Starting phenix.real_space_refine on Tue Sep 15 09:50:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5oik_3817/09_2026/5oik_3817.cif Found real_map, /net/cci-nas-00/data/ceres_data/5oik_3817/09_2026/5oik_3817.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5oik_3817/09_2026/5oik_3817.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5oik_3817/09_2026/5oik_3817.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5oik_3817/09_2026/5oik_3817.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5oik_3817/09_2026/5oik_3817.map" restraint_files = "/net/cci-nas-00/data/ceres_data/5oik_3817/09_2026/5oik_3817.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5oik_3817/09_2026/5oik_3817.cif" } resolution = 3.7 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 104 5.49 5 Mg 1 5.21 5 S 223 5.16 5 C 23677 2.51 5 N 6675 2.21 5 O 7300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.23s 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: 37988 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 11261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1421, 11261 Classifications: {'peptide': 1421} Link IDs: {'PCIS': 2, 'PTRANS': 68, 'TRANS': 1350} Chain breaks: 4 Chain: "B" Number of atoms: 9142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1147, 9142 Classifications: {'peptide': 1147} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 53, 'TRANS': 1093} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 2079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2079 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 15, 'TRANS': 243} Chain breaks: 1 Chain: "D" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1008 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 3, 'TRANS': 124} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "E" Number of atoms: 1711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1711 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 658 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "G" Number of atoms: 1341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1341 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 946 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "J" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 379 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "N" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 709 Classifications: {'DNA': 43} Modifications used: {'5*END': 1} Incomplete info: {'p_only': 9} Link IDs: {'rna3p': 42} Unresolved chain links: 9 Chain breaks: 1 Unresolved chain link angles: 39 Unresolved chain link dihedrals: 29 Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {' DT:plan': 5, ' DC:plan': 1, ' DC:plan2': 1, ' DA:plan': 2, ' DA:plan2': 2, ' DG:plan': 1, ' DG:plan2': 1} Unresolved non-hydrogen planarities: 101 Chain: "P" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 427 Classifications: {'RNAv2': 20} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 11, 'rna3p_pyr': 8} Link IDs: {'rna2p': 1, 'rna3p': 18} Chain: "T" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 874 Classifications: {'DNA': 43} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 42} Chain: "Y" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 911 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "Z" Number of atoms: 3894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3894 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 17, 'TRANS': 470} Chain breaks: 3 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: "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: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 464 SG CYS A 71 49.511 81.483 106.979 1.00174.43 S ATOM 486 SG CYS A 74 50.403 84.666 107.735 1.00166.79 S ATOM 533 SG CYS A 81 51.588 82.683 104.644 1.00162.13 S ATOM 768 SG CYS A 111 97.442 76.724 119.493 1.00183.09 S ATOM 796 SG CYS A 114 96.217 78.258 122.283 1.00182.27 S ATOM 1142 SG CYS A 184 98.201 74.807 122.510 1.00191.04 S ATOM 19973 SG CYS B1119 62.230 93.692 113.752 1.00148.10 S ATOM 19995 SG CYS B1122 64.520 91.088 113.113 1.00143.35 S ATOM 20110 SG CYS B1137 61.443 90.437 114.352 1.00165.79 S ATOM 20131 SG CYS B1140 64.951 91.110 116.464 1.00167.23 S ATOM 28452 SG CYS I 17 127.473 41.022 72.012 1.00155.52 S ATOM 28476 SG CYS I 20 124.329 40.644 74.643 1.00158.58 S ATOM 28637 SG CYS I 39 125.783 43.572 75.599 1.00159.23 S ATOM 28662 SG CYS I 42 128.090 40.618 75.763 1.00157.72 S ATOM 29014 SG CYS I 86 116.889 57.626 31.731 1.00154.36 S ATOM 29038 SG CYS I 89 116.360 54.569 29.565 1.00162.90 S ATOM 29242 SG CYS I 114 113.566 56.706 32.138 1.00146.80 S ATOM 29277 SG CYS I 119 116.034 54.241 33.009 1.00147.95 S ATOM 29387 SG CYS J 7 46.132 82.678 34.017 1.00 75.68 S ATOM 29411 SG CYS J 10 44.572 85.387 31.875 1.00 78.13 S ATOM 29675 SG CYS J 44 47.875 85.233 31.328 1.00 83.70 S ATOM 29681 SG CYS J 45 45.513 82.751 30.060 1.00 86.52 S ATOM 30834 SG CYS L 19 35.307 48.394 59.744 1.00138.04 S ATOM 30853 SG CYS L 22 33.360 46.285 57.805 1.00137.85 S ATOM 30970 SG CYS L 36 32.063 47.083 61.394 1.00146.22 S ATOM 30996 SG CYS L 39 35.347 45.135 60.694 1.00145.80 S ATOM 33293 SG CYS Y 16 75.126 24.130 126.306 1.00484.94 S ATOM 33315 SG CYS Y 19 78.449 24.783 124.495 1.00462.52 S ATOM 33427 SG CYS Y 33 76.998 21.604 123.861 1.00506.45 S ATOM 33449 SG CYS Y 36 78.411 22.354 127.424 1.00521.18 S Time building chain proxies: 7.73, per 1000 atoms: 0.20 Number of scatterers: 37988 At special positions: 0 Unit cell: (163.35, 167.4, 168.75, 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 223 16.00 P 104 15.00 Mg 1 11.99 O 7300 8.00 N 6675 7.00 C 23677 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: 3.36 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 84 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 184 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1140 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb=" ZN Y 201 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 33 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 16 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 36 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 19 " Number of angles added : 39 8934 Ramachandran restraints generated. 4467 Oldfield, 0 Emsley, 4467 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8474 Finding SS restraints... Secondary structure from input PDB file: 154 helices and 57 sheets defined 35.0% alpha, 19.9% beta 40 base pairs and 82 stacking pairs defined. Time for finding SS restraints: 4.93 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 removed outlier: 3.621A pdb=" N LYS A 32 " --> pdb=" O PRO A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 109 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 136 through 151 removed outlier: 3.931A pdb=" N LEU A 141 " --> pdb=" O PRO A 137 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP A 146 " --> pdb=" O THR A 142 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 227 removed outlier: 4.068A pdb=" N ARG A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 236 removed outlier: 3.536A pdb=" N LEU A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 257 through 261 Processing helix chain 'A' and resid 274 through 296 removed outlier: 3.535A pdb=" N ILE A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A 286 " --> pdb=" O ASP A 282 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 319 removed outlier: 3.571A pdb=" N ILE A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU A 305 " --> pdb=" O HIS A 301 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 344 removed outlier: 3.763A pdb=" N LEU A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 354 Processing helix chain 'A' and resid 381 through 388 removed outlier: 3.774A pdb=" N ASN A 387 " --> pdb=" O SER A 383 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N MET A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 409 removed outlier: 3.804A pdb=" N GLU A 404 " --> pdb=" O ASP A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 486 through 490 Processing helix chain 'A' and resid 508 through 519 removed outlier: 3.903A pdb=" N GLU A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE A 515 " --> pdb=" O THR A 511 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU A 517 " --> pdb=" O ALA A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 524 Processing helix chain 'A' and resid 539 through 550 removed outlier: 3.870A pdb=" N ARG A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 567 removed outlier: 3.556A pdb=" N MET A 561 " --> pdb=" O ARG A 557 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN A 562 " --> pdb=" O GLY A 558 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 563 " --> pdb=" O GLU A 559 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET A 565 " --> pdb=" O MET A 561 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 596 removed outlier: 4.113A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE A 595 " --> pdb=" O ILE A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 660 Processing helix chain 'A' and resid 665 through 678 removed outlier: 3.539A pdb=" N TYR A 669 " --> pdb=" O THR A 665 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER A 670 " --> pdb=" O ARG A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 684 removed outlier: 3.749A pdb=" N GLU A 683 " --> pdb=" O TRP A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'A' and resid 697 through 722 removed outlier: 3.530A pdb=" N THR A 705 " --> pdb=" O ASP A 701 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 714 " --> pdb=" O LYS A 710 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN A 722 " --> pdb=" O GLU A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 758 removed outlier: 3.649A pdb=" N ASN A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP A 747 " --> pdb=" O ARG A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 772 removed outlier: 3.769A pdb=" N SER A 772 " --> pdb=" O SER A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 786 removed outlier: 3.710A pdb=" N ILE A 781 " --> pdb=" O SER A 777 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER A 782 " --> pdb=" O LYS A 778 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN A 783 " --> pdb=" O ILE A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 869 removed outlier: 3.730A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N THR A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU A 856 " --> pdb=" O VAL A 852 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG A 863 " --> pdb=" O TYR A 859 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A 865 " --> pdb=" O GLN A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 920 removed outlier: 3.671A pdb=" N GLU A 917 " --> pdb=" O ASN A 913 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS A 918 " --> pdb=" O LYS A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 934 Processing helix chain 'A' and resid 935 through 945 removed outlier: 3.631A pdb=" N LYS A 940 " --> pdb=" O GLU A 936 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER A 944 " --> pdb=" O LYS A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 970 removed outlier: 3.538A pdb=" N GLN A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG A 967 " --> pdb=" O ARG A 963 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A 968 " --> pdb=" O GLU A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 974 removed outlier: 4.164A pdb=" N ASP A 974 " --> pdb=" O PRO A 971 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 971 through 974' Processing helix chain 'A' and resid 982 through 993 removed outlier: 3.682A pdb=" N LYS A 992 " --> pdb=" O TRP A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1018 removed outlier: 3.735A pdb=" N VAL A1010 " --> pdb=" O PRO A1006 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY A1012 " --> pdb=" O LYS A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1038 removed outlier: 3.566A pdb=" N ALA A1037 " --> pdb=" O ALA A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1049 removed outlier: 3.737A pdb=" N LEU A1049 " --> pdb=" O LEU A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1056 removed outlier: 3.530A pdb=" N ALA A1055 " --> pdb=" O SER A1051 " (cutoff:3.500A) Processing helix chain 'A' and resid 1061 through 1078 removed outlier: 3.545A pdb=" N GLY A1070 " --> pdb=" O ASP A1066 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU A1071 " --> pdb=" O TRP A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1087 through 1097 removed outlier: 3.527A pdb=" N LEU A1095 " --> pdb=" O ALA A1091 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A1096 " --> pdb=" O ALA A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1102 Processing helix chain 'A' and resid 1120 through 1130 removed outlier: 3.855A pdb=" N GLU A1126 " --> pdb=" O PRO A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1149 Processing helix chain 'A' and resid 1150 through 1162 removed outlier: 3.600A pdb=" N ILE A1157 " --> pdb=" O ARG A1153 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU A1162 " --> pdb=" O LEU A1158 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1169 removed outlier: 4.063A pdb=" N VAL A1169 " --> pdb=" O THR A1165 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1165 through 1169' Processing helix chain 'A' and resid 1180 through 1184 Processing helix chain 'A' and resid 1189 through 1199 removed outlier: 4.361A pdb=" N MET A1199 " --> pdb=" O VAL A1195 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1224 removed outlier: 3.507A pdb=" N ARG A1224 " --> pdb=" O HIS A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1240 Processing helix chain 'A' and resid 1262 through 1267 removed outlier: 3.829A pdb=" N GLU A1266 " --> pdb=" O MET A1262 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1296 removed outlier: 4.175A pdb=" N THR A1294 " --> pdb=" O SER A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1349 removed outlier: 3.674A pdb=" N VAL A1346 " --> pdb=" O SER A1342 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER A1348 " --> pdb=" O MET A1344 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU A1349 " --> pdb=" O ARG A1345 " (cutoff:3.500A) Processing helix chain 'A' and resid 1362 through 1370 removed outlier: 3.588A pdb=" N VAL A1368 " --> pdb=" O GLU A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1387 removed outlier: 3.579A pdb=" N VAL A1374 " --> pdb=" O GLY A1370 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU A1379 " --> pdb=" O ARG A1375 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1407 removed outlier: 3.653A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A1401 " --> pdb=" O HIS A1397 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR A1406 " --> pdb=" O CYS A1402 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1422 removed outlier: 3.886A pdb=" N GLN A1422 " --> pdb=" O GLY A1418 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1430 Processing helix chain 'A' and resid 1435 through 1445 removed outlier: 3.640A pdb=" N GLU A1441 " --> pdb=" O ASP A1437 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HIS A1445 " --> pdb=" O GLU A1441 " (cutoff:3.500A) Processing helix chain 'A' and resid 1453 through 1460 removed outlier: 3.780A pdb=" N ASN A1457 " --> pdb=" O GLY A1453 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A1460 " --> pdb=" O GLU A1456 " (cutoff:3.500A) Processing helix chain 'A' and resid 1478 through 1482 removed outlier: 3.589A pdb=" N LYS A1481 " --> pdb=" O GLU A1478 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 37 removed outlier: 3.989A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER B 31 " --> pdb=" O TRP B 27 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR B 33 " --> pdb=" O VAL B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 Processing helix chain 'B' and resid 53 through 61 removed outlier: 3.502A pdb=" N ILE B 58 " --> pdb=" O SER B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 246 through 253 removed outlier: 3.552A pdb=" N ALA B 251 " --> pdb=" O ALA B 247 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY B 253 " --> pdb=" O LYS B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 280 through 289 Processing helix chain 'B' and resid 294 through 308 removed outlier: 3.686A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Proline residue: B 303 - end of helix removed outlier: 3.674A pdb=" N GLU B 307 " --> pdb=" O PRO B 303 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 323 Processing helix chain 'B' and resid 331 through 345 Processing helix chain 'B' and resid 356 through 378 removed outlier: 4.191A pdb=" N LYS B 360 " --> pdb=" O PHE B 356 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE B 364 " --> pdb=" O LYS B 360 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA B 375 " --> pdb=" O ARG B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 424 removed outlier: 4.307A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR B 418 " --> pdb=" O GLU B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 451 removed outlier: 3.551A pdb=" N GLY B 451 " --> pdb=" O SER B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 483 removed outlier: 3.985A pdb=" N SER B 480 " --> pdb=" O ALA B 476 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N HIS B 481 " --> pdb=" O SER B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 516 through 520 removed outlier: 4.226A pdb=" N ALA B 519 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 547 removed outlier: 3.673A pdb=" N GLU B 547 " --> pdb=" O GLU B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 594 removed outlier: 3.562A pdb=" N LEU B 583 " --> pdb=" O ASP B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 645 removed outlier: 3.805A pdb=" N ILE B 640 " --> pdb=" O LYS B 636 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU B 645 " --> pdb=" O ASP B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 658 Processing helix chain 'B' and resid 678 through 683 Processing helix chain 'B' and resid 699 through 704 removed outlier: 3.577A pdb=" N ILE B 703 " --> pdb=" O PRO B 700 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU B 704 " --> pdb=" O SER B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 718 removed outlier: 3.613A pdb=" N ASN B 717 " --> pdb=" O PRO B 714 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLN B 718 " --> pdb=" O ASP B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 729 removed outlier: 3.662A pdb=" N THR B 723 " --> pdb=" O SER B 719 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN B 725 " --> pdb=" O ARG B 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 767 Processing helix chain 'B' and resid 798 through 802 Processing helix chain 'B' and resid 874 through 879 Processing helix chain 'B' and resid 950 through 954 removed outlier: 3.659A pdb=" N MET B 954 " --> pdb=" O GLN B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 976 removed outlier: 4.703A pdb=" N SER B 974 " --> pdb=" O HIS B 970 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 993 removed outlier: 3.540A pdb=" N CYS B 984 " --> pdb=" O HIS B 980 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS B 988 " --> pdb=" O CYS B 984 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 989 " --> pdb=" O LEU B 985 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN B 992 " --> pdb=" O LYS B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1016 removed outlier: 3.727A pdb=" N LEU B1014 " --> pdb=" O LYS B1010 " (cutoff:3.500A) Processing helix chain 'B' and resid 1017 through 1019 No H-bonds generated for 'chain 'B' and resid 1017 through 1019' Processing helix chain 'B' and resid 1087 through 1097 removed outlier: 3.561A pdb=" N ALA B1096 " --> pdb=" O ASP B1092 " (cutoff:3.500A) Processing helix chain 'B' and resid 1099 through 1108 removed outlier: 3.785A pdb=" N LEU B1103 " --> pdb=" O ALA B1099 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU B1105 " --> pdb=" O GLN B1101 " (cutoff:3.500A) Processing helix chain 'B' and resid 1152 through 1164 removed outlier: 3.514A pdb=" N SER B1164 " --> pdb=" O GLN B1160 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 36 removed outlier: 3.566A pdb=" N ARG C 35 " --> pdb=" O ALA C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 71 removed outlier: 3.575A pdb=" N GLY C 69 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU C 70 " --> pdb=" O HIS C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 129 through 133 Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 removed outlier: 3.565A pdb=" N GLU C 202 " --> pdb=" O LYS C 199 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TRP C 203 " --> pdb=" O PRO C 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 199 through 203' Processing helix chain 'C' and resid 241 through 271 removed outlier: 3.896A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER C 247 " --> pdb=" O THR C 243 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS C 254 " --> pdb=" O SER C 250 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS C 255 " --> pdb=" O GLY C 251 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR C 261 " --> pdb=" O SER C 257 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU C 266 " --> pdb=" O GLN C 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 20 Processing helix chain 'D' and resid 33 through 50 Processing helix chain 'D' and resid 58 through 71 Processing helix chain 'D' and resid 76 through 89 Processing helix chain 'D' and resid 93 through 104 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'E' and resid 3 through 24 removed outlier: 3.654A pdb=" N ARG E 14 " --> pdb=" O LEU E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 44 Processing helix chain 'E' and resid 83 through 98 removed outlier: 3.507A pdb=" N VAL E 89 " --> pdb=" O LYS E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 121 removed outlier: 4.148A pdb=" N GLN E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N MET E 121 " --> pdb=" O SER E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 163 Processing helix chain 'E' and resid 166 through 170 removed outlier: 3.677A pdb=" N LEU E 170 " --> pdb=" O GLU E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 183 removed outlier: 3.822A pdb=" N PHE E 183 " --> pdb=" O VAL E 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 74 removed outlier: 3.581A pdb=" N LEU F 66 " --> pdb=" O ARG F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 99 removed outlier: 3.545A pdb=" N LYS F 98 " --> pdb=" O MET F 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 22 through 35 Processing helix chain 'G' and resid 111 through 113 No H-bonds generated for 'chain 'G' and resid 111 through 113' Processing helix chain 'I' and resid 63 through 67 removed outlier: 3.539A pdb=" N THR I 66 " --> pdb=" O ASP I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 75 Processing helix chain 'J' and resid 17 through 26 removed outlier: 3.788A pdb=" N GLY J 23 " --> pdb=" O GLU J 19 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU J 24 " --> pdb=" O ALA J 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 4.084A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 9 removed outlier: 3.651A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 51 removed outlier: 3.845A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE K 46 " --> pdb=" O LEU K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 removed outlier: 3.554A pdb=" N ILE K 91 " --> pdb=" O PHE K 87 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU K 100 " --> pdb=" O SER K 96 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU K 103 " --> pdb=" O SER K 99 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 6 Processing helix chain 'Y' and resid 25 through 32 Processing helix chain 'Y' and resid 36 through 41 Processing helix chain 'Y' and resid 45 through 52 Processing helix chain 'Y' and resid 65 through 68 Processing helix chain 'Y' and resid 69 through 75 removed outlier: 3.702A pdb=" N LYS Y 73 " --> pdb=" O SER Y 69 " (cutoff:3.500A) Processing helix chain 'Y' and resid 94 through 104 Processing helix chain 'Z' and resid 188 through 204 Processing helix chain 'Z' and resid 231 through 240 removed outlier: 3.561A pdb=" N VAL Z 235 " --> pdb=" O LYS Z 231 " (cutoff:3.500A) Processing helix chain 'Z' and resid 242 through 249 removed outlier: 5.202A pdb=" N LEU Z 247 " --> pdb=" O ASN Z 244 " (cutoff:3.500A) Processing helix chain 'Z' and resid 256 through 260 Processing helix chain 'Z' and resid 261 through 265 Processing helix chain 'Z' and resid 341 through 349 Processing helix chain 'Z' and resid 389 through 396 Processing helix chain 'Z' and resid 464 through 466 No H-bonds generated for 'chain 'Z' and resid 464 through 466' Processing helix chain 'Z' and resid 514 through 516 No H-bonds generated for 'chain 'Z' and resid 514 through 516' Processing helix chain 'Z' and resid 573 through 575 No H-bonds generated for 'chain 'Z' and resid 573 through 575' Processing helix chain 'Z' and resid 630 through 633 removed outlier: 3.560A pdb=" N GLY Z 633 " --> pdb=" O VAL Z 630 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 630 through 633' Processing sheet with id=AA1, first strand: chain 'A' and resid 1448 through 1449 Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 95 removed outlier: 7.161A pdb=" N THR A 251 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 10.368A pdb=" N LYS A 92 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 10.387A pdb=" N ILE A 249 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 190 through 194 removed outlier: 4.579A pdb=" N LEU A 198 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 200 " --> pdb=" O ILE A 214 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 264 through 265 Processing sheet with id=AA5, first strand: chain 'A' and resid 357 through 359 removed outlier: 3.754A pdb=" N LEU B1084 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1060 through 1062 removed outlier: 3.872A pdb=" N THR A 365 " --> pdb=" O MET A 501 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N VAL A 378 " --> pdb=" O ARG A 475 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N PHE A 482 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL A 366 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LEU A 484 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N THR A 368 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 389 through 393 removed outlier: 3.707A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AA9, first strand: chain 'A' and resid 579 through 581 removed outlier: 5.812A pdb=" N ILE A 579 " --> pdb=" O TYR H 93 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N TYR H 93 " --> pdb=" O ILE A 579 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS A 581 " --> pdb=" O VAL H 91 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER H 139 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP H 11 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP H 38 " --> pdb=" O GLN H 126 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 602 through 605 removed outlier: 3.766A pdb=" N MET A 637 " --> pdb=" O VAL A 629 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 792 through 793 Processing sheet with id=AB3, first strand: chain 'A' and resid 872 through 873 removed outlier: 6.902A pdb=" N VAL A 879 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB5, first strand: chain 'A' and resid 1306 through 1310 removed outlier: 3.796A pdb=" N LYS A1306 " --> pdb=" O ASP A1339 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1243 through 1247 removed outlier: 4.399A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE A1261 " --> pdb=" O TRP A1210 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N TRP A1210 " --> pdb=" O ILE A1261 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU A1211 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE A1175 " --> pdb=" O LEU A1211 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ARG A1213 " --> pdb=" O THR A1173 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N THR A1173 " --> pdb=" O ARG A1213 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLU A1215 " --> pdb=" O ALA A1171 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N TYR A1177 " --> pdb=" O CYS I 52 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N CYS I 52 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1320 through 1322 Processing sheet with id=AB8, first strand: chain 'A' and resid 1472 through 1475 Processing sheet with id=AB9, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.675A pdb=" N ASP B 127 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ILE B 91 " --> pdb=" O TYR B 125 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TYR B 125 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LEU B 93 " --> pdb=" O PRO B 123 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ALA B 122 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLY B 150 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU B 124 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE B 148 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N VAL B 126 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LYS B 146 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AC2, first strand: chain 'B' and resid 185 through 187 removed outlier: 3.512A pdb=" N GLN B 468 " --> pdb=" O VAL B 193 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 391 through 394 Processing sheet with id=AC4, first strand: chain 'B' and resid 206 through 208 removed outlier: 3.832A pdb=" N TYR B 217 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LEU B 225 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 531 through 532 removed outlier: 3.565A pdb=" N ARG B 623 " --> pdb=" O ILE B 665 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 632 through 633 Processing sheet with id=AC7, first strand: chain 'B' and resid 572 through 577 removed outlier: 7.029A pdb=" N ILE B 567 " --> pdb=" O VAL B 574 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ILE B 576 " --> pdb=" O THR B 565 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N THR B 565 " --> pdb=" O ILE B 576 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 748 through 751 removed outlier: 6.215A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 748 through 751 removed outlier: 6.215A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AD2, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 7.026A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N ILE B 965 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ILE B 779 " --> pdb=" O ILE B 965 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ILE B 967 " --> pdb=" O ILE B 779 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ALA B 781 " --> pdb=" O ILE B 967 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 827 through 829 Processing sheet with id=AD4, first strand: chain 'B' and resid 865 through 867 removed outlier: 3.602A pdb=" N ILE B 867 " --> pdb=" O THR B 894 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 956 through 957 Processing sheet with id=AD6, first strand: chain 'B' and resid 1115 through 1119 Processing sheet with id=AD7, first strand: chain 'B' and resid 1127 through 1129 Processing sheet with id=AD8, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.608A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE C 21 " --> pdb=" O TYR C 231 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TYR C 230 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N PHE C 184 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ASN C 232 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N VAL C 182 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N GLU C 234 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.654A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 113 through 116 removed outlier: 3.557A pdb=" N VAL C 151 " --> pdb=" O VAL C 115 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 30 through 32 removed outlier: 3.609A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE G 2 " --> pdb=" O LEU D 32 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL G 66 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ILE G 54 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LYS G 71 " --> pdb=" O ASP G 52 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL G 48 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N PHE G 77 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ILE G 46 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 30 through 32 removed outlier: 3.609A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE G 2 " --> pdb=" O LEU D 32 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL G 66 " --> pdb=" O LEU G 13 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 60 through 61 removed outlier: 6.210A pdb=" N PHE E 73 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N VAL E 105 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N PHE E 75 " --> pdb=" O VAL E 105 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU E 128 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 81 through 82 removed outlier: 3.552A pdb=" N VAL E 82 " --> pdb=" O GLY E 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'E' and resid 147 through 150 removed outlier: 3.522A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 169 through 170 removed outlier: 6.609A pdb=" N ILE G 160 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N THR G 150 " --> pdb=" O PHE G 158 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N PHE G 158 " --> pdb=" O THR G 150 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL G 152 " --> pdb=" O ASP G 156 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ASP G 156 " --> pdb=" O VAL G 152 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER G 105 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU G 145 " --> pdb=" O VAL G 85 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 117 through 120 removed outlier: 3.523A pdb=" N ASP G 120 " --> pdb=" O CYS G 127 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N CYS G 127 " --> pdb=" O ASP G 120 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 25 through 28 Processing sheet with id=AF1, first strand: chain 'I' and resid 94 through 97 Processing sheet with id=AF2, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AF3, first strand: chain 'Y' and resid 22 through 24 Processing sheet with id=AF4, first strand: chain 'Y' and resid 83 through 89 removed outlier: 7.072A pdb=" N GLY Y 59 " --> pdb=" O VAL Y 87 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL Y 89 " --> pdb=" O PHE Y 57 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N PHE Y 57 " --> pdb=" O VAL Y 89 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER Z 214 " --> pdb=" O GLU Z 228 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Y' and resid 115 through 116 removed outlier: 7.315A pdb=" N ILE Y 115 " --> pdb=" O LYS Z 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'Z' and resid 352 through 355 removed outlier: 4.704A pdb=" N TYR Z 366 " --> pdb=" O PHE Z 373 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LYS Z 306 " --> pdb=" O VAL Z 293 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N VAL Z 293 " --> pdb=" O LYS Z 306 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Z' and resid 452 through 454 Processing sheet with id=AF8, first strand: chain 'Z' and resid 510 through 513 removed outlier: 3.548A pdb=" N ARG Z 494 " --> pdb=" O ILE Z 501 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N PHE Z 503 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ILE Z 492 " --> pdb=" O PHE Z 503 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Z' and resid 567 through 571 removed outlier: 7.065A pdb=" N THR Z 557 " --> pdb=" O LEU Z 553 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N LEU Z 553 " --> pdb=" O THR Z 557 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLN Z 559 " --> pdb=" O VAL Z 551 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Z' and resid 585 through 587 Processing sheet with id=AG2, first strand: chain 'Z' and resid 635 through 639 removed outlier: 6.382A pdb=" N HIS Z 625 " --> pdb=" O ILE Z 614 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ILE Z 614 " --> pdb=" O HIS Z 625 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'Z' and resid 742 through 746 removed outlier: 3.789A pdb=" N ASP Z 726 " --> pdb=" O ARG Z 733 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N GLU Z 735 " --> pdb=" O VAL Z 724 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N VAL Z 724 " --> pdb=" O GLU Z 735 " (cutoff:3.500A) 1355 hydrogen bonds defined for protein. 3696 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 94 hydrogen bonds 188 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 82 stacking parallelities Total time for adding SS restraints: 11.12 Time building geometry restraints manager: 4.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 9660 1.33 - 1.45: 8634 1.45 - 1.58: 20057 1.58 - 1.70: 187 1.70 - 1.83: 353 Bond restraints: 38891 Sorted by residual: bond pdb=" CA GLY Y 105 " pdb=" C GLY Y 105 " ideal model delta sigma weight residual 1.511 1.685 -0.174 1.40e-02 5.10e+03 1.54e+02 bond pdb=" CA ILE Z 450 " pdb=" C ILE Z 450 " ideal model delta sigma weight residual 1.522 1.448 0.074 1.16e-02 7.43e+03 4.09e+01 bond pdb=" CA THR Z 449 " pdb=" C THR Z 449 " ideal model delta sigma weight residual 1.530 1.459 0.071 1.17e-02 7.31e+03 3.71e+01 bond pdb=" O3' DA T 30 " pdb=" P DT T 31 " ideal model delta sigma weight residual 1.607 1.535 0.072 1.20e-02 6.94e+03 3.63e+01 bond pdb=" N ILE Z 450 " pdb=" CA ILE Z 450 " ideal model delta sigma weight residual 1.458 1.402 0.056 1.20e-02 6.94e+03 2.21e+01 ... (remaining 38886 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.54: 52153 3.54 - 7.08: 735 7.08 - 10.62: 44 10.62 - 14.16: 8 14.16 - 17.70: 4 Bond angle restraints: 52944 Sorted by residual: angle pdb=" N ARG Y 104 " pdb=" CA ARG Y 104 " pdb=" C ARG Y 104 " ideal model delta sigma weight residual 113.15 128.35 -15.20 1.19e+00 7.06e-01 1.63e+02 angle pdb=" N THR Z 449 " pdb=" CA THR Z 449 " pdb=" C THR Z 449 " ideal model delta sigma weight residual 111.28 94.49 16.79 1.35e+00 5.49e-01 1.55e+02 angle pdb=" N ILE Z 450 " pdb=" CA ILE Z 450 " pdb=" C ILE Z 450 " ideal model delta sigma weight residual 109.21 94.18 15.03 1.36e+00 5.41e-01 1.22e+02 angle pdb=" N GLY Z 423 " pdb=" CA GLY Z 423 " pdb=" C GLY Z 423 " ideal model delta sigma weight residual 114.69 127.01 -12.32 1.19e+00 7.06e-01 1.07e+02 angle pdb=" N LYS Z 447 " pdb=" CA LYS Z 447 " pdb=" C LYS Z 447 " ideal model delta sigma weight residual 109.15 96.48 12.67 1.44e+00 4.82e-01 7.74e+01 ... (remaining 52939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.28: 22599 23.28 - 46.57: 752 46.57 - 69.85: 193 69.85 - 93.14: 18 93.14 - 116.42: 1 Dihedral angle restraints: 23563 sinusoidal: 10453 harmonic: 13110 Sorted by residual: dihedral pdb=" C4' A P 36 " pdb=" C3' A P 36 " pdb=" C2' A P 36 " pdb=" C1' A P 36 " ideal model delta sinusoidal sigma weight residual 36.34 -32.94 69.28 1 3.10e+00 1.04e-01 6.46e+02 dihedral pdb=" O4' A P 36 " pdb=" C4' A P 36 " pdb=" C3' A P 36 " pdb=" C2' A P 36 " ideal model delta sinusoidal sigma weight residual -35.15 29.75 -64.90 1 4.00e+00 6.25e-02 3.45e+02 dihedral pdb=" O4' A P 36 " pdb=" C2' A P 36 " pdb=" C1' A P 36 " pdb=" C3' A P 36 " ideal model delta sinusoidal sigma weight residual 25.59 -25.31 50.91 3 3.80e+00 6.93e-02 1.40e+02 ... (remaining 23560 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 5089 0.087 - 0.175: 772 0.175 - 0.262: 59 0.262 - 0.350: 8 0.350 - 0.437: 3 Chirality restraints: 5931 Sorted by residual: chirality pdb=" CA ARG Y 104 " pdb=" N ARG Y 104 " pdb=" C ARG Y 104 " pdb=" CB ARG Y 104 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.78e+00 chirality pdb=" CA LYS Z 268 " pdb=" N LYS Z 268 " pdb=" C LYS Z 268 " pdb=" CB LYS Z 268 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.57e+00 chirality pdb=" CA SER Y 20 " pdb=" N SER Y 20 " pdb=" C SER Y 20 " pdb=" CB SER Y 20 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.58e+00 ... (remaining 5928 not shown) Planarity restraints: 6516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY Y 105 " 0.031 2.00e-02 2.50e+03 7.03e-02 4.95e+01 pdb=" C GLY Y 105 " -0.121 2.00e-02 2.50e+03 pdb=" O GLY Y 105 " 0.047 2.00e-02 2.50e+03 pdb=" N VAL Y 106 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA T 30 " 0.053 2.00e-02 2.50e+03 2.69e-02 1.98e+01 pdb=" N9 DA T 30 " -0.056 2.00e-02 2.50e+03 pdb=" C8 DA T 30 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DA T 30 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA T 30 " -0.015 2.00e-02 2.50e+03 pdb=" C6 DA T 30 " 0.036 2.00e-02 2.50e+03 pdb=" N6 DA T 30 " 0.000 2.00e-02 2.50e+03 pdb=" N1 DA T 30 " 0.000 2.00e-02 2.50e+03 pdb=" C2 DA T 30 " -0.000 2.00e-02 2.50e+03 pdb=" N3 DA T 30 " -0.020 2.00e-02 2.50e+03 pdb=" C4 DA T 30 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 872 " 0.019 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C THR B 872 " -0.063 2.00e-02 2.50e+03 pdb=" O THR B 872 " 0.023 2.00e-02 2.50e+03 pdb=" N LEU B 873 " 0.021 2.00e-02 2.50e+03 ... (remaining 6513 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 162 2.45 - 3.06: 25349 3.06 - 3.68: 53589 3.68 - 4.29: 85449 4.29 - 4.90: 141160 Nonbonded interactions: 305709 Sorted by model distance: nonbonded pdb=" OE2 GLU Z 417 " pdb=" NH1 ARG Z 516 " model vdw 1.841 3.120 nonbonded pdb=" OH TYR B 367 " pdb=" OE2 GLU B 611 " model vdw 2.038 3.040 nonbonded pdb=" OD2 ASP B 851 " pdb=" OH TYR L 17 " model vdw 2.059 3.040 nonbonded pdb=" NZ LYS B 327 " pdb=" CE3 TRP Z 250 " model vdw 2.090 3.420 nonbonded pdb=" OE1 GLN G 60 " pdb=" NH2 ARG G 63 " model vdw 2.094 3.120 ... (remaining 305704 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=0.65 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.510 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: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 44.710 Find NCS groups from input model: 0.210 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:1.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 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 : 0.012 0.691 38922 Z= 0.569 Angle : 1.148 39.596 52983 Z= 0.663 Chirality : 0.062 0.437 5931 Planarity : 0.006 0.086 6516 Dihedral : 12.434 116.421 15089 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.28 % Favored : 95.48 % Rotamer: Outliers : 0.33 % Allowed : 0.88 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.49 % 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: -3.26 (0.10), residues: 4467 helix: -3.80 (0.09), residues: 1332 sheet: -1.58 (0.16), residues: 706 loop : -1.26 (0.11), residues: 2429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG A 797 TYR 0.045 0.004 TYR B 752 PHE 0.044 0.004 PHE B 805 TRP 0.046 0.005 TRP A 570 HIS 0.021 0.003 HIS G 9 Details of bonding type rmsd/Z covalent geometry : bond 0.01140 / 0.56 (38891) covalent geometry : angle 1.08004 / 0.66 (52944) hydrogen bonds : bond 0.26284 / 17.67 ( 1416) hydrogen bonds : angle 10.01427 / 6.97 ( 3884) metal coordination : bond 0.16205 / 9.42 ( 31) metal coordination : angle 14.36008 / 11.14 ( 39) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8934 Ramachandran restraints generated. 4467 Oldfield, 0 Emsley, 4467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8934 Ramachandran restraints generated. 4467 Oldfield, 0 Emsley, 4467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 803 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.8974 (ttp) cc_final: 0.8692 (ttp) REVERT: A 321 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8366 (tm-30) REVERT: A 341 GLN cc_start: 0.8974 (mt0) cc_final: 0.8569 (mp10) REVERT: A 393 ILE cc_start: 0.9561 (mt) cc_final: 0.8953 (tp) REVERT: A 514 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7296 (mt-10) REVERT: A 637 MET cc_start: 0.8612 (ptm) cc_final: 0.8352 (ptp) REVERT: A 796 LYS cc_start: 0.9315 (mttt) cc_final: 0.8899 (mtpp) REVERT: A 845 GLU cc_start: 0.8588 (tt0) cc_final: 0.8204 (tt0) REVERT: A 959 MET cc_start: 0.8712 (mtp) cc_final: 0.7799 (mtp) REVERT: A 1095 LEU cc_start: 0.9355 (mt) cc_final: 0.9095 (mt) REVERT: A 1161 LEU cc_start: 0.9740 (mt) cc_final: 0.9463 (mt) REVERT: A 1243 LEU cc_start: 0.9510 (tp) cc_final: 0.9078 (mt) REVERT: A 1292 MET cc_start: 0.9089 (mtm) cc_final: 0.8764 (mtp) REVERT: A 1296 MET cc_start: 0.8755 (mmm) cc_final: 0.8375 (mmm) REVERT: A 1361 ASP cc_start: 0.8311 (t0) cc_final: 0.7443 (t0) REVERT: A 1422 GLN cc_start: 0.8807 (mt0) cc_final: 0.8522 (mt0) REVERT: A 1437 ASP cc_start: 0.9279 (m-30) cc_final: 0.8381 (m-30) REVERT: A 1447 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8290 (mp0) REVERT: A 1451 MET cc_start: 0.8980 (mmm) cc_final: 0.8385 (mmm) REVERT: B 54 SER cc_start: 0.9180 (m) cc_final: 0.8950 (p) REVERT: B 200 MET cc_start: 0.8541 (ttm) cc_final: 0.8272 (ttm) REVERT: B 674 MET cc_start: 0.8136 (mmm) cc_final: 0.7845 (tpt) REVERT: B 796 MET cc_start: 0.8142 (mtm) cc_final: 0.7655 (mtp) REVERT: B 802 ASP cc_start: 0.8518 (m-30) cc_final: 0.8201 (m-30) REVERT: B 1092 ASP cc_start: 0.8791 (m-30) cc_final: 0.8236 (m-30) REVERT: B 1101 GLN cc_start: 0.8389 (mt0) cc_final: 0.7697 (mt0) REVERT: B 1118 VAL cc_start: 0.9651 (t) cc_final: 0.9308 (p) REVERT: B 1130 THR cc_start: 0.9181 (m) cc_final: 0.8706 (t) REVERT: B 1151 MET cc_start: 0.9108 (ptm) cc_final: 0.8527 (ptm) REVERT: B 1165 MET cc_start: 0.9313 (mtm) cc_final: 0.9039 (mtt) REVERT: D 64 THR cc_start: 0.8893 (m) cc_final: 0.8606 (p) REVERT: G 7 LEU cc_start: 0.9288 (mt) cc_final: 0.8686 (tp) REVERT: G 8 GLU cc_start: 0.8610 (mm-30) cc_final: 0.7892 (mm-30) REVERT: G 21 ASN cc_start: 0.9074 (m-40) cc_final: 0.8499 (t0) REVERT: G 28 GLN cc_start: 0.9153 (mt0) cc_final: 0.8753 (mt0) REVERT: G 34 VAL cc_start: 0.8272 (OUTLIER) cc_final: 0.7543 (p) REVERT: G 52 ASP cc_start: 0.6871 (m-30) cc_final: 0.6387 (m-30) REVERT: G 72 TYR cc_start: 0.8304 (p90) cc_final: 0.7085 (p90) REVERT: G 81 LYS cc_start: 0.8569 (ttpt) cc_final: 0.8339 (tptp) REVERT: G 86 ASP cc_start: 0.6925 (m-30) cc_final: 0.6044 (p0) REVERT: G 116 GLU cc_start: 0.9183 (mp0) cc_final: 0.8878 (pm20) REVERT: G 166 ASP cc_start: 0.9440 (m-30) cc_final: 0.9064 (p0) REVERT: H 43 VAL cc_start: 0.9353 (t) cc_final: 0.9128 (p) REVERT: H 60 ILE cc_start: 0.9603 (mt) cc_final: 0.9383 (tp) REVERT: H 98 ARG cc_start: 0.8509 (ttt90) cc_final: 0.8294 (ttt180) REVERT: I 25 TYR cc_start: 0.8297 (m-80) cc_final: 0.5348 (m-80) REVERT: I 57 LYS cc_start: 0.9386 (mttt) cc_final: 0.9029 (mtmm) REVERT: I 78 LEU cc_start: 0.9425 (mt) cc_final: 0.8679 (mt) REVERT: K 24 ASP cc_start: 0.8317 (t0) cc_final: 0.8024 (t0) REVERT: L 16 ILE cc_start: 0.9222 (mt) cc_final: 0.9001 (tp) REVERT: L 21 GLU cc_start: 0.9116 (tp30) cc_final: 0.8856 (tm-30) REVERT: Z 627 LYS cc_start: 0.8946 (pttt) cc_final: 0.8176 (tmtt) REVERT: Z 705 LEU cc_start: 0.9267 (tp) cc_final: 0.9040 (tp) REVERT: Z 738 SER cc_start: 0.8910 (m) cc_final: 0.8387 (p) outliers start: 13 outliers final: 5 residues processed: 815 average time/residue: 0.2510 time to fit residues: 321.5524 Evaluate side-chains 434 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 428 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain Y residue 37 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 40.0000 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 20.0000 chunk 424 optimal weight: 9.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 GLN A1093 GLN A1163 HIS A1230 GLN ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1462 GLN B 111 ASN B 265 GLN B 312 GLN B 518 HIS ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 825 GLN B1021 HIS B1094 GLN B1097 HIS B1142 ASN C 32 ASN C 265 HIS D 34 ASN D 38 HIS F 72 GLN G 4 HIS ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN I 45 GLN I 60 HIS I 84 HIS K 69 HIS Y 12 HIS Y 41 GLN Z 534 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.086476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.056240 restraints weight = 131682.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.058315 restraints weight = 60669.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.059646 restraints weight = 37722.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.060446 restraints weight = 28156.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.060877 restraints weight = 23679.153| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3039 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3039 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 38922 Z= 0.196 Angle : 0.838 15.646 52983 Z= 0.421 Chirality : 0.051 0.455 5931 Planarity : 0.006 0.065 6516 Dihedral : 14.444 149.759 6021 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.13 % Favored : 96.84 % Rotamer: Outliers : 1.69 % Allowed : 8.14 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.49 % 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: -1.80 (0.11), residues: 4467 helix: -1.69 (0.12), residues: 1381 sheet: -1.05 (0.17), residues: 712 loop : -0.80 (0.12), residues: 2374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG Z 190 TYR 0.033 0.002 TYR B 766 PHE 0.033 0.002 PHE Z 583 TRP 0.016 0.002 TRP B 27 HIS 0.016 0.002 HIS B 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.20 (38891) covalent geometry : angle 0.81721 / 0.42 (52944) hydrogen bonds : bond 0.05650 / 3.73 ( 1416) hydrogen bonds : angle 6.15698 / 4.29 ( 3884) metal coordination : bond 0.01415 / 0.89 ( 31) metal coordination : angle 6.95911 / 4.88 ( 39) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8934 Ramachandran restraints generated. 4467 Oldfield, 0 Emsley, 4467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8934 Ramachandran restraints generated. 4467 Oldfield, 0 Emsley, 4467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 493 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8843 (tmm) cc_final: 0.8593 (tmm) REVERT: A 48 GLU cc_start: 0.8794 (tt0) cc_final: 0.8443 (pt0) REVERT: A 58 MET cc_start: 0.8845 (ttp) cc_final: 0.7997 (tmm) REVERT: A 266 MET cc_start: 0.6153 (mmm) cc_final: 0.5701 (mmt) REVERT: A 341 GLN cc_start: 0.8805 (mt0) cc_final: 0.7745 (mt0) REVERT: A 388 MET cc_start: 0.8400 (mtm) cc_final: 0.8197 (mtp) REVERT: A 447 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7936 (mt-10) REVERT: A 514 GLU cc_start: 0.8509 (mt-10) cc_final: 0.7906 (mt-10) REVERT: A 565 MET cc_start: 0.9059 (tpp) cc_final: 0.8465 (tpp) REVERT: A 794 GLU cc_start: 0.7548 (tm-30) cc_final: 0.7230 (tm-30) REVERT: A 849 ASP cc_start: 0.8744 (m-30) cc_final: 0.8311 (m-30) REVERT: A 869 GLU cc_start: 0.8552 (pm20) cc_final: 0.8289 (pp20) REVERT: A 872 MET cc_start: 0.8267 (ttp) cc_final: 0.7933 (ttp) REVERT: A 894 ASP cc_start: 0.8579 (t0) cc_final: 0.8372 (t0) REVERT: A 1199 MET cc_start: 0.8830 (ppp) cc_final: 0.8586 (tmm) REVERT: A 1292 MET cc_start: 0.8985 (mtm) cc_final: 0.8649 (ptp) REVERT: A 1361 ASP cc_start: 0.7837 (t0) cc_final: 0.7468 (t0) REVERT: A 1403 ASP cc_start: 0.8493 (m-30) cc_final: 0.8241 (m-30) REVERT: A 1437 ASP cc_start: 0.8530 (m-30) cc_final: 0.8303 (m-30) REVERT: A 1451 MET cc_start: 0.8844 (mmm) cc_final: 0.8524 (tpp) REVERT: B 39 LEU cc_start: 0.8789 (mp) cc_final: 0.8554 (mp) REVERT: B 54 SER cc_start: 0.9359 (m) cc_final: 0.8765 (p) REVERT: B 529 MET cc_start: 0.8847 (mmm) cc_final: 0.8632 (mmm) REVERT: B 617 ASP cc_start: 0.8275 (t0) cc_final: 0.8018 (t0) REVERT: B 764 MET cc_start: 0.8241 (mmm) cc_final: 0.8035 (mmm) REVERT: B 796 MET cc_start: 0.8344 (mtm) cc_final: 0.8015 (mtp) REVERT: B 930 GLN cc_start: 0.8753 (mt0) cc_final: 0.8374 (mt0) REVERT: B 1092 ASP cc_start: 0.8670 (m-30) cc_final: 0.8287 (m-30) REVERT: B 1101 GLN cc_start: 0.8529 (mt0) cc_final: 0.8171 (mt0) REVERT: B 1118 VAL cc_start: 0.9730 (t) cc_final: 0.9428 (p) REVERT: B 1138 ARG cc_start: 0.9146 (mmm-85) cc_final: 0.8817 (mmm-85) REVERT: B 1151 MET cc_start: 0.9227 (ptm) cc_final: 0.8545 (ptm) REVERT: D 34 ASN cc_start: 0.5818 (OUTLIER) cc_final: 0.5592 (t0) REVERT: D 44 ARG cc_start: 0.9290 (tpp-160) cc_final: 0.8926 (tpm170) REVERT: D 64 THR cc_start: 0.8904 (m) cc_final: 0.8597 (p) REVERT: D 128 GLN cc_start: 0.9742 (tp-100) cc_final: 0.9447 (mm110) REVERT: F 52 ILE cc_start: 0.9474 (OUTLIER) cc_final: 0.9215 (tp) REVERT: F 62 ARG cc_start: 0.8809 (tmm-80) cc_final: 0.8104 (ttm-80) REVERT: G 3 TYR cc_start: 0.7984 (m-80) cc_final: 0.7784 (m-80) REVERT: G 7 LEU cc_start: 0.9169 (mt) cc_final: 0.8602 (tp) REVERT: G 8 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8019 (mm-30) REVERT: G 21 ASN cc_start: 0.9096 (m-40) cc_final: 0.8452 (t0) REVERT: G 28 GLN cc_start: 0.9126 (mt0) cc_final: 0.8809 (mt0) REVERT: G 72 TYR cc_start: 0.8522 (p90) cc_final: 0.8049 (p90) REVERT: G 85 VAL cc_start: 0.9573 (OUTLIER) cc_final: 0.9210 (t) REVERT: G 86 ASP cc_start: 0.7339 (m-30) cc_final: 0.6333 (p0) REVERT: G 140 ASP cc_start: 0.9179 (m-30) cc_final: 0.8922 (p0) REVERT: G 141 ASP cc_start: 0.6037 (m-30) cc_final: 0.5306 (m-30) REVERT: H 98 ARG cc_start: 0.8525 (ttt90) cc_final: 0.8222 (ttt180) REVERT: H 145 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.7559 (ttt) REVERT: I 23 MET cc_start: 0.7342 (pmm) cc_final: 0.7127 (pmm) REVERT: I 25 TYR cc_start: 0.7642 (m-80) cc_final: 0.7245 (m-80) REVERT: I 46 GLN cc_start: 0.8466 (tm-30) cc_final: 0.8207 (tm-30) REVERT: I 75 ASP cc_start: 0.8031 (t0) cc_final: 0.7443 (t0) REVERT: K 24 ASP cc_start: 0.8490 (t0) cc_final: 0.8075 (t0) REVERT: K 102 GLU cc_start: 0.8036 (pp20) cc_final: 0.7630 (pp20) REVERT: K 103 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7868 (mm-30) REVERT: L 21 GLU cc_start: 0.9153 (tp30) cc_final: 0.8861 (tm-30) REVERT: L 44 MET cc_start: 0.8741 (mmm) cc_final: 0.7527 (mmm) REVERT: Y 64 MET cc_start: 0.9151 (mpp) cc_final: 0.8896 (ptp) REVERT: Z 288 ASP cc_start: 0.9274 (OUTLIER) cc_final: 0.8842 (t70) REVERT: Z 307 MET cc_start: 0.9262 (tpp) cc_final: 0.9016 (tpp) REVERT: Z 508 MET cc_start: 0.9136 (pmm) cc_final: 0.8805 (pmm) REVERT: Z 738 SER cc_start: 0.8950 (m) cc_final: 0.8673 (p) outliers start: 67 outliers final: 32 residues processed: 537 average time/residue: 0.2314 time to fit residues: 203.5314 Evaluate side-chains 427 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 390 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1115 LYS Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 958 CYS Chi-restraints excluded: chain B residue 1081 ASP Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 34 ASN Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 122 GLU Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain H residue 21 LYS Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain Y residue 22 VAL Chi-restraints excluded: chain Y residue 37 ASP Chi-restraints excluded: chain Z residue 190 ARG Chi-restraints excluded: chain Z residue 288 ASP Chi-restraints excluded: chain Z residue 580 ASP Chi-restraints excluded: chain Z residue 729 GLU Chi-restraints excluded: chain Z residue 739 THR Chi-restraints excluded: chain Z residue 745 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 370 optimal weight: 8.9990 chunk 295 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 356 optimal weight: 7.9990 chunk 246 optimal weight: 4.9990 chunk 225 optimal weight: 1.9990 chunk 430 optimal weight: 20.0000 chunk 343 optimal weight: 8.9990 chunk 411 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 GLN A 353 ASN ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 HIS ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 GLN ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN B 350 HIS B 825 GLN B 948 GLN B1120 ASN ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS F 49 GLN F 72 GLN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN J 52 HIS Z 519 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.082716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.052887 restraints weight = 133776.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.054793 restraints weight = 63660.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.056003 restraints weight = 40252.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.056757 restraints weight = 30397.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.057153 restraints weight = 25729.582| |-----------------------------------------------------------------------------| r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 38922 Z= 0.331 Angle : 0.812 16.793 52983 Z= 0.408 Chirality : 0.049 0.265 5931 Planarity : 0.005 0.066 6516 Dihedral : 14.309 147.130 6019 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.98 % Favored : 95.99 % Rotamer: Outliers : 2.55 % Allowed : 8.37 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.49 % 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: -1.06 (0.12), residues: 4467 helix: -0.53 (0.13), residues: 1408 sheet: -0.81 (0.17), residues: 723 loop : -0.66 (0.12), residues: 2336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B1091 TYR 0.027 0.002 TYR B 766 PHE 0.019 0.002 PHE G 119 TRP 0.016 0.002 TRP B 27 HIS 0.010 0.002 HIS B 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00721 / 0.33 (38891) covalent geometry : angle 0.79461 / 0.41 (52944) hydrogen bonds : bond 0.04961 / 3.29 ( 1416) hydrogen bonds : angle 5.70982 / 3.99 ( 3884) metal coordination : bond 0.01529 / 0.98 ( 31) metal coordination : angle 6.15583 / 4.11 ( 39) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8934 Ramachandran restraints generated. 4467 Oldfield, 0 Emsley, 4467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8934 Ramachandran restraints generated. 4467 Oldfield, 0 Emsley, 4467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 405 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8566 (tt0) cc_final: 0.8314 (pt0) REVERT: A 58 MET cc_start: 0.8836 (ttp) cc_final: 0.7984 (tmm) REVERT: A 148 CYS cc_start: 0.8782 (m) cc_final: 0.8398 (p) REVERT: A 266 MET cc_start: 0.6009 (mmm) cc_final: 0.5732 (mmt) REVERT: A 469 MET cc_start: 0.8582 (mtp) cc_final: 0.8250 (mtp) REVERT: A 501 MET cc_start: 0.9003 (mtp) cc_final: 0.8730 (mtp) REVERT: A 514 GLU cc_start: 0.8503 (mt-10) cc_final: 0.7365 (mt-10) REVERT: A 561 MET cc_start: 0.8559 (mtt) cc_final: 0.8193 (mtt) REVERT: A 845 GLU cc_start: 0.8206 (pp20) cc_final: 0.7810 (pp20) REVERT: A 849 ASP cc_start: 0.8771 (m-30) cc_final: 0.8375 (m-30) REVERT: A 869 GLU cc_start: 0.8530 (pm20) cc_final: 0.8233 (pp20) REVERT: A 1038 THR cc_start: 0.9147 (OUTLIER) cc_final: 0.8719 (p) REVERT: A 1228 MET cc_start: 0.8510 (pmm) cc_final: 0.8280 (pmm) REVERT: A 1292 MET cc_start: 0.8900 (mtm) cc_final: 0.8679 (mtp) REVERT: A 1296 MET cc_start: 0.8587 (mmm) cc_final: 0.8216 (mmm) REVERT: A 1403 ASP cc_start: 0.8638 (m-30) cc_final: 0.8422 (m-30) REVERT: A 1422 GLN cc_start: 0.8880 (mt0) cc_final: 0.8665 (mm-40) REVERT: A 1451 MET cc_start: 0.8896 (mmm) cc_final: 0.8639 (tpp) REVERT: B 529 MET cc_start: 0.8891 (mmm) cc_final: 0.8615 (mmm) REVERT: B 908 MET cc_start: 0.8769 (tmm) cc_final: 0.8522 (ppp) REVERT: B 1092 ASP cc_start: 0.8491 (m-30) cc_final: 0.8240 (m-30) REVERT: B 1101 GLN cc_start: 0.8662 (mt0) cc_final: 0.8046 (mt0) REVERT: B 1109 GLU cc_start: 0.8012 (mp0) cc_final: 0.7748 (mp0) REVERT: B 1118 VAL cc_start: 0.9685 (t) cc_final: 0.9404 (p) REVERT: B 1157 LEU cc_start: 0.9437 (tt) cc_final: 0.9185 (tt) REVERT: B 1161 GLU cc_start: 0.9104 (mt-10) cc_final: 0.8763 (mt-10) REVERT: D 62 MET cc_start: 0.9139 (mmm) cc_final: 0.8876 (mmm) REVERT: D 64 THR cc_start: 0.8953 (m) cc_final: 0.8689 (p) REVERT: D 128 GLN cc_start: 0.9790 (tp-100) cc_final: 0.9404 (mm110) REVERT: F 52 ILE cc_start: 0.9512 (OUTLIER) cc_final: 0.9234 (tp) REVERT: F 84 GLU cc_start: 0.8286 (pm20) cc_final: 0.7998 (pm20) REVERT: F 95 LYS cc_start: 0.9633 (ttmm) cc_final: 0.9315 (ttpt) REVERT: G 21 ASN cc_start: 0.9063 (m-40) cc_final: 0.8421 (t0) REVERT: G 28 GLN cc_start: 0.9140 (mt0) cc_final: 0.8815 (mt0) REVERT: G 71 LYS cc_start: 0.8509 (pttm) cc_final: 0.8255 (pttm) REVERT: G 83 GLU cc_start: 0.9197 (tp30) cc_final: 0.8389 (tp30) REVERT: G 85 VAL cc_start: 0.9578 (OUTLIER) cc_final: 0.9171 (t) REVERT: G 86 ASP cc_start: 0.7469 (m-30) cc_final: 0.6494 (p0) REVERT: G 104 MET cc_start: 0.8707 (tmm) cc_final: 0.8235 (tmm) REVERT: G 105 SER cc_start: 0.8599 (m) cc_final: 0.8328 (p) REVERT: G 139 GLN cc_start: 0.8126 (tp40) cc_final: 0.7567 (mm-40) REVERT: I 23 MET cc_start: 0.7587 (pmm) cc_final: 0.7339 (pmm) REVERT: I 25 TYR cc_start: 0.8153 (m-80) cc_final: 0.7707 (m-80) REVERT: K 24 ASP cc_start: 0.8610 (t0) cc_final: 0.8227 (t0) REVERT: K 38 GLU cc_start: 0.8292 (mm-30) cc_final: 0.8092 (mm-30) REVERT: K 103 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7795 (mm-30) REVERT: L 21 GLU cc_start: 0.9203 (tp30) cc_final: 0.8904 (tm-30) REVERT: L 44 MET cc_start: 0.8872 (mmm) cc_final: 0.7937 (mmm) REVERT: Z 197 MET cc_start: 0.7994 (tpp) cc_final: 0.7525 (tpt) REVERT: Z 288 ASP cc_start: 0.9423 (OUTLIER) cc_final: 0.8897 (t70) REVERT: Z 307 MET cc_start: 0.9246 (tpp) cc_final: 0.9000 (tpp) REVERT: Z 460 MET cc_start: 0.8922 (mmp) cc_final: 0.8571 (mmp) REVERT: Z 481 ILE cc_start: 0.9603 (OUTLIER) cc_final: 0.9126 (mp) REVERT: Z 508 MET cc_start: 0.9317 (pmm) cc_final: 0.9009 (pmm) outliers start: 101 outliers final: 63 residues processed: 474 average time/residue: 0.2266 time to fit residues: 176.8133 Evaluate side-chains 431 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 363 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1115 LYS Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1458 ILE Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 958 CYS Chi-restraints excluded: chain B residue 964 ASP Chi-restraints excluded: chain B residue 1081 ASP Chi-restraints excluded: chain B residue 1093 CYS Chi-restraints excluded: chain B residue 1130 THR Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 122 GLU Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 129 LYS Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain H residue 21 LYS Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 92 LYS Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain Y residue 22 VAL Chi-restraints excluded: chain Y residue 71 VAL Chi-restraints excluded: chain Z residue 190 ARG Chi-restraints excluded: chain Z residue 288 ASP Chi-restraints excluded: chain Z residue 481 ILE Chi-restraints excluded: chain Z residue 729 GLU Chi-restraints excluded: chain Z residue 739 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 146 optimal weight: 5.9990 chunk 357 optimal weight: 8.9990 chunk 29 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 chunk 263 optimal weight: 3.9990 chunk 294 optimal weight: 6.9990 chunk 144 optimal weight: 0.7980 chunk 289 optimal weight: 10.0000 chunk 390 optimal weight: 50.0000 chunk 446 optimal weight: 20.0000 chunk 396 optimal weight: 10.0000 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 757 GLN A 945 ASN ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 948 GLN ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 ASN F 72 GLN Z 592 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.082619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.052940 restraints weight = 132364.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.054848 restraints weight = 62648.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 73)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.056060 restraints weight = 39632.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.056812 restraints weight = 29869.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.057281 restraints weight = 25223.213| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 38922 Z= 0.244 Angle : 0.722 16.550 52983 Z= 0.362 Chirality : 0.047 0.232 5931 Planarity : 0.005 0.060 6516 Dihedral : 14.223 144.254 6017 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.96 % Favored : 95.99 % Rotamer: Outliers : 2.57 % Allowed : 9.53 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.49 % 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: -0.62 (0.12), residues: 4467 helix: 0.16 (0.13), residues: 1407 sheet: -0.64 (0.18), residues: 723 loop : -0.61 (0.13), residues: 2337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 151 TYR 0.024 0.002 TYR B 766 PHE 0.016 0.001 PHE A 668 TRP 0.017 0.002 TRP C 49 HIS 0.008 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.24 (38891) covalent geometry : angle 0.70636 / 0.36 (52944) hydrogen bonds : bond 0.04070 / 2.69 ( 1416) hydrogen bonds : angle 5.37413 / 3.75 ( 3884) metal coordination : bond 0.01250 / 0.81 ( 31) metal coordination : angle 5.54088 / 3.49 ( 39) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8934 Ramachandran restraints generated. 4467 Oldfield, 0 Emsley, 4467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8934 Ramachandran restraints generated. 4467 Oldfield, 0 Emsley, 4467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 386 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.8822 (ttp) cc_final: 0.7833 (tmm) REVERT: A 148 CYS cc_start: 0.8834 (m) cc_final: 0.8322 (p) REVERT: A 329 MET cc_start: 0.8278 (ptt) cc_final: 0.7827 (ttp) REVERT: A 447 GLU cc_start: 0.8366 (mt-10) cc_final: 0.7829 (mt-10) REVERT: A 514 GLU cc_start: 0.8556 (mt-10) cc_final: 0.7335 (mt-10) REVERT: A 561 MET cc_start: 0.8525 (mtt) cc_final: 0.8216 (mtt) REVERT: A 845 GLU cc_start: 0.8253 (pp20) cc_final: 0.7814 (pp20) REVERT: A 849 ASP cc_start: 0.8896 (m-30) cc_final: 0.8440 (m-30) REVERT: A 1038 THR cc_start: 0.9117 (OUTLIER) cc_final: 0.8721 (p) REVERT: A 1292 MET cc_start: 0.8907 (mtm) cc_final: 0.8590 (mtp) REVERT: A 1296 MET cc_start: 0.8596 (mmm) cc_final: 0.8341 (mmm) REVERT: A 1403 ASP cc_start: 0.8702 (m-30) cc_final: 0.8460 (m-30) REVERT: A 1422 GLN cc_start: 0.8863 (mt0) cc_final: 0.8487 (mt0) REVERT: A 1472 ASP cc_start: 0.8357 (p0) cc_final: 0.7999 (p0) REVERT: B 200 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8392 (ttm) REVERT: B 297 MET cc_start: 0.9137 (mmm) cc_final: 0.8875 (mmm) REVERT: B 365 LEU cc_start: 0.9891 (OUTLIER) cc_final: 0.9607 (tt) REVERT: B 513 GLU cc_start: 0.8662 (tp30) cc_final: 0.8040 (tm-30) REVERT: B 529 MET cc_start: 0.8878 (mmm) cc_final: 0.8601 (mmm) REVERT: B 908 MET cc_start: 0.8852 (tmm) cc_final: 0.8429 (ppp) REVERT: B 1092 ASP cc_start: 0.8348 (m-30) cc_final: 0.8015 (m-30) REVERT: B 1101 GLN cc_start: 0.8719 (mt0) cc_final: 0.7925 (mt0) REVERT: B 1131 ARG cc_start: 0.8446 (mmm160) cc_final: 0.8127 (mmm160) REVERT: D 64 THR cc_start: 0.8947 (m) cc_final: 0.8685 (p) REVERT: F 52 ILE cc_start: 0.9480 (OUTLIER) cc_final: 0.9198 (tp) REVERT: F 95 LYS cc_start: 0.9613 (ttmm) cc_final: 0.9373 (ttpt) REVERT: F 98 LYS cc_start: 0.9220 (OUTLIER) cc_final: 0.8435 (mtmm) REVERT: G 21 ASN cc_start: 0.9054 (m-40) cc_final: 0.8450 (t0) REVERT: G 28 GLN cc_start: 0.9152 (mt0) cc_final: 0.8823 (mt0) REVERT: G 83 GLU cc_start: 0.9103 (tp30) cc_final: 0.8244 (tp30) REVERT: G 104 MET cc_start: 0.8594 (tmm) cc_final: 0.8160 (tmm) REVERT: G 139 GLN cc_start: 0.7835 (tp40) cc_final: 0.7398 (tp40) REVERT: I 23 MET cc_start: 0.7552 (pmm) cc_final: 0.7162 (pmm) REVERT: I 25 TYR cc_start: 0.8114 (m-80) cc_final: 0.7592 (m-80) REVERT: I 60 HIS cc_start: 0.8458 (t70) cc_final: 0.8251 (t-170) REVERT: K 24 ASP cc_start: 0.8529 (t0) cc_final: 0.8185 (t0) REVERT: K 102 GLU cc_start: 0.8284 (pp20) cc_final: 0.8061 (pp20) REVERT: L 21 GLU cc_start: 0.9203 (tp30) cc_final: 0.8920 (tm-30) REVERT: L 44 MET cc_start: 0.8835 (mmm) cc_final: 0.7710 (mmm) REVERT: Z 197 MET cc_start: 0.8220 (tpp) cc_final: 0.7770 (tpt) REVERT: Z 278 TRP cc_start: 0.8808 (m-90) cc_final: 0.8515 (m100) REVERT: Z 288 ASP cc_start: 0.9385 (OUTLIER) cc_final: 0.8854 (t70) REVERT: Z 307 MET cc_start: 0.9323 (tpp) cc_final: 0.9090 (tpp) REVERT: Z 460 MET cc_start: 0.9023 (mmp) cc_final: 0.8670 (mmp) REVERT: Z 481 ILE cc_start: 0.9632 (OUTLIER) cc_final: 0.9146 (mp) REVERT: Z 508 MET cc_start: 0.9337 (pmm) cc_final: 0.9043 (pmm) outliers start: 102 outliers final: 55 residues processed: 455 average time/residue: 0.2163 time to fit residues: 163.6421 Evaluate side-chains 417 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 355 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 794 GLU Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1115 LYS Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1458 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 958 CYS Chi-restraints excluded: chain B residue 964 ASP Chi-restraints excluded: chain B residue 1081 ASP Chi-restraints excluded: chain B residue 1093 CYS Chi-restraints excluded: chain B residue 1130 THR Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 98 LYS Chi-restraints excluded: chain F residue 122 GLU Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain Y residue 71 VAL Chi-restraints excluded: chain Z residue 190 ARG Chi-restraints excluded: chain Z residue 288 ASP Chi-restraints excluded: chain Z residue 481 ILE Chi-restraints excluded: chain Z residue 580 ASP Chi-restraints excluded: chain Z residue 729 GLU Chi-restraints excluded: chain Z residue 739 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 372 optimal weight: 1.9990 chunk 349 optimal weight: 0.8980 chunk 257 optimal weight: 0.8980 chunk 116 optimal weight: 9.9990 chunk 120 optimal weight: 5.9990 chunk 412 optimal weight: 2.9990 chunk 310 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 275 optimal weight: 0.0770 chunk 292 optimal weight: 7.9990 chunk 266 optimal weight: 0.8980 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 725 GLN ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 GLN F 72 GLN I 22 ASN Z 519 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.082966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.053031 restraints weight = 132064.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.054978 restraints weight = 61478.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.056211 restraints weight = 38409.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.056982 restraints weight = 28729.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.057440 restraints weight = 24144.854| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 38922 Z= 0.126 Angle : 0.664 14.850 52983 Z= 0.332 Chirality : 0.045 0.226 5931 Planarity : 0.004 0.054 6516 Dihedral : 14.048 143.589 6017 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.90 % Favored : 96.06 % Rotamer: Outliers : 1.92 % Allowed : 10.84 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.49 % 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: -0.34 (0.12), residues: 4467 helix: 0.50 (0.14), residues: 1408 sheet: -0.48 (0.18), residues: 739 loop : -0.51 (0.13), residues: 2320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 230 TYR 0.022 0.001 TYR A 669 PHE 0.018 0.001 PHE A 458 TRP 0.016 0.001 TRP C 49 HIS 0.007 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (38891) covalent geometry : angle 0.65052 / 0.33 (52944) hydrogen bonds : bond 0.03661 / 2.43 ( 1416) hydrogen bonds : angle 5.14110 / 3.59 ( 3884) metal coordination : bond 0.00731 / 0.46 ( 31) metal coordination : angle 4.88180 / 2.99 ( 39) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8934 Ramachandran restraints generated. 4467 Oldfield, 0 Emsley, 4467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8934 Ramachandran restraints generated. 4467 Oldfield, 0 Emsley, 4467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 406 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 CYS cc_start: 0.8806 (m) cc_final: 0.8285 (p) REVERT: A 329 MET cc_start: 0.8302 (ptt) cc_final: 0.7867 (ttp) REVERT: A 467 MET cc_start: 0.8818 (mmt) cc_final: 0.8307 (mmt) REVERT: A 514 GLU cc_start: 0.8555 (mt-10) cc_final: 0.7700 (mt-10) REVERT: A 561 MET cc_start: 0.8387 (mtt) cc_final: 0.8136 (mtt) REVERT: A 845 GLU cc_start: 0.8240 (pp20) cc_final: 0.7760 (pp20) REVERT: A 849 ASP cc_start: 0.8859 (m-30) cc_final: 0.8491 (m-30) REVERT: A 868 MET cc_start: 0.8923 (mmm) cc_final: 0.8701 (mtp) REVERT: A 899 GLU cc_start: 0.8525 (pm20) cc_final: 0.8133 (mp0) REVERT: A 1038 THR cc_start: 0.9055 (OUTLIER) cc_final: 0.8661 (p) REVERT: A 1403 ASP cc_start: 0.8587 (m-30) cc_final: 0.8338 (m-30) REVERT: A 1422 GLN cc_start: 0.8878 (mt0) cc_final: 0.8628 (mm-40) REVERT: A 1472 ASP cc_start: 0.8346 (p0) cc_final: 0.7992 (p0) REVERT: B 176 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8412 (mm-30) REVERT: B 200 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8389 (ttm) REVERT: B 239 MET cc_start: 0.9081 (ttm) cc_final: 0.8818 (ttt) REVERT: B 297 MET cc_start: 0.9154 (mmm) cc_final: 0.8908 (mmm) REVERT: B 482 LEU cc_start: 0.9380 (mt) cc_final: 0.9144 (mt) REVERT: B 508 MET cc_start: 0.8595 (mtp) cc_final: 0.8068 (mtp) REVERT: B 513 GLU cc_start: 0.8666 (tp30) cc_final: 0.8043 (tm-30) REVERT: B 529 MET cc_start: 0.8815 (mmm) cc_final: 0.8580 (mmm) REVERT: B 603 MET cc_start: 0.7620 (mtm) cc_final: 0.7174 (ptt) REVERT: B 617 ASP cc_start: 0.8288 (t0) cc_final: 0.8016 (t0) REVERT: B 767 LEU cc_start: 0.9410 (mt) cc_final: 0.8707 (tt) REVERT: B 908 MET cc_start: 0.8783 (tmm) cc_final: 0.8358 (ppp) REVERT: B 1056 ASP cc_start: 0.8181 (p0) cc_final: 0.7963 (p0) REVERT: B 1092 ASP cc_start: 0.8337 (m-30) cc_final: 0.8043 (m-30) REVERT: B 1101 GLN cc_start: 0.8646 (mt0) cc_final: 0.7997 (mt0) REVERT: B 1161 GLU cc_start: 0.9100 (mt-10) cc_final: 0.8894 (tt0) REVERT: D 64 THR cc_start: 0.8879 (m) cc_final: 0.8634 (p) REVERT: E 94 MET cc_start: 0.8240 (ppp) cc_final: 0.8001 (ppp) REVERT: F 95 LYS cc_start: 0.9683 (ttmm) cc_final: 0.9321 (ttpt) REVERT: G 9 HIS cc_start: 0.7969 (m-70) cc_final: 0.7663 (m-70) REVERT: G 21 ASN cc_start: 0.8994 (m-40) cc_final: 0.8401 (t0) REVERT: G 28 GLN cc_start: 0.9141 (mt0) cc_final: 0.8793 (mt0) REVERT: G 83 GLU cc_start: 0.9016 (tp30) cc_final: 0.8009 (tp30) REVERT: G 104 MET cc_start: 0.8540 (tmm) cc_final: 0.8173 (tmm) REVERT: H 95 LYS cc_start: 0.9340 (ttmt) cc_final: 0.9019 (ttmm) REVERT: I 25 TYR cc_start: 0.7974 (m-80) cc_final: 0.7690 (m-80) REVERT: I 60 HIS cc_start: 0.8398 (t70) cc_final: 0.8163 (t-170) REVERT: K 24 ASP cc_start: 0.8498 (t0) cc_final: 0.8168 (t0) REVERT: K 102 GLU cc_start: 0.8284 (pp20) cc_final: 0.8063 (pp20) REVERT: L 21 GLU cc_start: 0.9153 (tp30) cc_final: 0.8722 (tp30) REVERT: L 44 MET cc_start: 0.8883 (mmm) cc_final: 0.7746 (mmm) REVERT: Y 50 TYR cc_start: 0.6144 (m-80) cc_final: 0.5675 (m-10) REVERT: Y 63 MET cc_start: 0.8775 (tpp) cc_final: 0.7886 (tmm) REVERT: Z 190 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.8000 (pmt-80) REVERT: Z 197 MET cc_start: 0.8273 (tpp) cc_final: 0.7871 (tpt) REVERT: Z 278 TRP cc_start: 0.8814 (m-90) cc_final: 0.8528 (m100) REVERT: Z 288 ASP cc_start: 0.9380 (OUTLIER) cc_final: 0.8857 (t70) REVERT: Z 307 MET cc_start: 0.9327 (tpp) cc_final: 0.9097 (tpp) REVERT: Z 460 MET cc_start: 0.9090 (mmp) cc_final: 0.8755 (mmp) REVERT: Z 481 ILE cc_start: 0.9653 (OUTLIER) cc_final: 0.9162 (mp) REVERT: Z 508 MET cc_start: 0.9356 (pmm) cc_final: 0.9093 (pmm) outliers start: 76 outliers final: 48 residues processed: 455 average time/residue: 0.2208 time to fit residues: 168.3737 Evaluate side-chains 426 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 373 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1115 LYS Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain A residue 1458 ILE Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 730 LYS Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 958 CYS Chi-restraints excluded: chain B residue 964 ASP Chi-restraints excluded: chain B residue 1081 ASP Chi-restraints excluded: chain B residue 1093 CYS Chi-restraints excluded: chain B residue 1130 THR Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain F residue 122 GLU Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 92 LYS Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain Y residue 22 VAL Chi-restraints excluded: chain Y residue 71 VAL Chi-restraints excluded: chain Z residue 190 ARG Chi-restraints excluded: chain Z residue 288 ASP Chi-restraints excluded: chain Z residue 481 ILE Chi-restraints excluded: chain Z residue 493 VAL Chi-restraints excluded: chain Z residue 580 ASP Chi-restraints excluded: chain Z residue 729 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 189 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 291 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 424 optimal weight: 7.9990 chunk 304 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 422 optimal weight: 30.0000 chunk 170 optimal weight: 7.9990 chunk 227 optimal weight: 30.0000 chunk 220 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 780 ASN A1230 GLN ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN B 631 GLN ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 GLN I 50 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.081602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.051848 restraints weight = 133746.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.053729 restraints weight = 63720.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.054940 restraints weight = 40358.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.055666 restraints weight = 30474.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.056131 restraints weight = 25820.343| |-----------------------------------------------------------------------------| r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 38922 Z= 0.287 Angle : 0.736 15.987 52983 Z= 0.366 Chirality : 0.046 0.213 5931 Planarity : 0.004 0.050 6516 Dihedral : 14.031 142.395 6016 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.32 % Favored : 95.63 % Rotamer: Outliers : 2.52 % Allowed : 11.04 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % 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: -0.15 (0.12), residues: 4467 helix: 0.82 (0.14), residues: 1416 sheet: -0.49 (0.18), residues: 740 loop : -0.47 (0.13), residues: 2311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 151 TYR 0.021 0.002 TYR A 413 PHE 0.020 0.002 PHE A 458 TRP 0.017 0.002 TRP C 49 HIS 0.007 0.001 HIS B 939 Details of bonding type rmsd/Z covalent geometry : bond 0.00624 / 0.29 (38891) covalent geometry : angle 0.72254 / 0.37 (52944) hydrogen bonds : bond 0.04224 / 2.85 ( 1416) hydrogen bonds : angle 5.18935 / 3.63 ( 3884) metal coordination : bond 0.01375 / 0.87 ( 31) metal coordination : angle 5.22449 / 3.23 ( 39) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8934 Ramachandran restraints generated. 4467 Oldfield, 0 Emsley, 4467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8934 Ramachandran restraints generated. 4467 Oldfield, 0 Emsley, 4467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 367 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.7910 (tmm) REVERT: A 104 MET cc_start: 0.9295 (mtp) cc_final: 0.8678 (tmm) REVERT: A 148 CYS cc_start: 0.8902 (m) cc_final: 0.8456 (p) REVERT: A 427 ILE cc_start: 0.9626 (OUTLIER) cc_final: 0.9343 (pt) REVERT: A 561 MET cc_start: 0.8453 (mtt) cc_final: 0.8161 (mtt) REVERT: A 634 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7702 (tm-30) REVERT: A 845 GLU cc_start: 0.8326 (pp20) cc_final: 0.7926 (pp20) REVERT: A 849 ASP cc_start: 0.8898 (m-30) cc_final: 0.8420 (m-30) REVERT: A 986 MET cc_start: 0.9071 (mtm) cc_final: 0.8810 (mtm) REVERT: A 1038 THR cc_start: 0.9174 (OUTLIER) cc_final: 0.8839 (p) REVERT: A 1403 ASP cc_start: 0.8698 (m-30) cc_final: 0.8485 (m-30) REVERT: A 1422 GLN cc_start: 0.8884 (mt0) cc_final: 0.8483 (mt0) REVERT: A 1451 MET cc_start: 0.8573 (tpp) cc_final: 0.8085 (mmm) REVERT: A 1472 ASP cc_start: 0.8227 (p0) cc_final: 0.7950 (p0) REVERT: B 200 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8522 (ttm) REVERT: B 239 MET cc_start: 0.9081 (ttm) cc_final: 0.8861 (ttt) REVERT: B 297 MET cc_start: 0.9162 (mmm) cc_final: 0.8743 (mmm) REVERT: B 410 ASN cc_start: 0.9398 (OUTLIER) cc_final: 0.9060 (t0) REVERT: B 513 GLU cc_start: 0.8700 (tp30) cc_final: 0.8105 (tm-30) REVERT: B 606 ASP cc_start: 0.8525 (t70) cc_final: 0.8254 (t0) REVERT: B 617 ASP cc_start: 0.8344 (t0) cc_final: 0.8097 (t0) REVERT: B 796 MET cc_start: 0.8483 (mtp) cc_final: 0.8226 (mtp) REVERT: B 908 MET cc_start: 0.8753 (tmm) cc_final: 0.8420 (tmm) REVERT: B 1089 MET cc_start: 0.8879 (mmp) cc_final: 0.8504 (mmm) REVERT: B 1092 ASP cc_start: 0.8298 (m-30) cc_final: 0.7989 (m-30) REVERT: B 1101 GLN cc_start: 0.8736 (mt0) cc_final: 0.8324 (mt0) REVERT: B 1131 ARG cc_start: 0.8478 (mmm160) cc_final: 0.8152 (mmm160) REVERT: D 62 MET cc_start: 0.9004 (mmm) cc_final: 0.8725 (mmm) REVERT: D 64 THR cc_start: 0.8906 (m) cc_final: 0.8664 (p) REVERT: F 95 LYS cc_start: 0.9636 (ttmm) cc_final: 0.9076 (ttpt) REVERT: G 9 HIS cc_start: 0.8013 (OUTLIER) cc_final: 0.7655 (m-70) REVERT: G 21 ASN cc_start: 0.9049 (m-40) cc_final: 0.8471 (t0) REVERT: G 28 GLN cc_start: 0.9101 (mt0) cc_final: 0.8763 (mt0) REVERT: G 104 MET cc_start: 0.8479 (tmm) cc_final: 0.8004 (tmm) REVERT: G 120 ASP cc_start: 0.9396 (p0) cc_final: 0.8996 (p0) REVERT: I 25 TYR cc_start: 0.8520 (m-80) cc_final: 0.8249 (m-80) REVERT: J 28 GLU cc_start: 0.8381 (mp0) cc_final: 0.8130 (mp0) REVERT: K 24 ASP cc_start: 0.8579 (t0) cc_final: 0.8250 (t0) REVERT: K 102 GLU cc_start: 0.8331 (pp20) cc_final: 0.8103 (pp20) REVERT: L 15 MET cc_start: 0.8536 (mmm) cc_final: 0.8057 (mmt) REVERT: L 44 MET cc_start: 0.8879 (mmm) cc_final: 0.7987 (mmm) REVERT: Y 50 TYR cc_start: 0.6173 (m-80) cc_final: 0.5870 (m-80) REVERT: Z 190 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.8048 (pmt-80) REVERT: Z 197 MET cc_start: 0.8335 (tpp) cc_final: 0.7938 (tpt) REVERT: Z 288 ASP cc_start: 0.9412 (OUTLIER) cc_final: 0.8941 (t70) REVERT: Z 307 MET cc_start: 0.9284 (tpp) cc_final: 0.9081 (tpp) REVERT: Z 460 MET cc_start: 0.9210 (mmp) cc_final: 0.8895 (mmp) REVERT: Z 481 ILE cc_start: 0.9664 (OUTLIER) cc_final: 0.9173 (mp) REVERT: Z 508 MET cc_start: 0.9281 (pmm) cc_final: 0.8979 (pmm) outliers start: 100 outliers final: 64 residues processed: 440 average time/residue: 0.2181 time to fit residues: 160.2038 Evaluate side-chains 426 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 353 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 794 GLU Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1115 LYS Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1458 ILE Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 958 CYS Chi-restraints excluded: chain B residue 964 ASP Chi-restraints excluded: chain B residue 1081 ASP Chi-restraints excluded: chain B residue 1093 CYS Chi-restraints excluded: chain B residue 1130 THR Chi-restraints excluded: chain B residue 1151 MET Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 122 GLU Chi-restraints excluded: chain G residue 9 HIS Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 92 LYS Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain Y residue 22 VAL Chi-restraints excluded: chain Y residue 71 VAL Chi-restraints excluded: chain Z residue 190 ARG Chi-restraints excluded: chain Z residue 288 ASP Chi-restraints excluded: chain Z residue 481 ILE Chi-restraints excluded: chain Z residue 493 VAL Chi-restraints excluded: chain Z residue 580 ASP Chi-restraints excluded: chain Z residue 729 GLU Chi-restraints excluded: chain Z residue 739 THR Chi-restraints excluded: chain Z residue 745 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 7 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 225 optimal weight: 4.9990 chunk 312 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 306 optimal weight: 2.9990 chunk 393 optimal weight: 50.0000 chunk 415 optimal weight: 7.9990 chunk 342 optimal weight: 1.9990 chunk 266 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 GLN I 60 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.082902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.053212 restraints weight = 132413.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.055154 restraints weight = 61871.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.056408 restraints weight = 38958.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.057175 restraints weight = 29227.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.057604 restraints weight = 24699.001| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 38922 Z= 0.141 Angle : 0.655 15.064 52983 Z= 0.328 Chirality : 0.045 0.214 5931 Planarity : 0.004 0.048 6516 Dihedral : 13.924 141.986 6016 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.01 % Favored : 95.95 % Rotamer: Outliers : 1.97 % Allowed : 11.82 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % 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: 0.08 (0.12), residues: 4467 helix: 1.04 (0.14), residues: 1417 sheet: -0.29 (0.18), residues: 735 loop : -0.38 (0.13), residues: 2315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 84 TYR 0.023 0.001 TYR A 669 PHE 0.018 0.001 PHE A 458 TRP 0.020 0.001 TRP Z 278 HIS 0.015 0.001 HIS I 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (38891) covalent geometry : angle 0.64189 / 0.33 (52944) hydrogen bonds : bond 0.03556 / 2.37 ( 1416) hydrogen bonds : angle 4.97736 / 3.47 ( 3884) metal coordination : bond 0.00789 / 0.51 ( 31) metal coordination : angle 4.82756 / 2.89 ( 39) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8934 Ramachandran restraints generated. 4467 Oldfield, 0 Emsley, 4467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8934 Ramachandran restraints generated. 4467 Oldfield, 0 Emsley, 4467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 386 time to evaluate : 1.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 CYS cc_start: 0.8864 (m) cc_final: 0.8390 (p) REVERT: A 329 MET cc_start: 0.8473 (ptt) cc_final: 0.8008 (ptt) REVERT: A 334 ARG cc_start: 0.8689 (mmp80) cc_final: 0.8438 (mmp80) REVERT: A 427 ILE cc_start: 0.9642 (OUTLIER) cc_final: 0.9357 (pt) REVERT: A 514 GLU cc_start: 0.8545 (mt-10) cc_final: 0.7774 (mt-10) REVERT: A 561 MET cc_start: 0.8426 (mtt) cc_final: 0.8173 (mtt) REVERT: A 634 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7707 (tm-30) REVERT: A 845 GLU cc_start: 0.8281 (pp20) cc_final: 0.7860 (pp20) REVERT: A 849 ASP cc_start: 0.8882 (m-30) cc_final: 0.8629 (m-30) REVERT: A 1038 THR cc_start: 0.9103 (OUTLIER) cc_final: 0.8717 (p) REVERT: A 1085 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7829 (mt-10) REVERT: A 1296 MET cc_start: 0.8681 (mmm) cc_final: 0.8420 (mmp) REVERT: A 1403 ASP cc_start: 0.8650 (m-30) cc_final: 0.8416 (m-30) REVERT: A 1422 GLN cc_start: 0.8876 (mt0) cc_final: 0.8480 (mt0) REVERT: A 1472 ASP cc_start: 0.8232 (p0) cc_final: 0.7885 (p0) REVERT: B 176 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8385 (mm-30) REVERT: B 200 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8464 (ttm) REVERT: B 297 MET cc_start: 0.9059 (mmm) cc_final: 0.8774 (mmm) REVERT: B 482 LEU cc_start: 0.9357 (mt) cc_final: 0.9135 (mt) REVERT: B 508 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.8086 (mtp) REVERT: B 513 GLU cc_start: 0.8676 (tp30) cc_final: 0.8089 (tm-30) REVERT: B 603 MET cc_start: 0.7597 (mtm) cc_final: 0.7170 (ptt) REVERT: B 606 ASP cc_start: 0.8502 (t70) cc_final: 0.8235 (t0) REVERT: B 616 THR cc_start: 0.9557 (OUTLIER) cc_final: 0.9181 (p) REVERT: B 908 MET cc_start: 0.8711 (tmm) cc_final: 0.8346 (tmm) REVERT: B 1056 ASP cc_start: 0.8156 (p0) cc_final: 0.7880 (p0) REVERT: B 1089 MET cc_start: 0.8826 (mmp) cc_final: 0.8445 (mmm) REVERT: B 1092 ASP cc_start: 0.8296 (m-30) cc_final: 0.7987 (m-30) REVERT: B 1101 GLN cc_start: 0.8729 (mt0) cc_final: 0.8001 (mt0) REVERT: D 64 THR cc_start: 0.8892 (m) cc_final: 0.8656 (p) REVERT: E 94 MET cc_start: 0.8362 (ppp) cc_final: 0.8092 (ppp) REVERT: E 151 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.8180 (ptp) REVERT: F 95 LYS cc_start: 0.9590 (ttmm) cc_final: 0.9384 (ttpt) REVERT: G 21 ASN cc_start: 0.9013 (m-40) cc_final: 0.8456 (t0) REVERT: G 28 GLN cc_start: 0.9148 (mt0) cc_final: 0.8775 (mt0) REVERT: G 104 MET cc_start: 0.8444 (tmm) cc_final: 0.8042 (tmm) REVERT: G 120 ASP cc_start: 0.9271 (p0) cc_final: 0.8892 (p0) REVERT: G 139 GLN cc_start: 0.8379 (mm-40) cc_final: 0.7339 (tp40) REVERT: G 141 ASP cc_start: 0.7630 (p0) cc_final: 0.6876 (p0) REVERT: K 24 ASP cc_start: 0.8505 (t0) cc_final: 0.8185 (t0) REVERT: K 102 GLU cc_start: 0.8309 (pp20) cc_final: 0.8080 (pp20) REVERT: L 15 MET cc_start: 0.8538 (mmm) cc_final: 0.8156 (mmt) REVERT: L 44 MET cc_start: 0.8922 (mmm) cc_final: 0.7798 (mmm) REVERT: Y 63 MET cc_start: 0.9082 (tpp) cc_final: 0.8756 (tpp) REVERT: Z 197 MET cc_start: 0.8318 (tpp) cc_final: 0.7662 (tpt) REVERT: Z 288 ASP cc_start: 0.9375 (OUTLIER) cc_final: 0.8871 (t70) REVERT: Z 307 MET cc_start: 0.9298 (tpp) cc_final: 0.9087 (tpp) REVERT: Z 460 MET cc_start: 0.9256 (mmp) cc_final: 0.8959 (mmp) REVERT: Z 481 ILE cc_start: 0.9674 (OUTLIER) cc_final: 0.9185 (mp) REVERT: Z 508 MET cc_start: 0.9354 (pmm) cc_final: 0.9068 (pmm) outliers start: 78 outliers final: 56 residues processed: 438 average time/residue: 0.2350 time to fit residues: 171.4949 Evaluate side-chains 420 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 356 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1115 LYS Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1458 ILE Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 730 LYS Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 958 CYS Chi-restraints excluded: chain B residue 964 ASP Chi-restraints excluded: chain B residue 1081 ASP Chi-restraints excluded: chain B residue 1093 CYS Chi-restraints excluded: chain B residue 1130 THR Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain L residue 41 TYR Chi-restraints excluded: chain Y residue 22 VAL Chi-restraints excluded: chain Y residue 71 VAL Chi-restraints excluded: chain Z residue 288 ASP Chi-restraints excluded: chain Z residue 481 ILE Chi-restraints excluded: chain Z residue 493 VAL Chi-restraints excluded: chain Z residue 580 ASP Chi-restraints excluded: chain Z residue 729 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 400 optimal weight: 40.0000 chunk 204 optimal weight: 0.7980 chunk 296 optimal weight: 10.0000 chunk 194 optimal weight: 0.0980 chunk 128 optimal weight: 0.3980 chunk 192 optimal weight: 0.0770 chunk 449 optimal weight: 9.9990 chunk 405 optimal weight: 20.0000 chunk 284 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 379 optimal weight: 3.9990 overall best weight: 1.0740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.083048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.053222 restraints weight = 132729.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.055178 restraints weight = 62356.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.056426 restraints weight = 39291.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 70)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.057196 restraints weight = 29623.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.057621 restraints weight = 25038.277| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 38922 Z= 0.129 Angle : 0.649 13.932 52983 Z= 0.324 Chirality : 0.044 0.209 5931 Planarity : 0.004 0.045 6516 Dihedral : 13.828 141.772 6016 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.19 % Favored : 95.77 % Rotamer: Outliers : 1.87 % Allowed : 12.35 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % 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: 0.18 (0.13), residues: 4467 helix: 1.17 (0.14), residues: 1410 sheet: -0.21 (0.18), residues: 731 loop : -0.36 (0.13), residues: 2326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 230 TYR 0.023 0.001 TYR G 17 PHE 0.023 0.001 PHE A 458 TRP 0.019 0.001 TRP A 988 HIS 0.006 0.001 HIS Y 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (38891) covalent geometry : angle 0.63501 / 0.32 (52944) hydrogen bonds : bond 0.03404 / 2.28 ( 1416) hydrogen bonds : angle 4.89619 / 3.40 ( 3884) metal coordination : bond 0.00874 / 0.51 ( 31) metal coordination : angle 4.94475 / 3.05 ( 39) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8934 Ramachandran restraints generated. 4467 Oldfield, 0 Emsley, 4467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8934 Ramachandran restraints generated. 4467 Oldfield, 0 Emsley, 4467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 375 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 CYS cc_start: 0.8864 (m) cc_final: 0.8384 (p) REVERT: A 329 MET cc_start: 0.8478 (ptt) cc_final: 0.7970 (ptt) REVERT: A 334 ARG cc_start: 0.8647 (mmp80) cc_final: 0.8411 (mmp80) REVERT: A 437 ASP cc_start: 0.9265 (m-30) cc_final: 0.9064 (p0) REVERT: A 467 MET cc_start: 0.8830 (mmt) cc_final: 0.8338 (mmt) REVERT: A 514 GLU cc_start: 0.8542 (mt-10) cc_final: 0.7783 (mt-10) REVERT: A 561 MET cc_start: 0.8407 (mtt) cc_final: 0.8153 (mtt) REVERT: A 565 MET cc_start: 0.8591 (mmm) cc_final: 0.8386 (mtp) REVERT: A 634 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7716 (tm-30) REVERT: A 849 ASP cc_start: 0.8899 (m-30) cc_final: 0.8669 (m-30) REVERT: A 868 MET cc_start: 0.8903 (mmm) cc_final: 0.8611 (mtp) REVERT: A 902 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7424 (pm20) REVERT: A 986 MET cc_start: 0.8975 (OUTLIER) cc_final: 0.8773 (mtm) REVERT: A 1038 THR cc_start: 0.9127 (OUTLIER) cc_final: 0.8744 (p) REVERT: A 1085 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7830 (mt-10) REVERT: A 1403 ASP cc_start: 0.8652 (m-30) cc_final: 0.8420 (m-30) REVERT: A 1422 GLN cc_start: 0.8885 (mt0) cc_final: 0.8496 (mt0) REVERT: A 1441 GLU cc_start: 0.8353 (tm-30) cc_final: 0.8102 (tm-30) REVERT: A 1451 MET cc_start: 0.8478 (tpp) cc_final: 0.8181 (mmm) REVERT: A 1472 ASP cc_start: 0.8229 (p0) cc_final: 0.7879 (p0) REVERT: B 176 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8338 (mm-30) REVERT: B 200 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8422 (ttm) REVERT: B 297 MET cc_start: 0.9049 (mmm) cc_final: 0.8749 (mmm) REVERT: B 410 ASN cc_start: 0.9418 (OUTLIER) cc_final: 0.9147 (t0) REVERT: B 482 LEU cc_start: 0.9339 (mt) cc_final: 0.9129 (mt) REVERT: B 508 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.8217 (mtp) REVERT: B 513 GLU cc_start: 0.8627 (tp30) cc_final: 0.8039 (tm-30) REVERT: B 603 MET cc_start: 0.7571 (mtm) cc_final: 0.7162 (ptt) REVERT: B 606 ASP cc_start: 0.8499 (t70) cc_final: 0.8227 (t0) REVERT: B 616 THR cc_start: 0.9573 (OUTLIER) cc_final: 0.9237 (p) REVERT: B 908 MET cc_start: 0.8764 (tmm) cc_final: 0.8467 (tmm) REVERT: B 1056 ASP cc_start: 0.8138 (p0) cc_final: 0.7854 (p0) REVERT: B 1089 MET cc_start: 0.8802 (mmp) cc_final: 0.8416 (mmm) REVERT: B 1092 ASP cc_start: 0.8284 (m-30) cc_final: 0.7987 (m-30) REVERT: B 1101 GLN cc_start: 0.8685 (mt0) cc_final: 0.7942 (mt0) REVERT: D 64 THR cc_start: 0.8890 (m) cc_final: 0.8664 (p) REVERT: D 128 GLN cc_start: 0.9850 (tp-100) cc_final: 0.9286 (mm110) REVERT: F 56 TYR cc_start: 0.9081 (m-80) cc_final: 0.8612 (m-80) REVERT: F 95 LYS cc_start: 0.9546 (ttmm) cc_final: 0.9287 (ttpt) REVERT: G 21 ASN cc_start: 0.9014 (m-40) cc_final: 0.8454 (t0) REVERT: G 28 GLN cc_start: 0.9057 (mt0) cc_final: 0.8683 (mt0) REVERT: G 86 ASP cc_start: 0.8122 (m-30) cc_final: 0.6964 (p0) REVERT: G 90 THR cc_start: 0.8993 (p) cc_final: 0.8112 (p) REVERT: G 104 MET cc_start: 0.8474 (tmm) cc_final: 0.8095 (tmm) REVERT: G 120 ASP cc_start: 0.9157 (p0) cc_final: 0.8762 (p0) REVERT: G 139 GLN cc_start: 0.8417 (mm-40) cc_final: 0.6939 (tp40) REVERT: G 141 ASP cc_start: 0.7900 (p0) cc_final: 0.6843 (p0) REVERT: H 60 ILE cc_start: 0.9545 (mp) cc_final: 0.9340 (mp) REVERT: I 93 GLU cc_start: 0.7005 (tp30) cc_final: 0.6777 (tp30) REVERT: K 24 ASP cc_start: 0.8486 (t0) cc_final: 0.8177 (t0) REVERT: K 102 GLU cc_start: 0.8331 (pp20) cc_final: 0.8110 (pp20) REVERT: L 15 MET cc_start: 0.8493 (mmm) cc_final: 0.8151 (mmt) REVERT: L 44 MET cc_start: 0.8940 (mmm) cc_final: 0.7629 (mmm) REVERT: Y 63 MET cc_start: 0.8942 (tpp) cc_final: 0.8598 (tpp) REVERT: Z 197 MET cc_start: 0.8335 (tpp) cc_final: 0.7949 (tpp) REVERT: Z 288 ASP cc_start: 0.9429 (OUTLIER) cc_final: 0.8899 (t70) REVERT: Z 307 MET cc_start: 0.9313 (tpp) cc_final: 0.9095 (tpp) REVERT: Z 460 MET cc_start: 0.9169 (mmp) cc_final: 0.8951 (mmp) REVERT: Z 481 ILE cc_start: 0.9679 (OUTLIER) cc_final: 0.9167 (mp) REVERT: Z 508 MET cc_start: 0.9334 (pmm) cc_final: 0.9067 (pmm) outliers start: 74 outliers final: 53 residues processed: 425 average time/residue: 0.2272 time to fit residues: 162.2622 Evaluate side-chains 417 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 356 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1115 LYS Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1458 ILE Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 958 CYS Chi-restraints excluded: chain B residue 964 ASP Chi-restraints excluded: chain B residue 1081 ASP Chi-restraints excluded: chain B residue 1093 CYS Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain Y residue 22 VAL Chi-restraints excluded: chain Y residue 71 VAL Chi-restraints excluded: chain Z residue 288 ASP Chi-restraints excluded: chain Z residue 481 ILE Chi-restraints excluded: chain Z residue 493 VAL Chi-restraints excluded: chain Z residue 580 ASP Chi-restraints excluded: chain Z residue 729 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 274 optimal weight: 3.9990 chunk 339 optimal weight: 4.9990 chunk 278 optimal weight: 1.9990 chunk 408 optimal weight: 30.0000 chunk 303 optimal weight: 9.9990 chunk 117 optimal weight: 0.8980 chunk 446 optimal weight: 30.0000 chunk 207 optimal weight: 0.6980 chunk 266 optimal weight: 8.9990 chunk 432 optimal weight: 9.9990 chunk 248 optimal weight: 0.7980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 GLN Z 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.082749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.053228 restraints weight = 133468.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.055170 restraints weight = 62507.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.056388 restraints weight = 39252.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.057145 restraints weight = 29590.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.057568 restraints weight = 25003.627| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 38922 Z= 0.151 Angle : 0.674 14.181 52983 Z= 0.335 Chirality : 0.045 0.207 5931 Planarity : 0.004 0.044 6516 Dihedral : 13.769 141.604 6016 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.23 % Favored : 95.72 % Rotamer: Outliers : 1.69 % Allowed : 12.86 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.22 (0.13), residues: 4467 helix: 1.22 (0.14), residues: 1420 sheet: -0.22 (0.18), residues: 741 loop : -0.34 (0.13), residues: 2306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 230 TYR 0.037 0.001 TYR I 25 PHE 0.029 0.001 PHE D 122 TRP 0.017 0.002 TRP C 49 HIS 0.007 0.001 HIS B 970 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (38891) covalent geometry : angle 0.65991 / 0.33 (52944) hydrogen bonds : bond 0.03460 / 2.31 ( 1416) hydrogen bonds : angle 4.84404 / 3.36 ( 3884) metal coordination : bond 0.00944 / 0.56 ( 31) metal coordination : angle 5.17064 / 3.16 ( 39) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8934 Ramachandran restraints generated. 4467 Oldfield, 0 Emsley, 4467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8934 Ramachandran restraints generated. 4467 Oldfield, 0 Emsley, 4467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 366 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 CYS cc_start: 0.8877 (m) cc_final: 0.8408 (p) REVERT: A 334 ARG cc_start: 0.8622 (mmp80) cc_final: 0.8385 (mmp80) REVERT: A 467 MET cc_start: 0.8877 (mmt) cc_final: 0.8402 (mmt) REVERT: A 561 MET cc_start: 0.8426 (mtt) cc_final: 0.8183 (mtt) REVERT: A 634 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7663 (tm-30) REVERT: A 660 MET cc_start: 0.8543 (mmt) cc_final: 0.8204 (mmm) REVERT: A 849 ASP cc_start: 0.8904 (m-30) cc_final: 0.8682 (m-30) REVERT: A 899 GLU cc_start: 0.8590 (pm20) cc_final: 0.8068 (mp0) REVERT: A 902 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7420 (pm20) REVERT: A 986 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.8783 (mtm) REVERT: A 1038 THR cc_start: 0.9137 (OUTLIER) cc_final: 0.8758 (p) REVERT: A 1085 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7884 (mt-10) REVERT: A 1279 MET cc_start: 0.7592 (OUTLIER) cc_final: 0.7086 (tpp) REVERT: A 1422 GLN cc_start: 0.8889 (mt0) cc_final: 0.8466 (mt0) REVERT: A 1441 GLU cc_start: 0.8352 (tm-30) cc_final: 0.8133 (tm-30) REVERT: A 1451 MET cc_start: 0.8433 (tpp) cc_final: 0.8049 (mmm) REVERT: A 1472 ASP cc_start: 0.8229 (p0) cc_final: 0.7889 (p0) REVERT: B 176 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8335 (mm-30) REVERT: B 200 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8484 (ttm) REVERT: B 297 MET cc_start: 0.9076 (mmm) cc_final: 0.8685 (mmm) REVERT: B 410 ASN cc_start: 0.9413 (OUTLIER) cc_final: 0.9162 (t0) REVERT: B 508 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8200 (mtp) REVERT: B 513 GLU cc_start: 0.8455 (tp30) cc_final: 0.8051 (tm-30) REVERT: B 603 MET cc_start: 0.7569 (mtm) cc_final: 0.7136 (ptt) REVERT: B 606 ASP cc_start: 0.8504 (t70) cc_final: 0.8234 (t0) REVERT: B 616 THR cc_start: 0.9510 (OUTLIER) cc_final: 0.9213 (p) REVERT: B 908 MET cc_start: 0.8751 (tmm) cc_final: 0.8450 (tmm) REVERT: B 1056 ASP cc_start: 0.8136 (p0) cc_final: 0.7863 (p0) REVERT: B 1089 MET cc_start: 0.8814 (mmp) cc_final: 0.8425 (mmm) REVERT: B 1092 ASP cc_start: 0.8268 (m-30) cc_final: 0.7964 (m-30) REVERT: B 1101 GLN cc_start: 0.8736 (mt0) cc_final: 0.8330 (mt0) REVERT: D 64 THR cc_start: 0.8896 (m) cc_final: 0.8667 (p) REVERT: F 56 TYR cc_start: 0.9081 (m-80) cc_final: 0.8610 (m-80) REVERT: F 95 LYS cc_start: 0.9600 (ttmm) cc_final: 0.9264 (ttpt) REVERT: G 21 ASN cc_start: 0.9007 (m-40) cc_final: 0.8465 (t0) REVERT: G 28 GLN cc_start: 0.9067 (mt0) cc_final: 0.8696 (mt0) REVERT: G 86 ASP cc_start: 0.8158 (m-30) cc_final: 0.6988 (p0) REVERT: G 104 MET cc_start: 0.8433 (tmm) cc_final: 0.8056 (tmm) REVERT: G 120 ASP cc_start: 0.9189 (p0) cc_final: 0.8757 (p0) REVERT: G 141 ASP cc_start: 0.7600 (p0) cc_final: 0.6883 (p0) REVERT: H 60 ILE cc_start: 0.9520 (mp) cc_final: 0.9306 (mp) REVERT: K 24 ASP cc_start: 0.8481 (t0) cc_final: 0.8166 (t0) REVERT: K 102 GLU cc_start: 0.8324 (pp20) cc_final: 0.8084 (pp20) REVERT: L 15 MET cc_start: 0.8429 (mmm) cc_final: 0.8101 (mmt) REVERT: L 21 GLU cc_start: 0.8279 (pt0) cc_final: 0.7891 (pp20) REVERT: L 44 MET cc_start: 0.8957 (mmm) cc_final: 0.7600 (mmm) REVERT: Z 197 MET cc_start: 0.8286 (tpp) cc_final: 0.7750 (tpt) REVERT: Z 288 ASP cc_start: 0.9434 (OUTLIER) cc_final: 0.8946 (t70) REVERT: Z 307 MET cc_start: 0.9301 (tpp) cc_final: 0.9086 (tpp) REVERT: Z 451 MET cc_start: 0.9364 (mmm) cc_final: 0.8578 (mmm) REVERT: Z 460 MET cc_start: 0.9017 (mmp) cc_final: 0.8765 (mmp) REVERT: Z 481 ILE cc_start: 0.9692 (OUTLIER) cc_final: 0.9192 (mp) REVERT: Z 508 MET cc_start: 0.9262 (pmm) cc_final: 0.8978 (pmm) outliers start: 67 outliers final: 51 residues processed: 411 average time/residue: 0.2309 time to fit residues: 159.8302 Evaluate side-chains 411 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 351 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1115 LYS Chi-restraints excluded: chain A residue 1279 MET Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1458 ILE Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 674 MET Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 958 CYS Chi-restraints excluded: chain B residue 964 ASP Chi-restraints excluded: chain B residue 1081 ASP Chi-restraints excluded: chain B residue 1093 CYS Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain Y residue 22 VAL Chi-restraints excluded: chain Y residue 71 VAL Chi-restraints excluded: chain Z residue 288 ASP Chi-restraints excluded: chain Z residue 481 ILE Chi-restraints excluded: chain Z residue 493 VAL Chi-restraints excluded: chain Z residue 580 ASP Chi-restraints excluded: chain Z residue 729 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 246 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 360 optimal weight: 4.9990 chunk 285 optimal weight: 10.0000 chunk 273 optimal weight: 4.9990 chunk 222 optimal weight: 6.9990 chunk 173 optimal weight: 9.9990 chunk 178 optimal weight: 7.9990 chunk 327 optimal weight: 0.9990 chunk 232 optimal weight: 0.4980 chunk 104 optimal weight: 0.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 GLN ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.082565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.053036 restraints weight = 132571.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.054982 restraints weight = 62421.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.056206 restraints weight = 39203.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.056942 restraints weight = 29484.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.057439 restraints weight = 24964.746| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 38922 Z= 0.158 Angle : 0.681 13.643 52983 Z= 0.337 Chirality : 0.044 0.229 5931 Planarity : 0.004 0.047 6516 Dihedral : 13.721 141.424 6016 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.30 % Favored : 95.68 % Rotamer: Outliers : 1.84 % Allowed : 12.98 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.24 (0.13), residues: 4467 helix: 1.24 (0.14), residues: 1422 sheet: -0.21 (0.18), residues: 745 loop : -0.33 (0.13), residues: 2300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 78 TYR 0.027 0.001 TYR G 17 PHE 0.019 0.001 PHE A 458 TRP 0.017 0.001 TRP C 49 HIS 0.004 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (38891) covalent geometry : angle 0.66584 / 0.34 (52944) hydrogen bonds : bond 0.03458 / 2.30 ( 1416) hydrogen bonds : angle 4.80856 / 3.33 ( 3884) metal coordination : bond 0.00966 / 0.57 ( 31) metal coordination : angle 5.24916 / 3.26 ( 39) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8934 Ramachandran restraints generated. 4467 Oldfield, 0 Emsley, 4467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8934 Ramachandran restraints generated. 4467 Oldfield, 0 Emsley, 4467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 364 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 CYS cc_start: 0.8878 (m) cc_final: 0.8412 (p) REVERT: A 334 ARG cc_start: 0.8530 (mmp80) cc_final: 0.8319 (mmp80) REVERT: A 341 GLN cc_start: 0.8660 (mt0) cc_final: 0.8405 (mp10) REVERT: A 467 MET cc_start: 0.8873 (mmt) cc_final: 0.8414 (mmt) REVERT: A 561 MET cc_start: 0.8445 (mtt) cc_final: 0.8233 (mtt) REVERT: A 565 MET cc_start: 0.8609 (mmm) cc_final: 0.8386 (mtp) REVERT: A 634 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7657 (tm-30) REVERT: A 660 MET cc_start: 0.8559 (mmt) cc_final: 0.8239 (mmm) REVERT: A 849 ASP cc_start: 0.8903 (m-30) cc_final: 0.8668 (m-30) REVERT: A 868 MET cc_start: 0.8435 (mtp) cc_final: 0.8217 (mtt) REVERT: A 899 GLU cc_start: 0.8610 (pm20) cc_final: 0.8104 (mp0) REVERT: A 902 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7246 (pm20) REVERT: A 986 MET cc_start: 0.9017 (OUTLIER) cc_final: 0.7380 (mtm) REVERT: A 1038 THR cc_start: 0.9145 (OUTLIER) cc_final: 0.8765 (p) REVERT: A 1085 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7941 (mt-10) REVERT: A 1279 MET cc_start: 0.7521 (OUTLIER) cc_final: 0.7085 (tpp) REVERT: A 1422 GLN cc_start: 0.8905 (mt0) cc_final: 0.8651 (mt0) REVERT: A 1441 GLU cc_start: 0.8358 (tm-30) cc_final: 0.8149 (tm-30) REVERT: A 1451 MET cc_start: 0.8347 (tpp) cc_final: 0.7994 (mmm) REVERT: A 1472 ASP cc_start: 0.8233 (p0) cc_final: 0.7893 (p0) REVERT: B 176 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8322 (mm-30) REVERT: B 200 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8372 (tpp) REVERT: B 297 MET cc_start: 0.9077 (mmm) cc_final: 0.8687 (mmm) REVERT: B 410 ASN cc_start: 0.9393 (OUTLIER) cc_final: 0.9162 (t0) REVERT: B 508 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8168 (mtp) REVERT: B 513 GLU cc_start: 0.8442 (tp30) cc_final: 0.8036 (tm-30) REVERT: B 603 MET cc_start: 0.7582 (mtm) cc_final: 0.7149 (ptt) REVERT: B 606 ASP cc_start: 0.8508 (t70) cc_final: 0.8238 (t0) REVERT: B 616 THR cc_start: 0.9499 (OUTLIER) cc_final: 0.9193 (p) REVERT: B 908 MET cc_start: 0.8759 (tmm) cc_final: 0.8432 (tmm) REVERT: B 1056 ASP cc_start: 0.8039 (p0) cc_final: 0.7769 (p0) REVERT: B 1089 MET cc_start: 0.8818 (mmp) cc_final: 0.8417 (mmm) REVERT: B 1092 ASP cc_start: 0.8211 (m-30) cc_final: 0.7908 (m-30) REVERT: B 1101 GLN cc_start: 0.8748 (mt0) cc_final: 0.8340 (mt0) REVERT: B 1171 MET cc_start: 0.8986 (mtm) cc_final: 0.8724 (mtt) REVERT: D 64 THR cc_start: 0.8906 (m) cc_final: 0.8680 (p) REVERT: F 56 TYR cc_start: 0.9078 (m-80) cc_final: 0.8605 (m-80) REVERT: F 95 LYS cc_start: 0.9630 (ttmm) cc_final: 0.9336 (ttpt) REVERT: G 21 ASN cc_start: 0.9047 (m-40) cc_final: 0.8205 (p0) REVERT: G 24 ASN cc_start: 0.9134 (OUTLIER) cc_final: 0.8711 (p0) REVERT: G 28 GLN cc_start: 0.9062 (mt0) cc_final: 0.8704 (mt0) REVERT: G 86 ASP cc_start: 0.8175 (m-30) cc_final: 0.7278 (p0) REVERT: G 94 LYS cc_start: 0.9457 (mmtt) cc_final: 0.9184 (mmmt) REVERT: G 120 ASP cc_start: 0.9131 (p0) cc_final: 0.8626 (p0) REVERT: G 139 GLN cc_start: 0.7864 (mm-40) cc_final: 0.7226 (tp40) REVERT: G 141 ASP cc_start: 0.7826 (p0) cc_final: 0.6862 (p0) REVERT: H 46 GLN cc_start: 0.8751 (mt0) cc_final: 0.8526 (mt0) REVERT: H 60 ILE cc_start: 0.9524 (mp) cc_final: 0.9314 (mp) REVERT: H 118 TYR cc_start: 0.8899 (m-80) cc_final: 0.8638 (m-80) REVERT: H 123 MET cc_start: 0.8735 (ptm) cc_final: 0.8358 (ttp) REVERT: I 108 MET cc_start: 0.8544 (mmm) cc_final: 0.8300 (mmm) REVERT: K 24 ASP cc_start: 0.8477 (t0) cc_final: 0.8172 (t0) REVERT: K 102 GLU cc_start: 0.8326 (pp20) cc_final: 0.7848 (pp20) REVERT: L 15 MET cc_start: 0.8409 (mmm) cc_final: 0.8097 (mmt) REVERT: L 21 GLU cc_start: 0.8284 (pt0) cc_final: 0.8031 (pp20) REVERT: L 44 MET cc_start: 0.8991 (mmm) cc_final: 0.7609 (mmm) REVERT: Z 190 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.8097 (pmt-80) REVERT: Z 197 MET cc_start: 0.8308 (tpp) cc_final: 0.7757 (tpt) REVERT: Z 288 ASP cc_start: 0.9409 (OUTLIER) cc_final: 0.8899 (t70) REVERT: Z 451 MET cc_start: 0.9355 (mmm) cc_final: 0.8587 (mmm) REVERT: Z 460 MET cc_start: 0.9024 (mmp) cc_final: 0.8767 (mmp) REVERT: Z 481 ILE cc_start: 0.9699 (OUTLIER) cc_final: 0.9363 (mp) REVERT: Z 508 MET cc_start: 0.9272 (pmm) cc_final: 0.8966 (pmm) outliers start: 73 outliers final: 50 residues processed: 415 average time/residue: 0.2350 time to fit residues: 164.0739 Evaluate side-chains 413 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 352 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1115 LYS Chi-restraints excluded: chain A residue 1279 MET Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1458 ILE Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 674 MET Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 958 CYS Chi-restraints excluded: chain B residue 964 ASP Chi-restraints excluded: chain B residue 1081 ASP Chi-restraints excluded: chain B residue 1093 CYS Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain Y residue 22 VAL Chi-restraints excluded: chain Y residue 71 VAL Chi-restraints excluded: chain Z residue 190 ARG Chi-restraints excluded: chain Z residue 288 ASP Chi-restraints excluded: chain Z residue 481 ILE Chi-restraints excluded: chain Z residue 493 VAL Chi-restraints excluded: chain Z residue 580 ASP Chi-restraints excluded: chain Z residue 729 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 184 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 226 optimal weight: 6.9990 chunk 332 optimal weight: 8.9990 chunk 344 optimal weight: 6.9990 chunk 170 optimal weight: 0.0010 chunk 223 optimal weight: 9.9990 chunk 218 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 chunk 273 optimal weight: 5.9990 overall best weight: 4.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 HIS ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 GLN I 100 HIS Z 519 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.081039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.051547 restraints weight = 134372.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.053413 restraints weight = 63797.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.054605 restraints weight = 40337.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.055327 restraints weight = 30498.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.055790 restraints weight = 25761.580| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.4804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 38922 Z= 0.292 Angle : 0.759 15.403 52983 Z= 0.373 Chirality : 0.046 0.328 5931 Planarity : 0.004 0.062 6516 Dihedral : 13.785 141.363 6016 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.93 % Favored : 95.05 % Rotamer: Outliers : 1.74 % Allowed : 13.28 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.15 (0.13), residues: 4467 helix: 1.19 (0.14), residues: 1425 sheet: -0.29 (0.18), residues: 726 loop : -0.39 (0.13), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 78 TYR 0.030 0.002 TYR G 17 PHE 0.022 0.002 PHE H 56 TRP 0.028 0.002 TRP A 988 HIS 0.006 0.001 HIS I 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00642 / 0.29 (38891) covalent geometry : angle 0.74281 / 0.37 (52944) hydrogen bonds : bond 0.03933 / 2.62 ( 1416) hydrogen bonds : angle 4.97078 / 3.45 ( 3884) metal coordination : bond 0.01377 / 0.86 ( 31) metal coordination : angle 5.71845 / 3.51 ( 39) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7917.44 seconds wall clock time: 137 minutes 14.93 seconds (8234.93 seconds total)