0.4700 (pttm) REVERT: M 863 MET cc_start: 0.8504 (mmm) cc_final: 0.8157 (mmt) REVERT: M 878 ASP cc_start: 0.8339 (m-30) cc_final: 0.7907 (t0) REVERT: M 907 LYS cc_start: 0.8106 (mttt) cc_final: 0.7259 (mmtt) outliers start: 68 outliers final: 47 residues processed: 424 average time/residue: 0.2107 time to fit residues: 144.5740 Evaluate side-chains 409 residues out of total 3697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 360 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1261 GLN Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 742 SER Chi-restraints excluded: chain B residue 796 GLU Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain C residue 116 GLN Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain I residue 75 ARG Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain M residue 8 ASN Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 107 ASP Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 287 LEU Chi-restraints excluded: chain M residue 464 VAL Chi-restraints excluded: chain M residue 525 SER Chi-restraints excluded: chain M residue 627 MET Chi-restraints excluded: chain M residue 725 VAL Chi-restraints excluded: chain M residue 835 GLN Chi-restraints excluded: chain M residue 1010 LEU Chi-restraints excluded: chain M residue 1057 ASP Chi-restraints excluded: chain M residue 1058 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 208 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 254 optimal weight: 4.9990 chunk 190 optimal weight: 0.7980 chunk 143 optimal weight: 20.0000 chunk 3 optimal weight: 0.7980 chunk 308 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 313 optimal weight: 1.9990 chunk 242 optimal weight: 10.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 HIS B1042 HIS ** M 582 GLN ** 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 = 0.3943 r_free = 0.3943 target = 0.173467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.134106 restraints weight = 39238.471| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.80 r_work: 0.3142 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 33488 Z= 0.140 Angle : 0.592 16.328 45773 Z= 0.279 Chirality : 0.046 0.362 5356 Planarity : 0.004 0.069 5571 Dihedral : 12.485 171.494 5381 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.34 % Allowed : 17.15 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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 are not related in a simple way. whole: -1.78 (0.13), residues: 4096 helix: -0.16 (0.15), residues: 1310 sheet: -1.25 (0.19), residues: 698 loop : -1.82 (0.13), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 22 TYR 0.013 0.001 TYR C 190 PHE 0.013 0.001 PHE M 311 TRP 0.024 0.001 TRP M 501 HIS 0.012 0.001 HIS A 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (33458) covalent geometry : angle 0.55822 / 0.28 (45742) hydrogen bonds : bond 0.03893 / 2.55 ( 1071) hydrogen bonds : angle 4.31697 / 3.03 ( 3097) metal coordination : bond 0.00858 / 0.66 ( 30) metal coordination : angle 7.64332 / 5.38 ( 31) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 375 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 602 ASP cc_start: 0.7689 (p0) cc_final: 0.7438 (t0) REVERT: A 1260 ASP cc_start: 0.7998 (p0) cc_final: 0.7634 (p0) REVERT: A 1261 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.7386 (pm20) REVERT: B 465 PHE cc_start: 0.7990 (m-80) cc_final: 0.7219 (m-80) REVERT: B 559 GLU cc_start: 0.8201 (tp30) cc_final: 0.7766 (tt0) REVERT: C 33 MET cc_start: 0.8297 (tpp) cc_final: 0.7988 (mmt) REVERT: C 55 ILE cc_start: 0.8694 (pt) cc_final: 0.8477 (mt) REVERT: E 8 LYS cc_start: 0.8217 (ttpp) cc_final: 0.7964 (mtpt) REVERT: F 73 ILE cc_start: 0.8688 (mt) cc_final: 0.8453 (mt) REVERT: F 95 THR cc_start: 0.7294 (t) cc_final: 0.6904 (p) REVERT: H 40 PHE cc_start: 0.8795 (t80) cc_final: 0.8209 (t80) REVERT: K 37 ARG cc_start: 0.8572 (mmt-90) cc_final: 0.7450 (mtm180) REVERT: K 96 LYS cc_start: 0.8925 (mtmm) cc_final: 0.8575 (mtpt) REVERT: L 17 GLN cc_start: 0.7235 (tt0) cc_final: 0.6647 (mm110) REVERT: M 466 PRO cc_start: 0.5600 (Cg_endo) cc_final: 0.5365 (Cg_exo) REVERT: M 608 MET cc_start: 0.7062 (mtt) cc_final: 0.6658 (mtt) REVERT: M 627 MET cc_start: 0.5877 (OUTLIER) cc_final: 0.5617 (ptp) REVERT: M 817 LYS cc_start: 0.6000 (mppt) cc_final: 0.4854 (pttm) REVERT: M 863 MET cc_start: 0.8492 (mmm) cc_final: 0.8178 (mmt) REVERT: M 878 ASP cc_start: 0.8365 (m-30) cc_final: 0.7946 (t0) REVERT: M 907 LYS cc_start: 0.7957 (mttt) cc_final: 0.7333 (mmtt) outliers start: 72 outliers final: 54 residues processed: 429 average time/residue: 0.2088 time to fit residues: 145.7029 Evaluate side-chains 419 residues out of total 3697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 363 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 693 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 879 SER Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1261 GLN Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 742 SER Chi-restraints excluded: chain B residue 796 GLU Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 1164 THR Chi-restraints excluded: chain C residue 116 GLN Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain I residue 75 ARG Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 107 ASP Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 235 THR Chi-restraints excluded: chain M residue 287 LEU Chi-restraints excluded: chain M residue 464 VAL Chi-restraints excluded: chain M residue 525 SER Chi-restraints excluded: chain M residue 541 ASP Chi-restraints excluded: chain M residue 627 MET Chi-restraints excluded: chain M residue 725 VAL Chi-restraints excluded: chain M residue 780 VAL Chi-restraints excluded: chain M residue 835 GLN Chi-restraints excluded: chain M residue 1010 LEU Chi-restraints excluded: chain M residue 1058 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 52 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 143 optimal weight: 20.0000 chunk 162 optimal weight: 2.9990 chunk 345 optimal weight: 5.9990 chunk 415 optimal weight: 9.9990 chunk 361 optimal weight: 9.9990 chunk 85 optimal weight: 30.0000 chunk 95 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 323 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 923 GLN M 892 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.169753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.129814 restraints weight = 39515.529| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.90 r_work: 0.3092 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 33488 Z= 0.253 Angle : 0.708 16.091 45773 Z= 0.338 Chirality : 0.050 0.386 5356 Planarity : 0.005 0.080 5571 Dihedral : 12.668 176.827 5381 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.77 % Allowed : 17.02 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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 are not related in a simple way. whole: -1.97 (0.13), residues: 4096 helix: -0.38 (0.15), residues: 1319 sheet: -1.36 (0.18), residues: 724 loop : -1.90 (0.13), residues: 2053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 70 TYR 0.018 0.002 TYR C 190 PHE 0.018 0.002 PHE C 66 TRP 0.028 0.002 TRP M 501 HIS 0.012 0.001 HIS A 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00616 / 0.25 (33458) covalent geometry : angle 0.67281 / 0.34 (45742) hydrogen bonds : bond 0.04646 / 3.08 ( 1071) hydrogen bonds : angle 4.59968 / 3.21 ( 3097) metal coordination : bond 0.01143 / 0.83 ( 30) metal coordination : angle 8.51746 / 5.91 ( 31) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 3697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 363 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 462 GLN cc_start: 0.9010 (tt0) cc_final: 0.8573 (mp10) REVERT: A 602 ASP cc_start: 0.7825 (p0) cc_final: 0.7419 (t0) REVERT: A 1261 GLN cc_start: 0.9134 (OUTLIER) cc_final: 0.7417 (pm20) REVERT: B 465 PHE cc_start: 0.8032 (m-80) cc_final: 0.7341 (m-80) REVERT: B 559 GLU cc_start: 0.8204 (tp30) cc_final: 0.7737 (tt0) REVERT: B 633 VAL cc_start: 0.9077 (OUTLIER) cc_final: 0.8820 (p) REVERT: C 33 MET cc_start: 0.8397 (tpp) cc_final: 0.8062 (mmt) REVERT: C 55 ILE cc_start: 0.8753 (pt) cc_final: 0.8378 (mt) REVERT: E 26 TYR cc_start: 0.8670 (OUTLIER) cc_final: 0.8224 (m-10) REVERT: F 95 THR cc_start: 0.7456 (t) cc_final: 0.7084 (p) REVERT: J 48 MET cc_start: 0.8958 (mmm) cc_final: 0.8692 (mmm) REVERT: K 37 ARG cc_start: 0.8548 (mmt-90) cc_final: 0.7419 (mtm180) REVERT: K 96 LYS cc_start: 0.8943 (mtmm) cc_final: 0.8598 (mtpt) REVERT: L 17 GLN cc_start: 0.7352 (tt0) cc_final: 0.6775 (mm110) REVERT: M 264 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.7087 (pt) REVERT: M 373 LEU cc_start: 0.5121 (OUTLIER) cc_final: 0.4697 (tt) REVERT: M 466 PRO cc_start: 0.5849 (Cg_endo) cc_final: 0.5618 (Cg_exo) REVERT: M 608 MET cc_start: 0.7034 (mtt) cc_final: 0.6678 (mtt) REVERT: M 627 MET cc_start: 0.5918 (OUTLIER) cc_final: 0.5550 (ptp) REVERT: M 738 MET cc_start: 0.5728 (OUTLIER) cc_final: 0.4707 (mtt) REVERT: M 817 LYS cc_start: 0.6104 (mppt) cc_final: 0.4902 (pttm) REVERT: M 835 GLN cc_start: 0.7207 (OUTLIER) cc_final: 0.6364 (mp10) REVERT: M 863 MET cc_start: 0.8583 (mmm) cc_final: 0.8299 (mmt) REVERT: M 878 ASP cc_start: 0.8457 (m-30) cc_final: 0.7972 (t0) REVERT: M 907 LYS cc_start: 0.8177 (mttt) cc_final: 0.7620 (mmtt) outliers start: 85 outliers final: 57 residues processed: 428 average time/residue: 0.2021 time to fit residues: 140.3521 Evaluate side-chains 421 residues out of total 3697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 356 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 693 SER Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 879 SER Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 997 SER Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1261 GLN Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 742 SER Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 1164 THR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 116 GLN Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain E residue 26 TYR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain I residue 75 ARG Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 32 SER Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain M residue 8 ASN Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 107 ASP Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain M residue 235 THR Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 287 LEU Chi-restraints excluded: chain M residue 373 LEU Chi-restraints excluded: chain M residue 464 VAL Chi-restraints excluded: chain M residue 483 SER Chi-restraints excluded: chain M residue 525 SER Chi-restraints excluded: chain M residue 541 ASP Chi-restraints excluded: chain M residue 617 MET Chi-restraints excluded: chain M residue 627 MET Chi-restraints excluded: chain M residue 648 MET Chi-restraints excluded: chain M residue 725 VAL Chi-restraints excluded: chain M residue 738 MET Chi-restraints excluded: chain M residue 780 VAL Chi-restraints excluded: chain M residue 835 GLN Chi-restraints excluded: chain M residue 905 SER Chi-restraints excluded: chain M residue 1010 LEU Chi-restraints excluded: chain M residue 1058 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 163 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 234 optimal weight: 0.4980 chunk 409 optimal weight: 10.0000 chunk 114 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 369 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 31 optimal weight: 0.0870 chunk 310 optimal weight: 0.8980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 892 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.173382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.133181 restraints weight = 39324.435| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.12 r_work: 0.3158 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 33488 Z= 0.102 Angle : 0.577 15.484 45773 Z= 0.274 Chirality : 0.044 0.354 5356 Planarity : 0.004 0.076 5571 Dihedral : 12.500 177.426 5381 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.89 % Allowed : 18.39 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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 are not related in a simple way. whole: -1.59 (0.13), residues: 4096 helix: -0.02 (0.15), residues: 1332 sheet: -1.10 (0.19), residues: 687 loop : -1.74 (0.13), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 396 TYR 0.011 0.001 TYR M 403 PHE 0.012 0.001 PHE M 311 TRP 0.030 0.001 TRP M 501 HIS 0.011 0.001 HIS A 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (33458) covalent geometry : angle 0.54691 / 0.27 (45742) hydrogen bonds : bond 0.03679 / 2.38 ( 1071) hydrogen bonds : angle 4.30949 / 3.03 ( 3097) metal coordination : bond 0.00818 / 0.65 ( 30) metal coordination : angle 7.13421 / 4.98 ( 31) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 365 time to evaluate : 1.120 Fit side-chains revert: symmetry clash REVERT: A 999 GLU cc_start: 0.8217 (mp0) cc_final: 0.7970 (mp0) REVERT: A 1260 ASP cc_start: 0.7988 (p0) cc_final: 0.7703 (p0) REVERT: A 1261 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.7434 (pm20) REVERT: B 465 PHE cc_start: 0.7868 (m-80) cc_final: 0.7185 (m-80) REVERT: B 558 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.7135 (mt-10) REVERT: B 559 GLU cc_start: 0.8135 (tp30) cc_final: 0.7783 (tt0) REVERT: C 33 MET cc_start: 0.8315 (tpp) cc_final: 0.7986 (mmt) REVERT: C 55 ILE cc_start: 0.8715 (pt) cc_final: 0.8433 (mt) REVERT: F 73 ILE cc_start: 0.8665 (mt) cc_final: 0.8458 (mt) REVERT: F 95 THR cc_start: 0.7290 (t) cc_final: 0.6890 (p) REVERT: F 107 GLN cc_start: 0.8060 (mt0) cc_final: 0.7707 (mt0) REVERT: H 40 PHE cc_start: 0.8650 (t80) cc_final: 0.8314 (t80) REVERT: J 48 MET cc_start: 0.8758 (mmm) cc_final: 0.8503 (mmm) REVERT: K 37 ARG cc_start: 0.8544 (mmt-90) cc_final: 0.7425 (mtm180) REVERT: K 96 LYS cc_start: 0.8903 (mtmm) cc_final: 0.8556 (mtpt) REVERT: L 17 GLN cc_start: 0.7215 (tt0) cc_final: 0.6627 (mm110) REVERT: L 36 ILE cc_start: 0.9375 (mt) cc_final: 0.9073 (mt) REVERT: M 373 LEU cc_start: 0.5107 (OUTLIER) cc_final: 0.4728 (tt) REVERT: M 466 PRO cc_start: 0.5714 (Cg_endo) cc_final: 0.5429 (Cg_exo) REVERT: M 608 MET cc_start: 0.6749 (mtt) cc_final: 0.6457 (mtt) REVERT: M 627 MET cc_start: 0.5911 (OUTLIER) cc_final: 0.5693 (ptp) REVERT: M 817 LYS cc_start: 0.6023 (mppt) cc_final: 0.4796 (pttm) REVERT: M 835 GLN cc_start: 0.7096 (OUTLIER) cc_final: 0.6320 (mp10) REVERT: M 863 MET cc_start: 0.8430 (mmm) cc_final: 0.8146 (mmt) REVERT: M 878 ASP cc_start: 0.8340 (m-30) cc_final: 0.7876 (t0) REVERT: M 907 LYS cc_start: 0.8109 (mttt) cc_final: 0.7430 (mmtt) outliers start: 58 outliers final: 43 residues processed: 412 average time/residue: 0.2066 time to fit residues: 137.9017 Evaluate side-chains 393 residues out of total 3697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 345 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 693 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1261 GLN Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 742 SER Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain C residue 116 GLN Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 32 SER Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain M residue 8 ASN Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain M residue 235 THR Chi-restraints excluded: chain M residue 287 LEU Chi-restraints excluded: chain M residue 373 LEU Chi-restraints excluded: chain M residue 464 VAL Chi-restraints excluded: chain M residue 525 SER Chi-restraints excluded: chain M residue 627 MET Chi-restraints excluded: chain M residue 725 VAL Chi-restraints excluded: chain M residue 835 GLN Chi-restraints excluded: chain M residue 1010 LEU Chi-restraints excluded: chain M residue 1058 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 37 optimal weight: 0.9990 chunk 237 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 369 optimal weight: 7.9990 chunk 246 optimal weight: 10.0000 chunk 215 optimal weight: 1.9990 chunk 239 optimal weight: 10.0000 chunk 269 optimal weight: 0.0980 chunk 312 optimal weight: 0.8980 chunk 257 optimal weight: 0.0020 chunk 75 optimal weight: 0.9980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.174503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.135685 restraints weight = 39208.013| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.75 r_work: 0.3166 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 33488 Z= 0.097 Angle : 0.568 17.363 45773 Z= 0.266 Chirality : 0.044 0.356 5356 Planarity : 0.003 0.063 5571 Dihedral : 12.430 178.069 5381 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.79 % Allowed : 18.49 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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 are not related in a simple way. whole: -1.31 (0.13), residues: 4096 helix: 0.28 (0.15), residues: 1317 sheet: -0.98 (0.19), residues: 705 loop : -1.59 (0.13), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 396 TYR 0.017 0.001 TYR M1006 PHE 0.018 0.001 PHE B 344 TRP 0.032 0.001 TRP M 501 HIS 0.009 0.001 HIS A 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (33458) covalent geometry : angle 0.53262 / 0.26 (45742) hydrogen bonds : bond 0.03511 / 2.27 ( 1071) hydrogen bonds : angle 4.14643 / 2.92 ( 3097) metal coordination : bond 0.00803 / 0.63 ( 30) metal coordination : angle 7.54922 / 5.37 ( 31) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 364 time to evaluate : 1.224 Fit side-chains revert: symmetry clash REVERT: B 71 PHE cc_start: 0.7400 (m-80) cc_final: 0.7087 (m-80) REVERT: B 465 PHE cc_start: 0.7941 (m-80) cc_final: 0.7191 (m-80) REVERT: B 558 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7296 (mt-10) REVERT: B 559 GLU cc_start: 0.8128 (tp30) cc_final: 0.7790 (tt0) REVERT: B 883 VAL cc_start: 0.9375 (OUTLIER) cc_final: 0.9017 (t) REVERT: C 33 MET cc_start: 0.8344 (tpp) cc_final: 0.8016 (mmt) REVERT: C 55 ILE cc_start: 0.8725 (pt) cc_final: 0.8514 (mt) REVERT: F 95 THR cc_start: 0.7296 (t) cc_final: 0.6907 (p) REVERT: F 107 GLN cc_start: 0.8116 (mt0) cc_final: 0.7742 (mt0) REVERT: H 33 ARG cc_start: 0.8514 (tpp-160) cc_final: 0.8309 (tpp-160) REVERT: H 40 PHE cc_start: 0.8634 (t80) cc_final: 0.8311 (t80) REVERT: J 48 MET cc_start: 0.8733 (mmm) cc_final: 0.8462 (mmm) REVERT: K 37 ARG cc_start: 0.8518 (mmt-90) cc_final: 0.7449 (mtm180) REVERT: K 96 LYS cc_start: 0.8909 (mtmm) cc_final: 0.8550 (mtpt) REVERT: L 36 ILE cc_start: 0.9364 (mt) cc_final: 0.9076 (mt) REVERT: M 316 MET cc_start: 0.6951 (mmm) cc_final: 0.6651 (mmm) REVERT: M 373 LEU cc_start: 0.5150 (OUTLIER) cc_final: 0.4742 (tt) REVERT: M 466 PRO cc_start: 0.5732 (Cg_endo) cc_final: 0.5417 (Cg_exo) REVERT: M 605 ARG cc_start: 0.6218 (mtm180) cc_final: 0.5601 (mtm-85) REVERT: M 608 MET cc_start: 0.6658 (mtt) cc_final: 0.6420 (mtt) REVERT: M 817 LYS cc_start: 0.6020 (mppt) cc_final: 0.4780 (pttm) REVERT: M 835 GLN cc_start: 0.7235 (OUTLIER) cc_final: 0.6418 (mp10) REVERT: M 863 MET cc_start: 0.8415 (mmm) cc_final: 0.8175 (mmt) REVERT: M 878 ASP cc_start: 0.8350 (m-30) cc_final: 0.7920 (t0) REVERT: M 907 LYS cc_start: 0.8096 (mttt) cc_final: 0.7433 (mmtt) REVERT: M 1063 MET cc_start: 0.4755 (tpt) cc_final: 0.4305 (tpt) outliers start: 55 outliers final: 44 residues processed: 407 average time/residue: 0.2070 time to fit residues: 137.0727 Evaluate side-chains 395 residues out of total 3697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 347 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 742 SER Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 796 GLU Chi-restraints excluded: chain B residue 812 VAL Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 116 GLN Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain M residue 8 ASN Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 235 THR Chi-restraints excluded: chain M residue 279 VAL Chi-restraints excluded: chain M residue 287 LEU Chi-restraints excluded: chain M residue 373 LEU Chi-restraints excluded: chain M residue 464 VAL Chi-restraints excluded: chain M residue 525 SER Chi-restraints excluded: chain M residue 725 VAL Chi-restraints excluded: chain M residue 835 GLN Chi-restraints excluded: chain M residue 1010 LEU Chi-restraints excluded: chain M residue 1058 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 18 optimal weight: 3.9990 chunk 406 optimal weight: 0.0980 chunk 302 optimal weight: 0.9980 chunk 129 optimal weight: 6.9990 chunk 363 optimal weight: 30.0000 chunk 418 optimal weight: 40.0000 chunk 174 optimal weight: 5.9990 chunk 318 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 175 optimal weight: 0.8980 chunk 398 optimal weight: 0.0370 overall best weight: 1.2060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 824 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.174404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.135004 restraints weight = 39684.621| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.25 r_work: 0.3130 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 33488 Z= 0.120 Angle : 0.579 18.233 45773 Z= 0.271 Chirality : 0.045 0.358 5356 Planarity : 0.003 0.049 5571 Dihedral : 12.432 179.041 5378 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.79 % Allowed : 18.59 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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 are not related in a simple way. whole: -1.27 (0.13), residues: 4096 helix: 0.29 (0.15), residues: 1321 sheet: -0.91 (0.19), residues: 707 loop : -1.57 (0.13), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 22 TYR 0.026 0.001 TYR M 551 PHE 0.015 0.001 PHE M 311 TRP 0.033 0.001 TRP M 501 HIS 0.010 0.001 HIS A 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (33458) covalent geometry : angle 0.54506 / 0.27 (45742) hydrogen bonds : bond 0.03621 / 2.35 ( 1071) hydrogen bonds : angle 4.13122 / 2.91 ( 3097) metal coordination : bond 0.00848 / 0.65 ( 30) metal coordination : angle 7.57681 / 5.40 ( 31) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 349 time to evaluate : 1.344 Fit side-chains revert: symmetry clash REVERT: A 1261 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.7384 (pm20) REVERT: B 465 PHE cc_start: 0.7743 (m-80) cc_final: 0.7058 (m-80) REVERT: B 558 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7294 (mt-10) REVERT: B 559 GLU cc_start: 0.8172 (tp30) cc_final: 0.7720 (tt0) REVERT: B 883 VAL cc_start: 0.9364 (OUTLIER) cc_final: 0.8990 (t) REVERT: F 95 THR cc_start: 0.7279 (t) cc_final: 0.6885 (p) REVERT: F 107 GLN cc_start: 0.8033 (mt0) cc_final: 0.7668 (mt0) REVERT: H 40 PHE cc_start: 0.8658 (t80) cc_final: 0.8356 (t80) REVERT: J 48 MET cc_start: 0.8804 (mmm) cc_final: 0.8509 (mmm) REVERT: K 37 ARG cc_start: 0.8558 (mmt-90) cc_final: 0.7404 (mtm180) REVERT: K 96 LYS cc_start: 0.8865 (mtmm) cc_final: 0.8500 (mtpt) REVERT: M 373 LEU cc_start: 0.5039 (OUTLIER) cc_final: 0.4616 (tt) REVERT: M 466 PRO cc_start: 0.5739 (Cg_endo) cc_final: 0.5426 (Cg_exo) REVERT: M 608 MET cc_start: 0.6453 (mtt) cc_final: 0.6167 (mtt) REVERT: M 817 LYS cc_start: 0.5928 (mppt) cc_final: 0.4771 (pttm) REVERT: M 835 GLN cc_start: 0.7153 (OUTLIER) cc_final: 0.6400 (mp10) REVERT: M 878 ASP cc_start: 0.8280 (m-30) cc_final: 0.7828 (t0) REVERT: M 907 LYS cc_start: 0.7940 (mttt) cc_final: 0.7248 (mmtt) REVERT: M 1063 MET cc_start: 0.4520 (tpt) cc_final: 0.4179 (tpt) outliers start: 55 outliers final: 48 residues processed: 395 average time/residue: 0.2095 time to fit residues: 134.5539 Evaluate side-chains 397 residues out of total 3697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 344 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 693 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1261 GLN Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 742 SER Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 796 GLU Chi-restraints excluded: chain B residue 812 VAL Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 116 GLN Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain M residue 8 ASN Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 235 THR Chi-restraints excluded: chain M residue 279 VAL Chi-restraints excluded: chain M residue 287 LEU Chi-restraints excluded: chain M residue 373 LEU Chi-restraints excluded: chain M residue 464 VAL Chi-restraints excluded: chain M residue 525 SER Chi-restraints excluded: chain M residue 725 VAL Chi-restraints excluded: chain M residue 835 GLN Chi-restraints excluded: chain M residue 1010 LEU Chi-restraints excluded: chain M residue 1058 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 371 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 244 optimal weight: 10.0000 chunk 355 optimal weight: 9.9990 chunk 82 optimal weight: 8.9990 chunk 410 optimal weight: 10.0000 chunk 360 optimal weight: 6.9990 chunk 382 optimal weight: 50.0000 chunk 74 optimal weight: 8.9990 chunk 255 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 454 HIS ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 892 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.168941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.133011 restraints weight = 39331.916| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.62 r_work: 0.3102 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.095 33488 Z= 0.423 Angle : 0.866 19.110 45773 Z= 0.416 Chirality : 0.058 0.408 5356 Planarity : 0.006 0.079 5571 Dihedral : 12.858 176.796 5378 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 2.25 % Allowed : 18.33 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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 are not related in a simple way. whole: -2.06 (0.12), residues: 4096 helix: -0.60 (0.14), residues: 1332 sheet: -1.35 (0.18), residues: 727 loop : -1.88 (0.13), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 70 TYR 0.033 0.003 TYR M 551 PHE 0.026 0.003 PHE C 66 TRP 0.029 0.003 TRP M 501 HIS 0.013 0.002 HIS A 454 Details of bonding type rmsd/Z covalent geometry : bond 0.01040 / 0.42 (33458) covalent geometry : angle 0.82984 / 0.41 (45742) hydrogen bonds : bond 0.05439 / 3.63 ( 1071) hydrogen bonds : angle 4.87190 / 3.40 ( 3097) metal coordination : bond 0.01408 / 0.99 ( 30) metal coordination : angle 9.50969 / 6.57 ( 31) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8958.26 seconds wall clock time: 153 minutes 38.83 seconds (9218.83 seconds total)