Starting phenix.real_space_refine on Sun Sep 13 13:07:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6bwd_7297/09_2026/6bwd_7297.cif Found real_map, /net/cci-nas-00/data/ceres_data/6bwd_7297/09_2026/6bwd_7297.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/6bwd_7297/09_2026/6bwd_7297.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6bwd_7297/09_2026/6bwd_7297.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6bwd_7297/09_2026/6bwd_7297.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6bwd_7297/09_2026/6bwd_7297.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6bwd_7297/09_2026/6bwd_7297.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6bwd_7297/09_2026/6bwd_7297.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= 0.006 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: 5 Type Number sf(0) Gaussians Mg 5 5.21 5 S 122 5.16 5 C 15156 2.51 5 N 3822 2.21 5 O 4082 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s 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: 23187 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 771, 5613 Classifications: {'peptide': 771} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 227} Link IDs: {'CIS': 48, 'PTRANS': 27, 'TRANS': 695} Chain breaks: 15 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 655 Unresolved non-hydrogen angles: 887 Unresolved non-hydrogen dihedrals: 478 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'UNK:plan-1': 121, 'PHE:plan': 2, 'ARG:plan': 9, 'GLU:plan': 8, 'GLN:plan1': 5, 'TYR:plan': 6, 'ASN:plan1': 6, 'HIS:plan': 5, 'ASP:plan': 4, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 345 Chain: "B" Number of atoms: 5618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 771, 5618 Classifications: {'peptide': 771} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 226} Link IDs: {'CIS': 47, 'PTRANS': 27, 'TRANS': 696} Chain breaks: 15 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 650 Unresolved non-hydrogen angles: 880 Unresolved non-hydrogen dihedrals: 475 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'UNK:plan-1': 121, 'PHE:plan': 2, 'ARG:plan': 8, 'GLU:plan': 8, 'GLN:plan1': 5, 'TYR:plan': 6, 'ASN:plan1': 6, 'HIS:plan': 5, 'ASP:plan': 3, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 337 Chain: "C" Number of atoms: 5628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 771, 5628 Classifications: {'peptide': 771} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 223} Link IDs: {'CIS': 45, 'PTRANS': 27, 'TRANS': 698} Chain breaks: 15 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 640 Unresolved non-hydrogen angles: 867 Unresolved non-hydrogen dihedrals: 468 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'UNK:plan-1': 121, 'PHE:plan': 2, 'ARG:plan': 8, 'GLU:plan': 6, 'GLN:plan1': 5, 'TYR:plan': 6, 'ASN:plan1': 5, 'HIS:plan': 5, 'ASP:plan': 3, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 326 Chain: "D" Number of atoms: 5593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 771, 5593 Classifications: {'peptide': 771} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 232} Link IDs: {'CIS': 46, 'PTRANS': 27, 'TRANS': 697} Chain breaks: 15 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 674 Unresolved non-hydrogen angles: 910 Unresolved non-hydrogen dihedrals: 492 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'UNK:plan-1': 121, 'PHE:plan': 2, 'ARG:plan': 9, 'GLU:plan': 11, 'GLN:plan1': 5, 'TYR:plan': 6, 'ASN:plan1': 6, 'HIS:plan': 5, 'ASP:plan': 5, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 360 Chain: "A" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 212 Unusual residues: {' MG': 2, 'Y01': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 142 Unusual residues: {' MG': 2, 'Y01': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 280 Unusual residues: {'Y01': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 71 Unusual residues: {' MG': 1, 'Y01': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Time building chain proxies: 5.78, per 1000 atoms: 0.25 Number of scatterers: 23187 At special positions: 0 Unit cell: (136.53, 136.53, 152.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 122 16.00 Mg 5 11.99 O 4082 8.00 N 3822 7.00 C 15156 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 894 " - pdb=" SG CYS A 904 " distance=2.02 Simple disulfide: pdb=" SG CYS B 894 " - pdb=" SG CYS B 904 " distance=2.02 Simple disulfide: pdb=" SG CYS C 711 " - pdb=" SG CYS C 721 " distance=2.02 Simple disulfide: pdb=" SG CYS D 894 " - pdb=" SG CYS D 904 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.50 Conformation dependent library (CDL) restraints added in 821.8 milliseconds 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5960 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 0 sheets defined 71.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 2 through 9 Processing helix chain 'A' and resid 10 through 16 Processing helix chain 'A' and resid 27 through 34 Processing helix chain 'A' and resid 226 through 231 Processing helix chain 'A' and resid 236 through 246 Processing helix chain 'A' and resid 273 through 285 removed outlier: 4.071A pdb=" N UNK A 285 " --> pdb=" O UNK A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 291 Processing helix chain 'A' and resid 308 through 317 removed outlier: 3.856A pdb=" N GLU A 313 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLU A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A 315 " --> pdb=" O ARG A 311 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASN A 317 " --> pdb=" O GLU A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 324 Processing helix chain 'A' and resid 344 through 349 Processing helix chain 'A' and resid 356 through 360 Processing helix chain 'A' and resid 414 through 418 removed outlier: 3.761A pdb=" N HIS A 417 " --> pdb=" O ARG A 414 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE A 418 " --> pdb=" O HIS A 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 414 through 418' Processing helix chain 'A' and resid 435 through 442 removed outlier: 3.555A pdb=" N LYS A 442 " --> pdb=" O LYS A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 470 removed outlier: 3.971A pdb=" N ILE A 465 " --> pdb=" O ASN A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 477 Processing helix chain 'A' and resid 485 through 503 removed outlier: 4.284A pdb=" N LEU A 491 " --> pdb=" O MET A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 517 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 527 through 538 removed outlier: 3.809A pdb=" N GLN A 538 " --> pdb=" O GLN A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 545 Processing helix chain 'A' and resid 546 through 548 No H-bonds generated for 'chain 'A' and resid 546 through 548' Processing helix chain 'A' and resid 574 through 587 Processing helix chain 'A' and resid 597 through 604 removed outlier: 3.540A pdb=" N SER A 602 " --> pdb=" O LYS A 598 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 613 removed outlier: 3.581A pdb=" N LEU A 612 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU A 613 " --> pdb=" O LEU A 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 609 through 613' Processing helix chain 'A' and resid 619 through 623 removed outlier: 3.891A pdb=" N ILE A 623 " --> pdb=" O MET A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 687 Processing helix chain 'A' and resid 689 through 714 removed outlier: 4.133A pdb=" N LEU A 702 " --> pdb=" O THR A 698 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL A 714 " --> pdb=" O PHE A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 743 removed outlier: 4.265A pdb=" N VAL A 727 " --> pdb=" O GLN A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 758 removed outlier: 3.788A pdb=" N TRP A 757 " --> pdb=" O LYS A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 779 removed outlier: 3.873A pdb=" N SER A 765 " --> pdb=" O TYR A 761 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE A 773 " --> pdb=" O ALA A 769 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY A 776 " --> pdb=" O SER A 772 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE A 777 " --> pdb=" O PHE A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 805 removed outlier: 3.903A pdb=" N ILE A 802 " --> pdb=" O ALA A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 819 removed outlier: 3.830A pdb=" N ARG A 813 " --> pdb=" O PHE A 809 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU A 814 " --> pdb=" O TRP A 810 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU A 815 " --> pdb=" O TYR A 811 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP A 816 " --> pdb=" O VAL A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 832 removed outlier: 4.087A pdb=" N TYR A 827 " --> pdb=" O GLN A 823 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY A 832 " --> pdb=" O VAL A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 861 removed outlier: 3.550A pdb=" N PHE A 839 " --> pdb=" O VAL A 835 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TYR A 840 " --> pdb=" O ALA A 836 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ILE A 841 " --> pdb=" O ASN A 837 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE A 844 " --> pdb=" O TYR A 840 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU A 849 " --> pdb=" O MET A 845 " (cutoff:3.500A) Proline residue: A 855 - end of helix removed outlier: 4.002A pdb=" N ILE A 859 " --> pdb=" O PRO A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 880 removed outlier: 4.587A pdb=" N HIS A 877 " --> pdb=" O ASP A 873 " (cutoff:3.500A) Proline residue: A 878 - end of helix Processing helix chain 'A' and resid 910 through 922 removed outlier: 3.506A pdb=" N ALA A 916 " --> pdb=" O PRO A 912 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE A 920 " --> pdb=" O ALA A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 933 Processing helix chain 'A' and resid 938 through 953 removed outlier: 4.240A pdb=" N ILE A 944 " --> pdb=" O GLN A 940 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE A 947 " --> pdb=" O ALA A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 958 Processing helix chain 'A' and resid 970 through 974 Processing helix chain 'A' and resid 1001 through 1023 removed outlier: 3.893A pdb=" N GLU A1017 " --> pdb=" O GLU A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1026 No H-bonds generated for 'chain 'A' and resid 1024 through 1026' Processing helix chain 'A' and resid 1031 through 1068 removed outlier: 3.665A pdb=" N ILE A1035 " --> pdb=" O SER A1031 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 9 Processing helix chain 'B' and resid 10 through 16 Processing helix chain 'B' and resid 27 through 34 Processing helix chain 'B' and resid 226 through 231 Processing helix chain 'B' and resid 236 through 246 Processing helix chain 'B' and resid 273 through 285 removed outlier: 4.072A pdb=" N UNK B 285 " --> pdb=" O UNK B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 291 Processing helix chain 'B' and resid 308 through 317 removed outlier: 3.857A pdb=" N GLU B 313 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLU B 314 " --> pdb=" O PRO B 310 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 315 " --> pdb=" O ARG B 311 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASN B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 324 Processing helix chain 'B' and resid 344 through 349 Processing helix chain 'B' and resid 353 through 360 Processing helix chain 'B' and resid 414 through 418 removed outlier: 3.760A pdb=" N HIS B 417 " --> pdb=" O ARG B 414 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE B 418 " --> pdb=" O HIS B 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 414 through 418' Processing helix chain 'B' and resid 435 through 442 removed outlier: 3.555A pdb=" N LYS B 442 " --> pdb=" O LYS B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 470 removed outlier: 3.970A pdb=" N ILE B 465 " --> pdb=" O ASN B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 477 Processing helix chain 'B' and resid 485 through 503 removed outlier: 4.284A pdb=" N LEU B 491 " --> pdb=" O MET B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 517 Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 527 through 538 removed outlier: 3.809A pdb=" N GLN B 538 " --> pdb=" O GLN B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 545 Processing helix chain 'B' and resid 546 through 548 No H-bonds generated for 'chain 'B' and resid 546 through 548' Processing helix chain 'B' and resid 574 through 587 Processing helix chain 'B' and resid 597 through 604 removed outlier: 3.770A pdb=" N SER B 602 " --> pdb=" O LYS B 598 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU B 604 " --> pdb=" O ILE B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 613 removed outlier: 4.257A pdb=" N MET B 611 " --> pdb=" O ALA B 608 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 612 " --> pdb=" O ILE B 609 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU B 613 " --> pdb=" O LEU B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 623 removed outlier: 3.890A pdb=" N ILE B 623 " --> pdb=" O MET B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 687 Processing helix chain 'B' and resid 689 through 714 removed outlier: 4.133A pdb=" N LEU B 702 " --> pdb=" O THR B 698 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL B 714 " --> pdb=" O PHE B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 743 removed outlier: 4.266A pdb=" N VAL B 727 " --> pdb=" O GLN B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 753 through 758 removed outlier: 3.788A pdb=" N TRP B 757 " --> pdb=" O LYS B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 779 removed outlier: 3.873A pdb=" N SER B 765 " --> pdb=" O TYR B 761 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE B 773 " --> pdb=" O ALA B 769 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY B 776 " --> pdb=" O SER B 772 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE B 777 " --> pdb=" O PHE B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 796 through 805 removed outlier: 3.902A pdb=" N ILE B 802 " --> pdb=" O ALA B 798 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 819 removed outlier: 3.831A pdb=" N ARG B 813 " --> pdb=" O PHE B 809 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU B 814 " --> pdb=" O TRP B 810 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU B 815 " --> pdb=" O TYR B 811 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP B 816 " --> pdb=" O VAL B 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 823 through 832 removed outlier: 4.086A pdb=" N TYR B 827 " --> pdb=" O GLN B 823 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY B 832 " --> pdb=" O VAL B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 861 removed outlier: 3.549A pdb=" N PHE B 839 " --> pdb=" O VAL B 835 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TYR B 840 " --> pdb=" O ALA B 836 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ILE B 841 " --> pdb=" O ASN B 837 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE B 844 " --> pdb=" O TYR B 840 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU B 849 " --> pdb=" O MET B 845 " (cutoff:3.500A) Proline residue: B 855 - end of helix removed outlier: 4.004A pdb=" N ILE B 859 " --> pdb=" O PRO B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 869 through 880 removed outlier: 4.587A pdb=" N HIS B 877 " --> pdb=" O ASP B 873 " (cutoff:3.500A) Proline residue: B 878 - end of helix Processing helix chain 'B' and resid 910 through 922 removed outlier: 3.507A pdb=" N ALA B 916 " --> pdb=" O PRO B 912 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE B 920 " --> pdb=" O ALA B 916 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 933 Processing helix chain 'B' and resid 938 through 953 removed outlier: 4.240A pdb=" N ILE B 944 " --> pdb=" O GLN B 940 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE B 947 " --> pdb=" O ALA B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 953 through 958 Processing helix chain 'B' and resid 970 through 974 Processing helix chain 'B' and resid 1001 through 1023 removed outlier: 3.893A pdb=" N GLU B1017 " --> pdb=" O GLU B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1024 through 1026 No H-bonds generated for 'chain 'B' and resid 1024 through 1026' Processing helix chain 'B' and resid 1031 through 1068 removed outlier: 3.666A pdb=" N ILE B1035 " --> pdb=" O SER B1031 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 9 Processing helix chain 'C' and resid 10 through 16 Processing helix chain 'C' and resid 27 through 34 Processing helix chain 'C' and resid 44 through 49 Processing helix chain 'C' and resid 54 through 64 Processing helix chain 'C' and resid 91 through 103 removed outlier: 4.071A pdb=" N UNK C 103 " --> pdb=" O UNK C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 109 Processing helix chain 'C' and resid 125 through 134 removed outlier: 3.857A pdb=" N GLU C 130 " --> pdb=" O ILE C 126 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLU C 131 " --> pdb=" O PRO C 127 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU C 132 " --> pdb=" O ARG C 128 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ASN C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 141 Processing helix chain 'C' and resid 161 through 166 Processing helix chain 'C' and resid 170 through 177 Processing helix chain 'C' and resid 231 through 235 removed outlier: 3.761A pdb=" N HIS C 234 " --> pdb=" O ARG C 231 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE C 235 " --> pdb=" O HIS C 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 231 through 235' Processing helix chain 'C' and resid 252 through 259 removed outlier: 3.556A pdb=" N LYS C 259 " --> pdb=" O LYS C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 287 removed outlier: 3.971A pdb=" N ILE C 282 " --> pdb=" O ASN C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 294 Processing helix chain 'C' and resid 302 through 320 removed outlier: 4.284A pdb=" N LEU C 308 " --> pdb=" O MET C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 334 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 344 through 355 removed outlier: 3.809A pdb=" N GLN C 355 " --> pdb=" O GLN C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 362 Processing helix chain 'C' and resid 363 through 365 No H-bonds generated for 'chain 'C' and resid 363 through 365' Processing helix chain 'C' and resid 391 through 404 Processing helix chain 'C' and resid 414 through 421 removed outlier: 3.809A pdb=" N SER C 419 " --> pdb=" O LYS C 415 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU C 421 " --> pdb=" O ILE C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 430 removed outlier: 4.914A pdb=" N MET C 428 " --> pdb=" O ALA C 425 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU C 429 " --> pdb=" O ILE C 426 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU C 430 " --> pdb=" O LEU C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 440 removed outlier: 3.891A pdb=" N ILE C 440 " --> pdb=" O MET C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 504 Processing helix chain 'C' and resid 506 through 531 removed outlier: 4.132A pdb=" N LEU C 519 " --> pdb=" O THR C 515 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL C 531 " --> pdb=" O PHE C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 560 removed outlier: 4.266A pdb=" N VAL C 544 " --> pdb=" O GLN C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 575 removed outlier: 3.789A pdb=" N TRP C 574 " --> pdb=" O LYS C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 596 removed outlier: 3.873A pdb=" N SER C 582 " --> pdb=" O TYR C 578 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE C 590 " --> pdb=" O ALA C 586 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY C 593 " --> pdb=" O SER C 589 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE C 594 " --> pdb=" O PHE C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 622 removed outlier: 3.903A pdb=" N ILE C 619 " --> pdb=" O ALA C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 636 removed outlier: 3.831A pdb=" N ARG C 630 " --> pdb=" O PHE C 626 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU C 631 " --> pdb=" O TRP C 627 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU C 632 " --> pdb=" O TYR C 628 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP C 633 " --> pdb=" O VAL C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 640 through 649 removed outlier: 4.086A pdb=" N TYR C 644 " --> pdb=" O GLN C 640 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY C 649 " --> pdb=" O VAL C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 678 removed outlier: 3.550A pdb=" N PHE C 656 " --> pdb=" O VAL C 652 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TYR C 657 " --> pdb=" O ALA C 653 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ILE C 658 " --> pdb=" O ASN C 654 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE C 661 " --> pdb=" O TYR C 657 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU C 666 " --> pdb=" O MET C 662 " (cutoff:3.500A) Proline residue: C 672 - end of helix removed outlier: 4.003A pdb=" N ILE C 676 " --> pdb=" O PRO C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 697 removed outlier: 4.586A pdb=" N HIS C 694 " --> pdb=" O ASP C 690 " (cutoff:3.500A) Proline residue: C 695 - end of helix Processing helix chain 'C' and resid 727 through 739 removed outlier: 3.506A pdb=" N ALA C 733 " --> pdb=" O PRO C 729 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE C 737 " --> pdb=" O ALA C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 745 through 750 Processing helix chain 'C' and resid 755 through 770 removed outlier: 4.240A pdb=" N ILE C 761 " --> pdb=" O GLN C 757 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE C 764 " --> pdb=" O ALA C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 770 through 775 Processing helix chain 'C' and resid 787 through 791 Processing helix chain 'C' and resid 818 through 840 removed outlier: 3.893A pdb=" N GLU C 834 " --> pdb=" O GLU C 830 " (cutoff:3.500A) Processing helix chain 'C' and resid 841 through 843 No H-bonds generated for 'chain 'C' and resid 841 through 843' Processing helix chain 'C' and resid 848 through 885 removed outlier: 3.666A pdb=" N ILE C 852 " --> pdb=" O SER C 848 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 9 Processing helix chain 'D' and resid 10 through 16 Processing helix chain 'D' and resid 27 through 34 Processing helix chain 'D' and resid 226 through 231 Processing helix chain 'D' and resid 236 through 246 Processing helix chain 'D' and resid 273 through 285 removed outlier: 4.071A pdb=" N UNK D 285 " --> pdb=" O UNK D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 291 Processing helix chain 'D' and resid 308 through 317 removed outlier: 3.856A pdb=" N GLU D 313 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLU D 314 " --> pdb=" O PRO D 310 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU D 315 " --> pdb=" O ARG D 311 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASN D 317 " --> pdb=" O GLU D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 324 Processing helix chain 'D' and resid 344 through 349 Processing helix chain 'D' and resid 353 through 360 removed outlier: 3.562A pdb=" N MET D 358 " --> pdb=" O GLU D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 418 removed outlier: 3.761A pdb=" N HIS D 417 " --> pdb=" O ARG D 414 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE D 418 " --> pdb=" O HIS D 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 414 through 418' Processing helix chain 'D' and resid 435 through 442 removed outlier: 3.556A pdb=" N LYS D 442 " --> pdb=" O LYS D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 470 removed outlier: 3.971A pdb=" N ILE D 465 " --> pdb=" O ASN D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 477 Processing helix chain 'D' and resid 485 through 503 removed outlier: 4.284A pdb=" N LEU D 491 " --> pdb=" O MET D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 517 Processing helix chain 'D' and resid 520 through 525 Processing helix chain 'D' and resid 527 through 538 removed outlier: 3.809A pdb=" N GLN D 538 " --> pdb=" O GLN D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 545 Processing helix chain 'D' and resid 546 through 548 No H-bonds generated for 'chain 'D' and resid 546 through 548' Processing helix chain 'D' and resid 574 through 587 Processing helix chain 'D' and resid 597 through 604 removed outlier: 3.802A pdb=" N SER D 602 " --> pdb=" O LYS D 598 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU D 604 " --> pdb=" O ILE D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 606 through 613 removed outlier: 4.256A pdb=" N MET D 611 " --> pdb=" O ALA D 608 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU D 612 " --> pdb=" O ILE D 609 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU D 613 " --> pdb=" O LEU D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 623 removed outlier: 3.891A pdb=" N ILE D 623 " --> pdb=" O MET D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 687 Processing helix chain 'D' and resid 689 through 714 removed outlier: 4.132A pdb=" N LEU D 702 " --> pdb=" O THR D 698 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL D 714 " --> pdb=" O PHE D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 723 through 743 removed outlier: 4.266A pdb=" N VAL D 727 " --> pdb=" O GLN D 723 " (cutoff:3.500A) Processing helix chain 'D' and resid 753 through 758 removed outlier: 3.789A pdb=" N TRP D 757 " --> pdb=" O LYS D 753 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 779 removed outlier: 3.873A pdb=" N SER D 765 " --> pdb=" O TYR D 761 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE D 773 " --> pdb=" O ALA D 769 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY D 776 " --> pdb=" O SER D 772 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) Processing helix chain 'D' and resid 796 through 805 removed outlier: 3.902A pdb=" N ILE D 802 " --> pdb=" O ALA D 798 " (cutoff:3.500A) Processing helix chain 'D' and resid 808 through 819 removed outlier: 3.829A pdb=" N ARG D 813 " --> pdb=" O PHE D 809 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU D 814 " --> pdb=" O TRP D 810 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU D 815 " --> pdb=" O TYR D 811 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP D 816 " --> pdb=" O VAL D 812 " (cutoff:3.500A) Processing helix chain 'D' and resid 823 through 832 removed outlier: 4.086A pdb=" N TYR D 827 " --> pdb=" O GLN D 823 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY D 832 " --> pdb=" O VAL D 828 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 861 removed outlier: 3.550A pdb=" N PHE D 839 " --> pdb=" O VAL D 835 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TYR D 840 " --> pdb=" O ALA D 836 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ILE D 841 " --> pdb=" O ASN D 837 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE D 844 " --> pdb=" O TYR D 840 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU D 849 " --> pdb=" O MET D 845 " (cutoff:3.500A) Proline residue: D 855 - end of helix removed outlier: 4.003A pdb=" N ILE D 859 " --> pdb=" O PRO D 855 " (cutoff:3.500A) Processing helix chain 'D' and resid 869 through 880 removed outlier: 4.586A pdb=" N HIS D 877 " --> pdb=" O ASP D 873 " (cutoff:3.500A) Proline residue: D 878 - end of helix Processing helix chain 'D' and resid 910 through 922 removed outlier: 3.506A pdb=" N ALA D 916 " --> pdb=" O PRO D 912 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N PHE D 920 " --> pdb=" O ALA D 916 " (cutoff:3.500A) Processing helix chain 'D' and resid 928 through 933 Processing helix chain 'D' and resid 938 through 953 removed outlier: 4.240A pdb=" N ILE D 944 " --> pdb=" O GLN D 940 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE D 947 " --> pdb=" O ALA D 943 " (cutoff:3.500A) Processing helix chain 'D' and resid 953 through 958 Processing helix chain 'D' and resid 970 through 974 Processing helix chain 'D' and resid 1001 through 1023 removed outlier: 3.893A pdb=" N GLU D1017 " --> pdb=" O GLU D1013 " (cutoff:3.500A) Processing helix chain 'D' and resid 1024 through 1026 No H-bonds generated for 'chain 'D' and resid 1024 through 1026' Processing helix chain 'D' and resid 1031 through 1068 removed outlier: 3.665A pdb=" N ILE D1035 " --> pdb=" O SER D1031 " (cutoff:3.500A) 994 hydrogen bonds defined for protein. 2856 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.71 Time building geometry restraints manager: 3.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3939 1.32 - 1.44: 6177 1.44 - 1.57: 13281 1.57 - 1.69: 36 1.69 - 1.81: 212 Bond restraints: 23645 Sorted by residual: bond pdb=" CAV Y01 C1303 " pdb=" CAZ Y01 C1303 " ideal model delta sigma weight residual 1.507 1.362 0.145 2.00e-02 2.50e+03 5.27e+01 bond pdb=" CAV Y01 C1306 " pdb=" CAZ Y01 C1306 " ideal model delta sigma weight residual 1.507 1.378 0.129 2.00e-02 2.50e+03 4.18e+01 bond pdb=" CAZ Y01 B1204 " pdb=" CBH Y01 B1204 " ideal model delta sigma weight residual 1.519 1.395 0.124 2.00e-02 2.50e+03 3.87e+01 bond pdb=" CAZ Y01 A1203 " pdb=" CBH Y01 A1203 " ideal model delta sigma weight residual 1.519 1.395 0.124 2.00e-02 2.50e+03 3.87e+01 bond pdb=" CAV Y01 D1203 " pdb=" CAZ Y01 D1203 " ideal model delta sigma weight residual 1.507 1.390 0.117 2.00e-02 2.50e+03 3.45e+01 ... (remaining 23640 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.88: 31018 3.88 - 7.75: 996 7.75 - 11.63: 159 11.63 - 15.51: 46 15.51 - 19.38: 10 Bond angle restraints: 32229 Sorted by residual: angle pdb=" C ILE C 167 " pdb=" N GLY C 168 " pdb=" CA GLY C 168 " ideal model delta sigma weight residual 121.41 140.79 -19.38 1.96e+00 2.60e-01 9.78e+01 angle pdb=" C TRP A 480 " pdb=" N GLN A 481 " pdb=" CA GLN A 481 " ideal model delta sigma weight residual 122.82 134.84 -12.02 1.42e+00 4.96e-01 7.16e+01 angle pdb=" C TRP B 480 " pdb=" N GLN B 481 " pdb=" CA GLN B 481 " ideal model delta sigma weight residual 122.82 134.83 -12.01 1.42e+00 4.96e-01 7.15e+01 angle pdb=" C TRP C 297 " pdb=" N GLN C 298 " pdb=" CA GLN C 298 " ideal model delta sigma weight residual 122.82 134.83 -12.01 1.42e+00 4.96e-01 7.15e+01 angle pdb=" C TRP D 480 " pdb=" N GLN D 481 " pdb=" CA GLN D 481 " ideal model delta sigma weight residual 122.82 134.82 -12.00 1.42e+00 4.96e-01 7.14e+01 ... (remaining 32224 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.92: 13309 26.92 - 53.84: 407 53.84 - 80.76: 26 80.76 - 107.68: 15 107.68 - 134.60: 6 Dihedral angle restraints: 13763 sinusoidal: 4651 harmonic: 9112 Sorted by residual: dihedral pdb=" CA TRP A 480 " pdb=" C TRP A 480 " pdb=" N GLN A 481 " pdb=" CA GLN A 481 " ideal model delta harmonic sigma weight residual 180.00 45.40 134.60 0 5.00e+00 4.00e-02 7.25e+02 dihedral pdb=" CA TRP D 480 " pdb=" C TRP D 480 " pdb=" N GLN D 481 " pdb=" CA GLN D 481 " ideal model delta harmonic sigma weight residual 180.00 45.45 134.55 0 5.00e+00 4.00e-02 7.24e+02 dihedral pdb=" CA TRP C 297 " pdb=" C TRP C 297 " pdb=" N GLN C 298 " pdb=" CA GLN C 298 " ideal model delta harmonic sigma weight residual 180.00 45.47 134.53 0 5.00e+00 4.00e-02 7.24e+02 ... (remaining 13760 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 3292 0.106 - 0.212: 334 0.212 - 0.318: 81 0.318 - 0.425: 43 0.425 - 0.531: 25 Chirality restraints: 3775 Sorted by residual: chirality pdb=" CBF Y01 A1206 " pdb=" CAS Y01 A1206 " pdb=" CBD Y01 A1206 " pdb=" CBH Y01 A1206 " both_signs ideal model delta sigma weight residual False -2.45 -2.98 0.53 2.00e-01 2.50e+01 7.04e+00 chirality pdb=" CBG Y01 C1303 " pdb=" CAQ Y01 C1303 " pdb=" CBD Y01 C1303 " pdb=" CBI Y01 C1303 " both_signs ideal model delta sigma weight residual False -2.33 -2.84 0.51 2.00e-01 2.50e+01 6.54e+00 chirality pdb=" CBG Y01 B1205 " pdb=" CAQ Y01 B1205 " pdb=" CBD Y01 B1205 " pdb=" CBI Y01 B1205 " both_signs ideal model delta sigma weight residual False -2.33 -2.84 0.51 2.00e-01 2.50e+01 6.51e+00 ... (remaining 3772 not shown) Planarity restraints: 3968 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 167 " -0.033 2.00e-02 2.50e+03 6.63e-02 4.39e+01 pdb=" C ILE C 167 " 0.115 2.00e-02 2.50e+03 pdb=" O ILE C 167 " -0.043 2.00e-02 2.50e+03 pdb=" N GLY C 168 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL D 605 " 0.092 5.00e-02 4.00e+02 1.35e-01 2.90e+01 pdb=" N PRO D 606 " -0.232 5.00e-02 4.00e+02 pdb=" CA PRO D 606 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO D 606 " 0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 353 " 0.020 2.00e-02 2.50e+03 3.96e-02 1.57e+01 pdb=" C VAL A 353 " -0.068 2.00e-02 2.50e+03 pdb=" O VAL A 353 " 0.026 2.00e-02 2.50e+03 pdb=" N ILE A 354 " 0.023 2.00e-02 2.50e+03 ... (remaining 3965 not shown) Histogram of nonbonded interaction distances: 1.25 - 1.98: 1 1.98 - 2.71: 1268 2.71 - 3.44: 32255 3.44 - 4.17: 51645 4.17 - 4.90: 88268 Nonbonded interactions: 173437 Sorted by model distance: nonbonded pdb="MG MG D1201 " pdb=" O HOH D1307 " model vdw 1.254 2.170 nonbonded pdb="MG MG A1201 " pdb=" O HOH B1301 " model vdw 2.039 2.170 nonbonded pdb="MG MG A1201 " pdb=" O HOH A1304 " model vdw 2.047 2.170 nonbonded pdb="MG MG A1201 " pdb=" O HOH C1404 " model vdw 2.073 2.170 nonbonded pdb="MG MG A1201 " pdb=" O HOH D1303 " model vdw 2.079 2.170 ... (remaining 173432 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 346 or (resid 347 through 348 and (name N or nam \ e CA or name C or name O or name CB )) or resid 349 through 351 or (resid 352 an \ d (name N or name CA or name C or name O or name CB )) or resid 353 through 362 \ or (resid 363 through 365 and (name N or name CA or name C or name O or name CB \ )) or resid 366 through 432 or (resid 433 through 434 and (name N or name CA or \ name C or name O or name CB )) or resid 435 through 443 or (resid 454 and (name \ N or name CA or name C or name O or name CB )) or resid 455 through 484 or (resi \ d 485 and (name N or name CA or name C or name O or name CB )) or resid 486 thro \ ugh 514 or (resid 515 through 516 and (name N or name CA or name C or name O or \ name CB )) or resid 517 through 538 or (resid 539 through 540 and (name N or nam \ e CA or name C or name O or name CB )) or resid 541 through 550 or (resid 551 an \ d (name N or name CA or name C or name O or name CB )) or resid 552 through 1068 \ or resid 1203)) selection = (chain 'B' and (resid 1 through 307 or (resid 308 and (name N or name CA or name \ C or name O or name CB )) or resid 309 through 346 or (resid 347 through 348 an \ d (name N or name CA or name C or name O or name CB )) or resid 349 through 353 \ or (resid 354 through 355 and (name N or name CA or name C or name O or name CB \ )) or resid 356 through 362 or (resid 363 through 365 and (name N or name CA or \ name C or name O or name CB )) or resid 366 through 439 or (resid 440 and (name \ N or name CA or name C or name O or name CB )) or resid 441 through 443 or (resi \ d 454 and (name N or name CA or name C or name O or name CB )) or resid 455 thro \ ugh 484 or (resid 485 and (name N or name CA or name C or name O or name CB )) o \ r resid 486 through 514 or (resid 515 through 516 and (name N or name CA or name \ C or name O or name CB )) or resid 517 through 522 or (resid 523 and (name N or \ name CA or name C or name O or name CB )) or resid 524 through 538 or (resid 53 \ 9 through 540 and (name N or name CA or name C or name O or name CB )) or resid \ 541 through 1068 or resid 1203)) selection = (chain 'C' and (resid 1 through 124 or (resid 125 and (name N or name CA or name \ C or name O or name CB )) or resid 126 through 163 or (resid 164 through 165 an \ d (name N or name CA or name C or name O or name CB )) or resid 166 through 170 \ or (resid 171 through 172 and (name N or name CA or name C or name O or name CB \ )) or resid 173 through 179 or (resid 180 through 182 and (name N or name CA or \ name C or name O or name CB )) or resid 183 through 232 or (resid 233 through 23 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 235 through \ 249 or (resid 250 through 251 and (name N or name CA or name C or name O or name \ CB )) or resid 252 through 256 or (resid 257 and (name N or name CA or name C o \ r name O or name CB )) or resid 258 through 300 or (resid 301 through 302 and (n \ ame N or name CA or name C or name O or name CB )) or resid 303 through 331 or ( \ resid 332 through 333 and (name N or name CA or name C or name O or name CB )) o \ r resid 334 through 339 or (resid 340 and (name N or name CA or name C or name O \ or name CB )) or resid 341 through 355 or (resid 356 through 357 and (name N or \ name CA or name C or name O or name CB )) or resid 358 through 885 or resid 130 \ 3)) selection = (chain 'D' and (resid 1 through 307 or (resid 308 and (name N or name CA or name \ C or name O or name CB )) or resid 309 through 353 or (resid 354 through 355 an \ d (name N or name CA or name C or name O or name CB )) or resid 356 through 433 \ or (resid 434 and (name N or name CA or name C or name O or name CB )) or resid \ 435 through 439 or (resid 440 and (name N or name CA or name C or name O or name \ CB )) or resid 441 through 443 or (resid 454 and (name N or name CA or name C o \ r name O or name CB )) or resid 455 through 550 or (resid 551 and (name N or nam \ e CA or name C or name O or name CB )) or resid 552 through 605 or (resid 606 an \ d (name N or name CA or name C or name O or name CB )) or resid 607 through 1068 \ or resid 1203)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.210 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.680 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 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 : 0.011 0.145 23649 Z= 0.545 Angle : 1.676 19.383 32237 Z= 0.897 Chirality : 0.092 0.531 3775 Planarity : 0.009 0.135 3968 Dihedral : 13.726 134.605 7791 Min Nonbonded Distance : 1.254 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 1.19 % Allowed : 12.50 % Favored : 86.31 % Rotamer: Outliers : 0.57 % Allowed : 5.51 % Favored : 93.92 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.33 % Twisted Proline : 3.70 % Twisted General : 3.75 % 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: -5.69 (0.12), residues: 2528 helix: -3.51 (0.09), residues: 1578 sheet: None (None), residues: 0 loop : -4.03 (0.17), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 477 TYR 0.035 0.003 TYR A 708 PHE 0.041 0.003 PHE D 999 TRP 0.032 0.004 TRP B 868 HIS 0.009 0.002 HIS D 415 Details of bonding type rmsd/Z covalent geometry : bond 0.01139 / 0.54 (23645) covalent geometry : angle 1.67584 / 0.90 (32229) SS BOND : bond 0.00844 / 0.42 ( 4) SS BOND : angle 1.26265 / 0.65 ( 8) hydrogen bonds : bond 0.18906 / 11.10 ( 994) hydrogen bonds : angle 10.87707 / 6.87 ( 2856) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 628 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 350 ILE cc_start: 0.7732 (mt) cc_final: 0.7529 (mt) REVERT: A 429 MET cc_start: 0.5428 (ppp) cc_final: 0.5004 (ppp) REVERT: A 513 THR cc_start: 0.7569 (p) cc_final: 0.7087 (t) REVERT: A 586 MET cc_start: 0.8072 (mtt) cc_final: 0.7793 (mtm) REVERT: A 753 LYS cc_start: 0.6326 (mttt) cc_final: 0.6071 (mttm) REVERT: A 818 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8793 (tp) REVERT: A 1006 LYS cc_start: 0.8394 (mttt) cc_final: 0.7619 (mttt) REVERT: A 1010 ASP cc_start: 0.7502 (m-30) cc_final: 0.7288 (m-30) REVERT: A 1045 MET cc_start: 0.8244 (tmm) cc_final: 0.7629 (tmm) REVERT: B 374 ILE cc_start: 0.7987 (mt) cc_final: 0.7616 (tp) REVERT: B 429 MET cc_start: 0.6810 (ppp) cc_final: 0.6566 (ppp) REVERT: B 518 LYS cc_start: 0.8585 (tttt) cc_final: 0.8330 (ttpp) REVERT: B 561 LYS cc_start: 0.8396 (mtmt) cc_final: 0.8030 (ptpt) REVERT: B 583 ASP cc_start: 0.8034 (m-30) cc_final: 0.7758 (m-30) REVERT: B 1010 ASP cc_start: 0.7845 (m-30) cc_final: 0.7591 (m-30) REVERT: C 162 ILE cc_start: 0.8565 (mt) cc_final: 0.8313 (mt) REVERT: C 408 MET cc_start: 0.6121 (OUTLIER) cc_final: 0.5782 (mmm) REVERT: C 533 MET cc_start: 0.7612 (mmm) cc_final: 0.7356 (mmm) REVERT: C 623 ASN cc_start: 0.8543 (t0) cc_final: 0.8191 (t0) REVERT: C 689 LYS cc_start: 0.7215 (mttt) cc_final: 0.6845 (tptp) REVERT: C 745 ASN cc_start: 0.8763 (t160) cc_final: 0.8445 (m-40) REVERT: C 823 LYS cc_start: 0.8384 (mttt) cc_final: 0.7842 (mttt) REVERT: C 827 ASP cc_start: 0.7339 (m-30) cc_final: 0.7066 (m-30) REVERT: C 853 ARG cc_start: 0.8303 (tmm-80) cc_final: 0.8032 (ttp-170) REVERT: C 862 MET cc_start: 0.8409 (tmm) cc_final: 0.8166 (tmm) REVERT: D 354 ILE cc_start: 0.7951 (mp) cc_final: 0.7546 (mp) REVERT: D 429 MET cc_start: 0.6572 (ppp) cc_final: 0.6299 (ppp) REVERT: D 470 MET cc_start: 0.8256 (mmm) cc_final: 0.7651 (mmm) REVERT: D 487 MET cc_start: 0.9020 (tmt) cc_final: 0.8784 (tmm) REVERT: D 598 LYS cc_start: 0.8139 (mttt) cc_final: 0.7821 (ptmm) REVERT: D 767 THR cc_start: 0.8173 (p) cc_final: 0.7929 (p) REVERT: D 1039 PHE cc_start: 0.8402 (t80) cc_final: 0.8171 (t80) outliers start: 11 outliers final: 2 residues processed: 637 average time/residue: 0.1572 time to fit residues: 158.0643 Evaluate side-chains 431 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 427 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain D residue 576 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.0270 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 0.7980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 ASN A 578 GLN ** A 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 928 ASN A 935 ASN A1005 GLN A1048 GLN ** B 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 553 ASN B 578 GLN B 590 ASN B 806 ASN C 370 ASN C 395 GLN C 745 ASN C 752 ASN ** C 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 865 GLN D 522 ASN D 553 ASN D 578 GLN D 590 ASN D1005 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.173314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.144597 restraints weight = 33550.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.147614 restraints weight = 20133.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.148368 restraints weight = 13333.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.148740 restraints weight = 10319.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.148852 restraints weight = 9467.315| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 23649 Z= 0.186 Angle : 0.985 14.549 32237 Z= 0.497 Chirality : 0.049 0.279 3775 Planarity : 0.005 0.080 3968 Dihedral : 10.628 109.486 3515 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.99 % Allowed : 8.58 % Favored : 90.43 % Rotamer: Outliers : 4.11 % Allowed : 11.38 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 6.19 % Twisted Proline : 3.70 % Twisted General : 1.26 % 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: -3.95 (0.15), residues: 2528 helix: -1.93 (0.11), residues: 1673 sheet: None (None), residues: 0 loop : -3.86 (0.18), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D1034 TYR 0.025 0.002 TYR D 960 PHE 0.023 0.002 PHE B 418 TRP 0.023 0.002 TRP B 949 HIS 0.005 0.001 HIS D 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.19 (23645) covalent geometry : angle 0.98531 / 0.50 (32229) SS BOND : bond 0.00272 / 0.14 ( 4) SS BOND : angle 0.83251 / 0.44 ( 8) hydrogen bonds : bond 0.04163 / 2.49 ( 994) hydrogen bonds : angle 5.15038 / 3.25 ( 2856) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 503 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 487 MET cc_start: 0.8625 (tmm) cc_final: 0.8419 (ttp) REVERT: A 591 MET cc_start: 0.6010 (ptp) cc_final: 0.4981 (ptp) REVERT: A 816 ASP cc_start: 0.8276 (t0) cc_final: 0.7857 (t0) REVERT: A 1006 LYS cc_start: 0.8385 (mttt) cc_final: 0.7872 (ttpt) REVERT: B 307 LEU cc_start: 0.8418 (tp) cc_final: 0.8154 (tt) REVERT: B 429 MET cc_start: 0.6672 (ppp) cc_final: 0.6469 (ppp) REVERT: B 561 LYS cc_start: 0.8232 (mtmt) cc_final: 0.7835 (mttm) REVERT: B 755 LYS cc_start: 0.7022 (pttm) cc_final: 0.6797 (tppt) REVERT: B 891 ILE cc_start: 0.8441 (mt) cc_final: 0.8226 (mt) REVERT: B 1006 LYS cc_start: 0.8455 (mttt) cc_final: 0.8139 (mttt) REVERT: C 232 HIS cc_start: 0.8479 (p90) cc_final: 0.8110 (p90) REVERT: C 246 MET cc_start: 0.6349 (ppp) cc_final: 0.5827 (ppp) REVERT: C 257 ARG cc_start: 0.7335 (mtp180) cc_final: 0.7100 (mtm-85) REVERT: C 378 LYS cc_start: 0.8037 (mtmt) cc_final: 0.7639 (mttp) REVERT: C 408 MET cc_start: 0.7012 (mmm) cc_final: 0.6715 (mmm) REVERT: C 651 MET cc_start: 0.8600 (ttm) cc_final: 0.8373 (mtt) REVERT: C 745 ASN cc_start: 0.8842 (t0) cc_final: 0.8508 (m-40) REVERT: C 780 LYS cc_start: 0.7588 (mmmt) cc_final: 0.7348 (mmmt) REVERT: C 823 LYS cc_start: 0.8489 (mttt) cc_final: 0.7590 (tppt) REVERT: C 824 LYS cc_start: 0.8609 (mttt) cc_final: 0.7994 (tmtt) REVERT: C 835 MET cc_start: 0.8439 (ttm) cc_final: 0.8231 (ttm) REVERT: C 853 ARG cc_start: 0.8331 (tmm-80) cc_final: 0.8040 (ttp-170) REVERT: C 860 GLU cc_start: 0.6653 (mm-30) cc_final: 0.6261 (mm-30) REVERT: D 561 LYS cc_start: 0.7904 (mtmt) cc_final: 0.7670 (mttm) REVERT: D 591 MET cc_start: 0.5900 (OUTLIER) cc_final: 0.5039 (ttm) REVERT: D 598 LYS cc_start: 0.7976 (mttt) cc_final: 0.7638 (ptmm) REVERT: D 818 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8910 (tp) REVERT: D 834 MET cc_start: 0.8478 (ttm) cc_final: 0.8237 (mtt) REVERT: D 1006 LYS cc_start: 0.8317 (mttt) cc_final: 0.7802 (ttmt) REVERT: D 1017 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7501 (tm-30) REVERT: D 1021 ASP cc_start: 0.8124 (m-30) cc_final: 0.7885 (m-30) REVERT: D 1043 GLU cc_start: 0.5913 (mm-30) cc_final: 0.5191 (mm-30) outliers start: 79 outliers final: 41 residues processed: 550 average time/residue: 0.1451 time to fit residues: 128.3587 Evaluate side-chains 464 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 421 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 803 TYR Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 482 HIS Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 754 ILE Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 999 PHE Chi-restraints excluded: chain B residue 1012 GLU Chi-restraints excluded: chain B residue 1047 ILE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 299 HIS Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 744 VAL Chi-restraints excluded: chain C residue 816 PHE Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 518 LYS Chi-restraints excluded: chain D residue 557 SER Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 589 LEU Chi-restraints excluded: chain D residue 591 MET Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 807 ILE Chi-restraints excluded: chain D residue 818 LEU Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain D residue 874 ILE Chi-restraints excluded: chain D residue 927 VAL Chi-restraints excluded: chain D residue 931 ILE Chi-restraints excluded: chain D residue 999 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 123 optimal weight: 0.6980 chunk 73 optimal weight: 6.9990 chunk 260 optimal weight: 0.0770 chunk 246 optimal weight: 1.9990 chunk 225 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 265 optimal weight: 0.4980 chunk 292 optimal weight: 0.0050 chunk 97 optimal weight: 1.9990 chunk 259 optimal weight: 0.8980 overall best weight: 0.4352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 GLN ** A 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 ASN B 481 GLN B 896 ASN ** B 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 GLN C 861 GLN C 865 GLN D 395 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.175186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.145295 restraints weight = 33532.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.148383 restraints weight = 20782.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.150006 restraints weight = 12643.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.149964 restraints weight = 9625.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.150426 restraints weight = 9794.870| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23649 Z= 0.159 Angle : 0.916 13.586 32237 Z= 0.461 Chirality : 0.048 0.275 3775 Planarity : 0.005 0.067 3968 Dihedral : 9.778 106.198 3508 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.91 % Allowed : 9.02 % Favored : 90.07 % Rotamer: Outliers : 4.89 % Allowed : 14.29 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 6.43 % Twisted Proline : 0.00 % Twisted General : 0.57 % 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: -3.06 (0.16), residues: 2528 helix: -1.21 (0.12), residues: 1672 sheet: None (None), residues: 0 loop : -3.62 (0.19), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B1034 TYR 0.019 0.001 TYR D 960 PHE 0.019 0.002 PHE B 777 TRP 0.025 0.002 TRP A 480 HIS 0.003 0.001 HIS C 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.16 (23645) covalent geometry : angle 0.91650 / 0.46 (32229) SS BOND : bond 0.00228 / 0.12 ( 4) SS BOND : angle 0.50088 / 0.26 ( 8) hydrogen bonds : bond 0.03721 / 2.23 ( 994) hydrogen bonds : angle 4.52016 / 2.84 ( 2856) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 446 time to evaluate : 0.810 Fit side-chains REVERT: A 429 MET cc_start: 0.5109 (ppp) cc_final: 0.4186 (ppp) REVERT: A 487 MET cc_start: 0.8688 (tmm) cc_final: 0.8368 (ttt) REVERT: A 779 LEU cc_start: 0.6665 (tp) cc_final: 0.6009 (pt) REVERT: A 881 MET cc_start: 0.8928 (tpp) cc_final: 0.8151 (mmt) REVERT: A 882 ILE cc_start: 0.7560 (OUTLIER) cc_final: 0.7015 (pt) REVERT: B 356 TYR cc_start: 0.6846 (m-10) cc_final: 0.6566 (m-10) REVERT: B 429 MET cc_start: 0.6633 (ppp) cc_final: 0.6330 (ppp) REVERT: B 523 ASP cc_start: 0.6349 (m-30) cc_final: 0.6048 (m-30) REVERT: B 532 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7450 (tp) REVERT: B 561 LYS cc_start: 0.8376 (mtmt) cc_final: 0.7966 (mttm) REVERT: B 834 MET cc_start: 0.8526 (tpp) cc_final: 0.8040 (mtt) REVERT: B 1036 ARG cc_start: 0.8362 (tmm-80) cc_final: 0.7991 (ttp-170) REVERT: B 1040 GLU cc_start: 0.8266 (mt-10) cc_final: 0.8005 (mt-10) REVERT: B 1044 GLN cc_start: 0.8448 (tm-30) cc_final: 0.7897 (mm-40) REVERT: C 246 MET cc_start: 0.6484 (ppp) cc_final: 0.5902 (ppp) REVERT: C 257 ARG cc_start: 0.7472 (mtp180) cc_final: 0.7211 (mtm-85) REVERT: C 378 LYS cc_start: 0.8096 (mtmt) cc_final: 0.7772 (mttm) REVERT: C 408 MET cc_start: 0.6509 (mmm) cc_final: 0.6228 (mmm) REVERT: C 651 MET cc_start: 0.8566 (ttm) cc_final: 0.8294 (mtt) REVERT: C 728 THR cc_start: 0.9516 (OUTLIER) cc_final: 0.9303 (m) REVERT: C 745 ASN cc_start: 0.8770 (t0) cc_final: 0.8539 (m-40) REVERT: C 823 LYS cc_start: 0.8433 (mttt) cc_final: 0.8039 (tppt) REVERT: C 824 LYS cc_start: 0.8582 (mttt) cc_final: 0.7941 (tmtt) REVERT: C 853 ARG cc_start: 0.8142 (tmm-80) cc_final: 0.7781 (tmm160) REVERT: D 375 TYR cc_start: 0.6523 (OUTLIER) cc_final: 0.6059 (t80) REVERT: D 400 HIS cc_start: 0.5926 (m-70) cc_final: 0.5694 (m-70) REVERT: D 561 LYS cc_start: 0.8131 (mtmt) cc_final: 0.7775 (mttm) REVERT: D 598 LYS cc_start: 0.7937 (mttt) cc_final: 0.7597 (ptmm) REVERT: D 818 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8979 (tp) REVERT: D 834 MET cc_start: 0.8460 (ttm) cc_final: 0.8215 (mtt) REVERT: D 911 THR cc_start: 0.9635 (OUTLIER) cc_final: 0.9303 (m) REVERT: D 1017 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7448 (tm-30) REVERT: D 1036 ARG cc_start: 0.8397 (tmm-80) cc_final: 0.8170 (ttp80) REVERT: D 1043 GLU cc_start: 0.5780 (mm-30) cc_final: 0.5056 (mm-30) outliers start: 94 outliers final: 50 residues processed: 505 average time/residue: 0.1426 time to fit residues: 116.3272 Evaluate side-chains 459 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 403 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 418 PHE Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 803 TYR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 926 MET Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 482 HIS Chi-restraints excluded: chain B residue 500 MET Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 754 ILE Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain B residue 874 ILE Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 999 PHE Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1015 CYS Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 299 HIS Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 728 THR Chi-restraints excluded: chain C residue 744 VAL Chi-restraints excluded: chain C residue 816 PHE Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain C residue 865 GLN Chi-restraints excluded: chain D residue 375 TYR Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 521 SER Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 797 VAL Chi-restraints excluded: chain D residue 818 LEU Chi-restraints excluded: chain D residue 874 ILE Chi-restraints excluded: chain D residue 911 THR Chi-restraints excluded: chain D residue 927 VAL Chi-restraints excluded: chain D residue 999 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 148 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 258 optimal weight: 4.9990 chunk 242 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 203 optimal weight: 0.9980 chunk 19 optimal weight: 9.9990 chunk 304 optimal weight: 4.9990 chunk 307 optimal weight: 7.9990 chunk 193 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 806 ASN A 837 ASN ** A 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 ASN ** B 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 ASN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 713 ASN D 482 HIS ** D 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 935 ASN D1057 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.162865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.132477 restraints weight = 33915.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.135023 restraints weight = 23688.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.136406 restraints weight = 14595.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.136857 restraints weight = 11815.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.137273 restraints weight = 11063.744| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 23649 Z= 0.262 Angle : 1.012 14.610 32237 Z= 0.507 Chirality : 0.052 0.316 3775 Planarity : 0.005 0.064 3968 Dihedral : 10.003 111.272 3506 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.79 % Allowed : 10.21 % Favored : 89.00 % Rotamer: Outliers : 5.61 % Allowed : 15.80 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 6.35 % Twisted Proline : 0.93 % Twisted General : 0.81 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.98 (0.16), residues: 2528 helix: -1.10 (0.12), residues: 1675 sheet: None (None), residues: 0 loop : -3.70 (0.19), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1034 TYR 0.024 0.002 TYR D 708 PHE 0.038 0.002 PHE B 777 TRP 0.024 0.002 TRP A 480 HIS 0.005 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00602 / 0.26 (23645) covalent geometry : angle 1.01187 / 0.51 (32229) SS BOND : bond 0.00432 / 0.22 ( 4) SS BOND : angle 1.15663 / 0.62 ( 8) hydrogen bonds : bond 0.04143 / 2.50 ( 994) hydrogen bonds : angle 4.45660 / 2.79 ( 2856) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 449 time to evaluate : 0.824 Fit side-chains revert: symmetry clash REVERT: A 312 LEU cc_start: 0.8968 (mt) cc_final: 0.8758 (mt) REVERT: A 429 MET cc_start: 0.5953 (ppp) cc_final: 0.5140 (ppp) REVERT: A 470 MET cc_start: 0.8493 (tpp) cc_final: 0.8266 (mmm) REVERT: A 487 MET cc_start: 0.9016 (tmm) cc_final: 0.8796 (ttp) REVERT: A 505 LYS cc_start: 0.7783 (mmtm) cc_final: 0.7476 (mmtm) REVERT: A 561 LYS cc_start: 0.8308 (mtmt) cc_final: 0.7833 (mttp) REVERT: A 591 MET cc_start: 0.5656 (ptp) cc_final: 0.5133 (ptp) REVERT: A 837 ASN cc_start: 0.8278 (t160) cc_final: 0.8041 (t160) REVERT: A 872 LYS cc_start: 0.7139 (mttt) cc_final: 0.6364 (tttp) REVERT: A 882 ILE cc_start: 0.7835 (OUTLIER) cc_final: 0.7410 (pt) REVERT: A 1003 GLU cc_start: 0.7005 (pm20) cc_final: 0.6753 (pm20) REVERT: A 1007 LYS cc_start: 0.8388 (mttt) cc_final: 0.8179 (tmtt) REVERT: B 429 MET cc_start: 0.7081 (ppp) cc_final: 0.6474 (ppp) REVERT: B 470 MET cc_start: 0.8802 (tpp) cc_final: 0.8584 (mmm) REVERT: B 561 LYS cc_start: 0.8503 (mtmt) cc_final: 0.8152 (mttm) REVERT: B 755 LYS cc_start: 0.7586 (pttm) cc_final: 0.7027 (tppt) REVERT: B 847 LEU cc_start: 0.9138 (tp) cc_final: 0.8905 (tp) REVERT: B 872 LYS cc_start: 0.7167 (mttt) cc_final: 0.6643 (tttp) REVERT: B 882 ILE cc_start: 0.7897 (OUTLIER) cc_final: 0.7558 (pt) REVERT: B 1036 ARG cc_start: 0.8623 (tmm-80) cc_final: 0.8314 (ttp-170) REVERT: B 1044 GLN cc_start: 0.8494 (tm-30) cc_final: 0.7985 (mm-40) REVERT: C 246 MET cc_start: 0.6563 (ppp) cc_final: 0.5996 (ppp) REVERT: C 257 ARG cc_start: 0.7577 (mtp180) cc_final: 0.7317 (mtm-85) REVERT: C 378 LYS cc_start: 0.8444 (mtmt) cc_final: 0.8110 (mttm) REVERT: C 664 LEU cc_start: 0.9114 (tp) cc_final: 0.8908 (tp) REVERT: C 748 ILE cc_start: 0.9238 (mm) cc_final: 0.8918 (mt) REVERT: C 823 LYS cc_start: 0.8446 (mttt) cc_final: 0.8104 (tppt) REVERT: C 824 LYS cc_start: 0.8597 (mttt) cc_final: 0.8309 (tmtt) REVERT: C 853 ARG cc_start: 0.8180 (tmm-80) cc_final: 0.7871 (tmm160) REVERT: D 375 TYR cc_start: 0.6862 (OUTLIER) cc_final: 0.6220 (t80) REVERT: D 533 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7530 (tm-30) REVERT: D 561 LYS cc_start: 0.8412 (mtmt) cc_final: 0.8103 (mttm) REVERT: D 732 PHE cc_start: 0.8518 (t80) cc_final: 0.8221 (t80) REVERT: D 935 ASN cc_start: 0.8615 (OUTLIER) cc_final: 0.8109 (t0) REVERT: D 1006 LYS cc_start: 0.8111 (ttmt) cc_final: 0.7263 (tppt) REVERT: D 1007 LYS cc_start: 0.8483 (mttt) cc_final: 0.8158 (tmtt) REVERT: D 1036 ARG cc_start: 0.8581 (tmm-80) cc_final: 0.8219 (ttp80) REVERT: D 1043 GLU cc_start: 0.6222 (mm-30) cc_final: 0.5972 (mm-30) outliers start: 108 outliers final: 67 residues processed: 511 average time/residue: 0.1459 time to fit residues: 121.3064 Evaluate side-chains 471 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 400 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 803 TYR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 397 ARG Chi-restraints excluded: chain B residue 482 HIS Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 736 ILE Chi-restraints excluded: chain B residue 754 ILE Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain B residue 830 MET Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 874 ILE Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 947 ILE Chi-restraints excluded: chain B residue 999 PHE Chi-restraints excluded: chain B residue 1047 ILE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 299 HIS Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 621 CYS Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 728 THR Chi-restraints excluded: chain C residue 744 VAL Chi-restraints excluded: chain C residue 816 PHE Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 371 PHE Chi-restraints excluded: chain D residue 375 TYR Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 482 HIS Chi-restraints excluded: chain D residue 521 SER Chi-restraints excluded: chain D residue 531 LEU Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 768 ILE Chi-restraints excluded: chain D residue 797 VAL Chi-restraints excluded: chain D residue 818 LEU Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain D residue 874 ILE Chi-restraints excluded: chain D residue 911 THR Chi-restraints excluded: chain D residue 927 VAL Chi-restraints excluded: chain D residue 935 ASN Chi-restraints excluded: chain D residue 999 PHE Chi-restraints excluded: chain D residue 1049 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 18 optimal weight: 0.9990 chunk 113 optimal weight: 0.6980 chunk 200 optimal weight: 4.9990 chunk 187 optimal weight: 6.9990 chunk 296 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 288 optimal weight: 0.5980 chunk 11 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 chunk 12 optimal weight: 0.0570 chunk 292 optimal weight: 0.0670 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 806 ASN ** A 936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 HIS ** B 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 ASN B1044 GLN B1048 GLN C 540 GLN C 861 GLN C 865 GLN D 473 GLN D 481 GLN D 935 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.170664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.140905 restraints weight = 33254.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.142485 restraints weight = 19442.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.144070 restraints weight = 13805.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.144690 restraints weight = 11254.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.144802 restraints weight = 10061.566| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.5376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23649 Z= 0.153 Angle : 0.898 13.691 32237 Z= 0.452 Chirality : 0.047 0.268 3775 Planarity : 0.004 0.050 3968 Dihedral : 9.355 104.753 3506 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.71 % Allowed : 9.02 % Favored : 90.27 % Rotamer: Outliers : 4.05 % Allowed : 19.96 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 6.43 % Twisted Proline : 0.00 % Twisted General : 0.49 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.45 (0.16), residues: 2528 helix: -0.63 (0.13), residues: 1657 sheet: None (None), residues: 0 loop : -3.59 (0.18), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 567 TYR 0.017 0.001 TYR C 525 PHE 0.034 0.002 PHE D 934 TRP 0.031 0.002 TRP D 480 HIS 0.003 0.000 HIS C 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (23645) covalent geometry : angle 0.89785 / 0.45 (32229) SS BOND : bond 0.00140 / 0.07 ( 4) SS BOND : angle 0.49862 / 0.18 ( 8) hydrogen bonds : bond 0.03410 / 2.03 ( 994) hydrogen bonds : angle 4.07155 / 2.54 ( 2856) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 446 time to evaluate : 0.770 Fit side-chains revert: symmetry clash REVERT: A 349 ASP cc_start: 0.6863 (p0) cc_final: 0.6509 (t0) REVERT: A 429 MET cc_start: 0.5748 (ppp) cc_final: 0.5039 (ppp) REVERT: A 487 MET cc_start: 0.8832 (tmm) cc_final: 0.8517 (ttp) REVERT: A 505 LYS cc_start: 0.7571 (mmtm) cc_final: 0.7274 (mmtm) REVERT: A 561 LYS cc_start: 0.8354 (mtmt) cc_final: 0.7921 (mttp) REVERT: A 710 PHE cc_start: 0.8872 (t80) cc_final: 0.8413 (t80) REVERT: A 933 PHE cc_start: 0.8495 (t80) cc_final: 0.8274 (t80) REVERT: A 1003 GLU cc_start: 0.6829 (pm20) cc_final: 0.6265 (pm20) REVERT: A 1004 ASP cc_start: 0.6649 (m-30) cc_final: 0.6239 (m-30) REVERT: A 1006 LYS cc_start: 0.8262 (ttpt) cc_final: 0.7334 (tppt) REVERT: B 429 MET cc_start: 0.7043 (ppp) cc_final: 0.6438 (ppp) REVERT: B 561 LYS cc_start: 0.8436 (mtmt) cc_final: 0.8050 (mttm) REVERT: B 847 LEU cc_start: 0.9051 (tp) cc_final: 0.8850 (tp) REVERT: B 872 LYS cc_start: 0.7230 (mttt) cc_final: 0.6720 (tptt) REVERT: B 882 ILE cc_start: 0.7559 (OUTLIER) cc_final: 0.7126 (pt) REVERT: B 1044 GLN cc_start: 0.8474 (tm130) cc_final: 0.8260 (tm-30) REVERT: C 246 MET cc_start: 0.6600 (ppp) cc_final: 0.5965 (ppp) REVERT: C 317 MET cc_start: 0.8642 (mtm) cc_final: 0.8438 (mtm) REVERT: C 336 GLN cc_start: 0.8359 (tm-30) cc_final: 0.8152 (tm-30) REVERT: C 378 LYS cc_start: 0.8290 (mtmt) cc_final: 0.7956 (mttm) REVERT: C 385 LEU cc_start: 0.0794 (OUTLIER) cc_final: 0.0531 (pt) REVERT: C 549 PHE cc_start: 0.8604 (t80) cc_final: 0.8306 (t80) REVERT: C 651 MET cc_start: 0.8486 (ttm) cc_final: 0.8260 (mtt) REVERT: C 664 LEU cc_start: 0.9046 (tp) cc_final: 0.8715 (tp) REVERT: C 699 ILE cc_start: 0.7644 (OUTLIER) cc_final: 0.7247 (pt) REVERT: C 728 THR cc_start: 0.9445 (OUTLIER) cc_final: 0.9180 (m) REVERT: C 823 LYS cc_start: 0.8386 (mttt) cc_final: 0.7995 (tppt) REVERT: C 824 LYS cc_start: 0.8591 (mttt) cc_final: 0.8281 (tmtt) REVERT: C 853 ARG cc_start: 0.7948 (tmm-80) cc_final: 0.7694 (ttp-170) REVERT: C 861 GLN cc_start: 0.8580 (tm130) cc_final: 0.8359 (tm-30) REVERT: D 375 TYR cc_start: 0.6758 (OUTLIER) cc_final: 0.6335 (t80) REVERT: D 429 MET cc_start: 0.7552 (ppp) cc_final: 0.7176 (ppp) REVERT: D 470 MET cc_start: 0.8586 (mmm) cc_final: 0.8232 (mmp) REVERT: D 508 ASP cc_start: 0.7273 (OUTLIER) cc_final: 0.6464 (m-30) REVERT: D 561 LYS cc_start: 0.8293 (mtmt) cc_final: 0.8023 (mttm) REVERT: D 818 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8887 (tp) REVERT: D 882 ILE cc_start: 0.7671 (OUTLIER) cc_final: 0.7356 (pt) REVERT: D 911 THR cc_start: 0.9439 (OUTLIER) cc_final: 0.9162 (m) REVERT: D 935 ASN cc_start: 0.8338 (OUTLIER) cc_final: 0.7537 (t0) REVERT: D 1006 LYS cc_start: 0.8106 (ttmt) cc_final: 0.7288 (tppt) REVERT: D 1007 LYS cc_start: 0.8525 (mttt) cc_final: 0.8158 (tmtt) REVERT: D 1033 GLU cc_start: 0.7630 (tp30) cc_final: 0.7373 (tp30) REVERT: D 1043 GLU cc_start: 0.6058 (mm-30) cc_final: 0.5636 (mm-30) outliers start: 78 outliers final: 53 residues processed: 492 average time/residue: 0.1476 time to fit residues: 117.4066 Evaluate side-chains 458 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 395 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 418 PHE Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain A residue 521 SER Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain A residue 803 TYR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 418 PHE Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 482 HIS Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 830 MET Chi-restraints excluded: chain B residue 834 MET Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 874 ILE Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 999 PHE Chi-restraints excluded: chain B residue 1009 HIS Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 299 HIS Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 621 CYS Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 647 MET Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain C residue 728 THR Chi-restraints excluded: chain C residue 744 VAL Chi-restraints excluded: chain C residue 816 PHE Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain D residue 371 PHE Chi-restraints excluded: chain D residue 375 TYR Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 471 LYS Chi-restraints excluded: chain D residue 482 HIS Chi-restraints excluded: chain D residue 508 ASP Chi-restraints excluded: chain D residue 521 SER Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 797 VAL Chi-restraints excluded: chain D residue 818 LEU Chi-restraints excluded: chain D residue 874 ILE Chi-restraints excluded: chain D residue 882 ILE Chi-restraints excluded: chain D residue 911 THR Chi-restraints excluded: chain D residue 927 VAL Chi-restraints excluded: chain D residue 935 ASN Chi-restraints excluded: chain D residue 999 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 169 optimal weight: 3.9990 chunk 119 optimal weight: 0.7980 chunk 176 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 216 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 136 optimal weight: 0.0570 chunk 242 optimal weight: 20.0000 chunk 292 optimal weight: 0.9980 chunk 179 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 461 ASN ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 ASN ** B 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 ASN D 482 HIS D 935 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.168663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.139270 restraints weight = 33603.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.140174 restraints weight = 20456.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.141298 restraints weight = 14799.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.142044 restraints weight = 12976.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.142074 restraints weight = 10945.266| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.5669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23649 Z= 0.162 Angle : 0.900 13.626 32237 Z= 0.451 Chirality : 0.048 0.266 3775 Planarity : 0.004 0.058 3968 Dihedral : 9.121 108.248 3506 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.67 % Allowed : 9.77 % Favored : 89.56 % Rotamer: Outliers : 4.68 % Allowed : 22.40 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 6.47 % Twisted Proline : 0.00 % Twisted General : 0.45 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.17), residues: 2528 helix: -0.43 (0.13), residues: 1664 sheet: None (None), residues: 0 loop : -3.49 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1036 TYR 0.015 0.001 TYR A 840 PHE 0.026 0.002 PHE D 773 TRP 0.024 0.002 TRP A 480 HIS 0.004 0.001 HIS C 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (23645) covalent geometry : angle 0.89975 / 0.45 (32229) SS BOND : bond 0.00219 / 0.11 ( 4) SS BOND : angle 0.40965 / 0.22 ( 8) hydrogen bonds : bond 0.03408 / 2.05 ( 994) hydrogen bonds : angle 3.92827 / 2.45 ( 2856) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 419 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 429 MET cc_start: 0.5743 (ppp) cc_final: 0.5043 (ppp) REVERT: A 487 MET cc_start: 0.8908 (tmm) cc_final: 0.8430 (ttt) REVERT: A 505 LYS cc_start: 0.7674 (mmtm) cc_final: 0.7418 (mmtm) REVERT: A 834 MET cc_start: 0.8546 (ttm) cc_final: 0.8236 (mtt) REVERT: A 1003 GLU cc_start: 0.6981 (pm20) cc_final: 0.6279 (pm20) REVERT: A 1004 ASP cc_start: 0.6526 (m-30) cc_final: 0.6007 (m-30) REVERT: A 1006 LYS cc_start: 0.8187 (ttpt) cc_final: 0.7331 (tppt) REVERT: B 429 MET cc_start: 0.7108 (ppp) cc_final: 0.6440 (ppp) REVERT: B 523 ASP cc_start: 0.6388 (m-30) cc_final: 0.6086 (m-30) REVERT: B 561 LYS cc_start: 0.8483 (mtmt) cc_final: 0.8171 (mttm) REVERT: B 847 LEU cc_start: 0.9064 (tp) cc_final: 0.8766 (tp) REVERT: B 872 LYS cc_start: 0.7123 (mttt) cc_final: 0.6466 (tptt) REVERT: B 882 ILE cc_start: 0.7541 (OUTLIER) cc_final: 0.7166 (pt) REVERT: B 1005 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.8344 (mt0) REVERT: B 1044 GLN cc_start: 0.8527 (tm130) cc_final: 0.7879 (mm-40) REVERT: C 246 MET cc_start: 0.6637 (ppp) cc_final: 0.6005 (ppp) REVERT: C 350 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7523 (tm-30) REVERT: C 378 LYS cc_start: 0.8363 (mtmt) cc_final: 0.8041 (mttm) REVERT: C 385 LEU cc_start: 0.0253 (OUTLIER) cc_final: 0.0025 (pt) REVERT: C 549 PHE cc_start: 0.8588 (t80) cc_final: 0.8356 (t80) REVERT: C 664 LEU cc_start: 0.9107 (tp) cc_final: 0.8747 (tp) REVERT: C 699 ILE cc_start: 0.7509 (OUTLIER) cc_final: 0.7159 (pt) REVERT: C 728 THR cc_start: 0.9542 (OUTLIER) cc_final: 0.9223 (m) REVERT: C 739 GLN cc_start: 0.8664 (mm110) cc_final: 0.8423 (tp40) REVERT: C 823 LYS cc_start: 0.8484 (mttt) cc_final: 0.8092 (tppt) REVERT: C 824 LYS cc_start: 0.8628 (mttt) cc_final: 0.8299 (tmtt) REVERT: C 861 GLN cc_start: 0.8563 (tm130) cc_final: 0.8338 (tm-30) REVERT: D 375 TYR cc_start: 0.6817 (OUTLIER) cc_final: 0.6325 (t80) REVERT: D 470 MET cc_start: 0.8669 (mmm) cc_final: 0.8327 (mmp) REVERT: D 508 ASP cc_start: 0.7276 (OUTLIER) cc_final: 0.6479 (m-30) REVERT: D 568 LEU cc_start: 0.0728 (OUTLIER) cc_final: 0.0472 (pt) REVERT: D 882 ILE cc_start: 0.7663 (OUTLIER) cc_final: 0.7330 (pt) REVERT: D 911 THR cc_start: 0.9460 (OUTLIER) cc_final: 0.9209 (m) REVERT: D 922 GLN cc_start: 0.8689 (mm110) cc_final: 0.8448 (tp40) REVERT: D 958 MET cc_start: 0.8794 (mmm) cc_final: 0.8555 (mmm) REVERT: D 1006 LYS cc_start: 0.8097 (ttmt) cc_final: 0.7266 (tppt) REVERT: D 1007 LYS cc_start: 0.8526 (mttt) cc_final: 0.8194 (tmtt) REVERT: D 1041 ARG cc_start: 0.8532 (tpp80) cc_final: 0.7887 (mtt-85) REVERT: D 1043 GLU cc_start: 0.5970 (mm-30) cc_final: 0.5539 (mm-30) outliers start: 90 outliers final: 64 residues processed: 474 average time/residue: 0.1460 time to fit residues: 112.8859 Evaluate side-chains 472 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 398 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 418 PHE Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain A residue 521 SER Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain A residue 803 TYR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1009 HIS Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 397 ARG Chi-restraints excluded: chain B residue 418 PHE Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 482 HIS Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 579 MET Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 834 MET Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 874 ILE Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 999 PHE Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1009 HIS Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 299 HIS Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 340 ASP Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 621 CYS Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 647 MET Chi-restraints excluded: chain C residue 666 LEU Chi-restraints excluded: chain C residue 668 SER Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain C residue 728 THR Chi-restraints excluded: chain C residue 744 VAL Chi-restraints excluded: chain C residue 816 PHE Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain D residue 375 TYR Chi-restraints excluded: chain D residue 418 PHE Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 471 LYS Chi-restraints excluded: chain D residue 508 ASP Chi-restraints excluded: chain D residue 521 SER Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 753 LYS Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 797 VAL Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain D residue 820 VAL Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain D residue 874 ILE Chi-restraints excluded: chain D residue 882 ILE Chi-restraints excluded: chain D residue 911 THR Chi-restraints excluded: chain D residue 927 VAL Chi-restraints excluded: chain D residue 999 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 64 optimal weight: 0.5980 chunk 116 optimal weight: 0.0170 chunk 268 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 139 optimal weight: 0.4980 chunk 233 optimal weight: 9.9990 chunk 249 optimal weight: 8.9990 chunk 225 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 158 optimal weight: 10.0000 chunk 224 optimal weight: 8.9990 overall best weight: 1.6222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 806 ASN A1005 GLN ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 ASN ** B 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 ASN D 590 ASN D 935 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.159352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.128919 restraints weight = 33876.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.132203 restraints weight = 22261.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.133130 restraints weight = 13373.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.133690 restraints weight = 11251.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.134111 restraints weight = 10334.773| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.5914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 23649 Z= 0.226 Angle : 0.967 13.543 32237 Z= 0.482 Chirality : 0.050 0.293 3775 Planarity : 0.005 0.055 3968 Dihedral : 9.405 110.497 3506 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.79 % Allowed : 10.44 % Favored : 88.77 % Rotamer: Outliers : 5.46 % Allowed : 22.14 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 6.39 % Twisted Proline : 1.85 % Twisted General : 0.69 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.17), residues: 2528 helix: -0.51 (0.13), residues: 1673 sheet: None (None), residues: 0 loop : -3.49 (0.19), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D1036 TYR 0.018 0.002 TYR D 708 PHE 0.022 0.002 PHE D 773 TRP 0.034 0.002 TRP A 480 HIS 0.005 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.23 (23645) covalent geometry : angle 0.96715 / 0.48 (32229) SS BOND : bond 0.00334 / 0.17 ( 4) SS BOND : angle 0.98896 / 0.52 ( 8) hydrogen bonds : bond 0.03693 / 2.21 ( 994) hydrogen bonds : angle 4.07772 / 2.54 ( 2856) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 417 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 429 MET cc_start: 0.5998 (ppp) cc_final: 0.5300 (ppp) REVERT: A 487 MET cc_start: 0.9031 (tmm) cc_final: 0.8822 (ttp) REVERT: A 505 LYS cc_start: 0.7855 (mmtm) cc_final: 0.7514 (mmtm) REVERT: A 533 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7798 (tm-30) REVERT: A 834 MET cc_start: 0.8553 (ttm) cc_final: 0.8222 (mtt) REVERT: A 882 ILE cc_start: 0.7475 (OUTLIER) cc_final: 0.7091 (pt) REVERT: A 1003 GLU cc_start: 0.7104 (pm20) cc_final: 0.6407 (pm20) REVERT: A 1004 ASP cc_start: 0.6723 (m-30) cc_final: 0.6178 (m-30) REVERT: A 1006 LYS cc_start: 0.8182 (ttpt) cc_final: 0.7313 (tppt) REVERT: A 1007 LYS cc_start: 0.8346 (mttt) cc_final: 0.8079 (tmtt) REVERT: B 429 MET cc_start: 0.7100 (ppp) cc_final: 0.6452 (ppp) REVERT: B 524 PHE cc_start: 0.9039 (OUTLIER) cc_final: 0.7438 (t80) REVERT: B 561 LYS cc_start: 0.8442 (mtmt) cc_final: 0.8113 (mttm) REVERT: B 568 LEU cc_start: 0.0465 (OUTLIER) cc_final: 0.0106 (pt) REVERT: B 777 PHE cc_start: 0.7879 (OUTLIER) cc_final: 0.7474 (m-10) REVERT: B 847 LEU cc_start: 0.9018 (tp) cc_final: 0.8685 (tp) REVERT: B 872 LYS cc_start: 0.7109 (mttt) cc_final: 0.6314 (tttp) REVERT: B 882 ILE cc_start: 0.7813 (OUTLIER) cc_final: 0.7437 (pt) REVERT: B 922 GLN cc_start: 0.8897 (mm-40) cc_final: 0.8687 (mm110) REVERT: B 1005 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8413 (mt0) REVERT: B 1039 PHE cc_start: 0.9088 (t80) cc_final: 0.8522 (t80) REVERT: C 246 MET cc_start: 0.6611 (ppp) cc_final: 0.5996 (ppp) REVERT: C 350 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7701 (tm-30) REVERT: C 378 LYS cc_start: 0.8387 (mtmt) cc_final: 0.8036 (mttm) REVERT: C 385 LEU cc_start: 0.0544 (OUTLIER) cc_final: 0.0198 (pt) REVERT: C 664 LEU cc_start: 0.9049 (tp) cc_final: 0.8761 (tp) REVERT: C 699 ILE cc_start: 0.7742 (OUTLIER) cc_final: 0.7332 (pt) REVERT: C 728 THR cc_start: 0.9450 (OUTLIER) cc_final: 0.9114 (m) REVERT: C 823 LYS cc_start: 0.8370 (mttt) cc_final: 0.8020 (tppt) REVERT: C 824 LYS cc_start: 0.8651 (mttt) cc_final: 0.8287 (tmtt) REVERT: C 861 GLN cc_start: 0.8597 (tm130) cc_final: 0.8260 (tm-30) REVERT: D 375 TYR cc_start: 0.7018 (OUTLIER) cc_final: 0.6539 (t80) REVERT: D 470 MET cc_start: 0.8767 (mmm) cc_final: 0.8395 (mmp) REVERT: D 508 ASP cc_start: 0.7165 (OUTLIER) cc_final: 0.6204 (m-30) REVERT: D 533 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7445 (tm-30) REVERT: D 568 LEU cc_start: 0.0747 (OUTLIER) cc_final: 0.0443 (pt) REVERT: D 882 ILE cc_start: 0.7792 (OUTLIER) cc_final: 0.7507 (pt) REVERT: D 911 THR cc_start: 0.9457 (OUTLIER) cc_final: 0.9144 (m) REVERT: D 1006 LYS cc_start: 0.8095 (ttmt) cc_final: 0.7286 (tppt) REVERT: D 1007 LYS cc_start: 0.8443 (mttt) cc_final: 0.8101 (tmtt) REVERT: D 1041 ARG cc_start: 0.8562 (tpp80) cc_final: 0.7906 (mtt-85) REVERT: D 1043 GLU cc_start: 0.5930 (mm-30) cc_final: 0.5469 (mm-30) outliers start: 105 outliers final: 77 residues processed: 478 average time/residue: 0.1446 time to fit residues: 112.1842 Evaluate side-chains 491 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 400 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 PHE Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain A residue 521 SER Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 803 TYR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 851 SER Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 397 ARG Chi-restraints excluded: chain B residue 418 PHE Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 482 HIS Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 524 PHE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 586 MET Chi-restraints excluded: chain B residue 777 PHE Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 803 TYR Chi-restraints excluded: chain B residue 834 MET Chi-restraints excluded: chain B residue 874 ILE Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 935 ASN Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 999 PHE Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1009 HIS Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 299 HIS Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 340 ASP Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 621 CYS Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 647 MET Chi-restraints excluded: chain C residue 666 LEU Chi-restraints excluded: chain C residue 668 SER Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain C residue 728 THR Chi-restraints excluded: chain C residue 744 VAL Chi-restraints excluded: chain C residue 754 VAL Chi-restraints excluded: chain C residue 816 PHE Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain C residue 854 VAL Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 371 PHE Chi-restraints excluded: chain D residue 375 TYR Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 418 PHE Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 471 LYS Chi-restraints excluded: chain D residue 482 HIS Chi-restraints excluded: chain D residue 508 ASP Chi-restraints excluded: chain D residue 521 SER Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 599 VAL Chi-restraints excluded: chain D residue 719 LEU Chi-restraints excluded: chain D residue 753 LYS Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 797 VAL Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain D residue 874 ILE Chi-restraints excluded: chain D residue 882 ILE Chi-restraints excluded: chain D residue 911 THR Chi-restraints excluded: chain D residue 927 VAL Chi-restraints excluded: chain D residue 999 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 153 optimal weight: 10.0000 chunk 197 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 191 optimal weight: 9.9990 chunk 202 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 ASN ** B 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 ASN ** B1048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1057 ASN C 778 HIS D 763 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.154399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.124330 restraints weight = 33972.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.126439 restraints weight = 23566.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.127897 restraints weight = 15105.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.128591 restraints weight = 12283.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.129126 restraints weight = 11186.261| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.6225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 23649 Z= 0.286 Angle : 1.024 14.047 32237 Z= 0.510 Chirality : 0.053 0.310 3775 Planarity : 0.005 0.062 3968 Dihedral : 9.769 109.588 3506 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.79 % Allowed : 10.92 % Favored : 88.29 % Rotamer: Outliers : 6.55 % Allowed : 21.41 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 6.35 % Twisted Proline : 1.85 % Twisted General : 0.73 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.17), residues: 2528 helix: -0.64 (0.13), residues: 1686 sheet: None (None), residues: 0 loop : -3.41 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 800 TYR 0.016 0.002 TYR D 708 PHE 0.024 0.002 PHE D 773 TRP 0.024 0.002 TRP A 480 HIS 0.006 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00666 / 0.29 (23645) covalent geometry : angle 1.02429 / 0.51 (32229) SS BOND : bond 0.00331 / 0.17 ( 4) SS BOND : angle 1.19272 / 0.60 ( 8) hydrogen bonds : bond 0.03882 / 2.32 ( 994) hydrogen bonds : angle 4.25479 / 2.65 ( 2856) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 421 time to evaluate : 0.618 Fit side-chains revert: symmetry clash REVERT: A 425 TYR cc_start: 0.7764 (m-80) cc_final: 0.7352 (m-80) REVERT: A 429 MET cc_start: 0.6397 (ppp) cc_final: 0.5855 (ppp) REVERT: A 524 PHE cc_start: 0.9192 (OUTLIER) cc_final: 0.7288 (t80) REVERT: A 561 LYS cc_start: 0.8330 (mtmt) cc_final: 0.7917 (mttp) REVERT: A 567 ARG cc_start: 0.6928 (OUTLIER) cc_final: 0.6455 (ptp90) REVERT: A 568 LEU cc_start: 0.1149 (OUTLIER) cc_final: 0.0909 (pt) REVERT: A 741 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7587 (tt0) REVERT: A 834 MET cc_start: 0.8536 (ttm) cc_final: 0.8105 (mtt) REVERT: A 872 LYS cc_start: 0.6816 (mttt) cc_final: 0.6008 (tttp) REVERT: A 882 ILE cc_start: 0.7689 (OUTLIER) cc_final: 0.7448 (pt) REVERT: A 1003 GLU cc_start: 0.7348 (pm20) cc_final: 0.6676 (pm20) REVERT: A 1004 ASP cc_start: 0.7200 (m-30) cc_final: 0.6516 (m-30) REVERT: A 1007 LYS cc_start: 0.8338 (mttt) cc_final: 0.8082 (tmtt) REVERT: B 429 MET cc_start: 0.7112 (ppp) cc_final: 0.6436 (ppp) REVERT: B 470 MET cc_start: 0.8856 (mmp) cc_final: 0.8625 (mmp) REVERT: B 524 PHE cc_start: 0.9056 (OUTLIER) cc_final: 0.7613 (t80) REVERT: B 561 LYS cc_start: 0.8458 (mtmt) cc_final: 0.8126 (mttm) REVERT: B 568 LEU cc_start: 0.1494 (OUTLIER) cc_final: 0.1124 (pt) REVERT: B 719 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7973 (mp) REVERT: B 777 PHE cc_start: 0.8186 (OUTLIER) cc_final: 0.7694 (m-10) REVERT: B 872 LYS cc_start: 0.7153 (mttt) cc_final: 0.6450 (tttp) REVERT: B 1005 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8449 (mt0) REVERT: B 1032 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7723 (mm-30) REVERT: C 180 ARG cc_start: 0.8224 (ttm-80) cc_final: 0.7949 (ttm110) REVERT: C 246 MET cc_start: 0.6796 (ppp) cc_final: 0.6062 (ppp) REVERT: C 341 PHE cc_start: 0.9124 (OUTLIER) cc_final: 0.7041 (t80) REVERT: C 350 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7815 (tm-30) REVERT: C 378 LYS cc_start: 0.8376 (mtmt) cc_final: 0.8052 (mttm) REVERT: C 385 LEU cc_start: 0.0364 (OUTLIER) cc_final: -0.0004 (pt) REVERT: C 664 LEU cc_start: 0.9081 (tp) cc_final: 0.8792 (tp) REVERT: C 699 ILE cc_start: 0.7839 (OUTLIER) cc_final: 0.7569 (pt) REVERT: C 728 THR cc_start: 0.9415 (OUTLIER) cc_final: 0.9123 (m) REVERT: C 823 LYS cc_start: 0.8258 (mttt) cc_final: 0.7843 (tppt) REVERT: C 824 LYS cc_start: 0.8654 (mttt) cc_final: 0.8267 (tmtt) REVERT: D 375 TYR cc_start: 0.7196 (OUTLIER) cc_final: 0.6541 (t80) REVERT: D 429 MET cc_start: 0.7682 (ppp) cc_final: 0.7239 (ppp) REVERT: D 470 MET cc_start: 0.8774 (mmm) cc_final: 0.8401 (mmp) REVERT: D 508 ASP cc_start: 0.7276 (OUTLIER) cc_final: 0.6276 (m-30) REVERT: D 524 PHE cc_start: 0.9174 (OUTLIER) cc_final: 0.7207 (t80) REVERT: D 533 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7707 (tm-30) REVERT: D 561 LYS cc_start: 0.8314 (mtmt) cc_final: 0.7900 (mttp) REVERT: D 568 LEU cc_start: 0.0417 (OUTLIER) cc_final: 0.0036 (pt) REVERT: D 806 ASN cc_start: 0.8962 (t0) cc_final: 0.8605 (t0) REVERT: D 882 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7735 (pt) REVERT: D 911 THR cc_start: 0.9458 (OUTLIER) cc_final: 0.9107 (m) REVERT: D 1006 LYS cc_start: 0.8108 (ttmt) cc_final: 0.7299 (tppt) REVERT: D 1007 LYS cc_start: 0.8448 (mttt) cc_final: 0.8153 (tmtt) REVERT: D 1041 ARG cc_start: 0.8517 (tpp80) cc_final: 0.7897 (mtt-85) REVERT: D 1043 GLU cc_start: 0.6136 (mm-30) cc_final: 0.5610 (mm-30) outliers start: 126 outliers final: 84 residues processed: 495 average time/residue: 0.1383 time to fit residues: 112.1561 Evaluate side-chains 516 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 413 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 PHE Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain A residue 521 SER Chi-restraints excluded: chain A residue 524 PHE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 803 TYR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 851 SER Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 926 MET Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 397 ARG Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 482 HIS Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 524 PHE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 754 ILE Chi-restraints excluded: chain B residue 777 PHE Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 803 TYR Chi-restraints excluded: chain B residue 834 MET Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 874 ILE Chi-restraints excluded: chain B residue 883 PHE Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 999 PHE Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 217 HIS Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 299 HIS Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 340 ASP Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 621 CYS Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 666 LEU Chi-restraints excluded: chain C residue 668 SER Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain C residue 700 PHE Chi-restraints excluded: chain C residue 728 THR Chi-restraints excluded: chain C residue 744 VAL Chi-restraints excluded: chain C residue 754 VAL Chi-restraints excluded: chain C residue 816 PHE Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 371 PHE Chi-restraints excluded: chain D residue 375 TYR Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 418 PHE Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 465 ILE Chi-restraints excluded: chain D residue 471 LYS Chi-restraints excluded: chain D residue 482 HIS Chi-restraints excluded: chain D residue 508 ASP Chi-restraints excluded: chain D residue 521 SER Chi-restraints excluded: chain D residue 524 PHE Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 719 LEU Chi-restraints excluded: chain D residue 753 LYS Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 797 VAL Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain D residue 874 ILE Chi-restraints excluded: chain D residue 882 ILE Chi-restraints excluded: chain D residue 883 PHE Chi-restraints excluded: chain D residue 911 THR Chi-restraints excluded: chain D residue 927 VAL Chi-restraints excluded: chain D residue 999 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 46 optimal weight: 0.8980 chunk 202 optimal weight: 4.9990 chunk 287 optimal weight: 0.5980 chunk 95 optimal weight: 4.9990 chunk 228 optimal weight: 0.8980 chunk 291 optimal weight: 0.5980 chunk 180 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 12 optimal weight: 0.3980 chunk 48 optimal weight: 0.7980 chunk 11 optimal weight: 10.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 461 ASN A 806 ASN A 936 ASN ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 ASN B1044 GLN C 278 ASN ** C 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1044 GLN D1048 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.163670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.133359 restraints weight = 33688.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.135967 restraints weight = 21754.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.137349 restraints weight = 13739.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.138144 restraints weight = 11056.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.138625 restraints weight = 10067.563| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.6437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23649 Z= 0.163 Angle : 0.905 13.019 32237 Z= 0.453 Chirality : 0.047 0.254 3775 Planarity : 0.004 0.055 3968 Dihedral : 9.139 106.509 3506 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.67 % Allowed : 9.69 % Favored : 89.64 % Rotamer: Outliers : 4.89 % Allowed : 23.54 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 6.35 % Twisted Proline : 0.00 % Twisted General : 0.65 % 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: -1.95 (0.17), residues: 2528 helix: -0.28 (0.13), residues: 1686 sheet: None (None), residues: 0 loop : -3.39 (0.19), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 800 TYR 0.016 0.001 TYR A 840 PHE 0.034 0.002 PHE A 478 TRP 0.033 0.002 TRP A 480 HIS 0.003 0.001 HIS C 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (23645) covalent geometry : angle 0.90517 / 0.45 (32229) SS BOND : bond 0.00110 / 0.06 ( 4) SS BOND : angle 0.71895 / 0.38 ( 8) hydrogen bonds : bond 0.03360 / 2.01 ( 994) hydrogen bonds : angle 3.95173 / 2.46 ( 2856) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 431 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 ARG cc_start: 0.7371 (ttt180) cc_final: 0.7085 (ttt180) REVERT: A 429 MET cc_start: 0.6024 (ppp) cc_final: 0.5616 (ppp) REVERT: A 524 PHE cc_start: 0.9169 (OUTLIER) cc_final: 0.7313 (t80) REVERT: A 533 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7722 (tm-30) REVERT: A 567 ARG cc_start: 0.6821 (OUTLIER) cc_final: 0.6025 (ptp90) REVERT: A 741 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7698 (tt0) REVERT: A 882 ILE cc_start: 0.7556 (OUTLIER) cc_final: 0.7216 (pt) REVERT: A 1003 GLU cc_start: 0.7210 (pm20) cc_final: 0.6989 (pm20) REVERT: A 1004 ASP cc_start: 0.7050 (m-30) cc_final: 0.6392 (m-30) REVERT: B 429 MET cc_start: 0.7060 (ppp) cc_final: 0.6396 (ppp) REVERT: B 523 ASP cc_start: 0.6761 (m-30) cc_final: 0.6475 (m-30) REVERT: B 561 LYS cc_start: 0.8261 (mtmt) cc_final: 0.7905 (mttp) REVERT: B 568 LEU cc_start: 0.1044 (OUTLIER) cc_final: 0.0774 (pt) REVERT: B 719 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7975 (mp) REVERT: B 777 PHE cc_start: 0.7805 (OUTLIER) cc_final: 0.7472 (m-10) REVERT: B 872 LYS cc_start: 0.7221 (mttt) cc_final: 0.6489 (tttp) REVERT: B 1005 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8396 (mt0) REVERT: B 1039 PHE cc_start: 0.8947 (t80) cc_final: 0.8296 (t80) REVERT: C 246 MET cc_start: 0.6588 (ppp) cc_final: 0.5835 (ppp) REVERT: C 341 PHE cc_start: 0.9125 (OUTLIER) cc_final: 0.6836 (t80) REVERT: C 350 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7734 (tm-30) REVERT: C 385 LEU cc_start: 0.0827 (OUTLIER) cc_final: 0.0586 (pt) REVERT: C 664 LEU cc_start: 0.9019 (tp) cc_final: 0.8666 (tp) REVERT: C 699 ILE cc_start: 0.7577 (OUTLIER) cc_final: 0.7185 (pt) REVERT: C 728 THR cc_start: 0.9468 (OUTLIER) cc_final: 0.9158 (m) REVERT: C 823 LYS cc_start: 0.8064 (mttt) cc_final: 0.7611 (tppt) REVERT: C 824 LYS cc_start: 0.8529 (mttt) cc_final: 0.8172 (tmtt) REVERT: C 861 GLN cc_start: 0.8654 (tm-30) cc_final: 0.8037 (mm-40) REVERT: D 375 TYR cc_start: 0.7108 (OUTLIER) cc_final: 0.6704 (t80) REVERT: D 429 MET cc_start: 0.7680 (ppp) cc_final: 0.7270 (ppp) REVERT: D 470 MET cc_start: 0.8636 (mmm) cc_final: 0.8256 (mmp) REVERT: D 508 ASP cc_start: 0.7232 (OUTLIER) cc_final: 0.6373 (m-30) REVERT: D 568 LEU cc_start: 0.1199 (OUTLIER) cc_final: 0.0958 (pt) REVERT: D 882 ILE cc_start: 0.7668 (OUTLIER) cc_final: 0.7223 (pt) REVERT: D 911 THR cc_start: 0.9434 (OUTLIER) cc_final: 0.9123 (m) REVERT: D 1006 LYS cc_start: 0.8049 (ttmt) cc_final: 0.7278 (tppt) REVERT: D 1007 LYS cc_start: 0.8382 (mttt) cc_final: 0.8082 (tmtt) REVERT: D 1041 ARG cc_start: 0.8567 (tpp80) cc_final: 0.8027 (tpp80) REVERT: D 1043 GLU cc_start: 0.6159 (mm-30) cc_final: 0.5681 (mm-30) outliers start: 94 outliers final: 68 residues processed: 488 average time/residue: 0.1439 time to fit residues: 114.6207 Evaluate side-chains 499 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 415 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 418 PHE Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain A residue 521 SER Chi-restraints excluded: chain A residue 524 PHE Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 803 TYR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 851 SER Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 883 PHE Chi-restraints excluded: chain A residue 926 MET Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 418 PHE Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 482 HIS Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 754 ILE Chi-restraints excluded: chain B residue 777 PHE Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 803 TYR Chi-restraints excluded: chain B residue 834 MET Chi-restraints excluded: chain B residue 874 ILE Chi-restraints excluded: chain B residue 883 PHE Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 999 PHE Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1009 HIS Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 299 HIS Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 621 CYS Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 666 LEU Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain C residue 728 THR Chi-restraints excluded: chain C residue 744 VAL Chi-restraints excluded: chain C residue 816 PHE Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain D residue 371 PHE Chi-restraints excluded: chain D residue 375 TYR Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 418 PHE Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 471 LYS Chi-restraints excluded: chain D residue 508 ASP Chi-restraints excluded: chain D residue 521 SER Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 753 LYS Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 797 VAL Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 874 ILE Chi-restraints excluded: chain D residue 882 ILE Chi-restraints excluded: chain D residue 883 PHE Chi-restraints excluded: chain D residue 911 THR Chi-restraints excluded: chain D residue 927 VAL Chi-restraints excluded: chain D residue 937 VAL Chi-restraints excluded: chain D residue 999 PHE Chi-restraints excluded: chain D residue 1004 ASP Chi-restraints excluded: chain D residue 1048 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 142 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 chunk 267 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 191 optimal weight: 4.9990 chunk 275 optimal weight: 3.9990 chunk 193 optimal weight: 0.9990 chunk 287 optimal weight: 0.2980 chunk 2 optimal weight: 10.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 936 ASN ** B1048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.164949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.136855 restraints weight = 32732.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.139314 restraints weight = 23990.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.140228 restraints weight = 16258.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.140890 restraints weight = 12904.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.140910 restraints weight = 12142.909| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.6554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23649 Z= 0.167 Angle : 0.918 14.004 32237 Z= 0.459 Chirality : 0.047 0.267 3775 Planarity : 0.005 0.057 3968 Dihedral : 8.984 108.153 3506 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.79 % Allowed : 9.77 % Favored : 89.44 % Rotamer: Outliers : 4.63 % Allowed : 25.26 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 6.47 % Twisted Proline : 0.00 % Twisted General : 0.45 % 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: -1.82 (0.17), residues: 2528 helix: -0.21 (0.13), residues: 1701 sheet: None (None), residues: 0 loop : -3.34 (0.20), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 800 TYR 0.017 0.001 TYR B 840 PHE 0.021 0.002 PHE B1039 TRP 0.026 0.002 TRP A 480 HIS 0.004 0.001 HIS C 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 (23645) covalent geometry : angle 0.91791 / 0.46 (32229) SS BOND : bond 0.00174 / 0.09 ( 4) SS BOND : angle 0.39602 / 0.19 ( 8) hydrogen bonds : bond 0.03353 / 2.01 ( 994) hydrogen bonds : angle 3.88874 / 2.41 ( 2856) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 420 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 ASP cc_start: 0.6371 (p0) cc_final: 0.6018 (t0) REVERT: A 429 MET cc_start: 0.6213 (ppp) cc_final: 0.5575 (ppp) REVERT: A 487 MET cc_start: 0.8933 (tmm) cc_final: 0.8594 (ttp) REVERT: A 524 PHE cc_start: 0.9154 (OUTLIER) cc_final: 0.7426 (t80) REVERT: A 533 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7626 (tm-30) REVERT: A 567 ARG cc_start: 0.6954 (OUTLIER) cc_final: 0.6739 (ptp90) REVERT: A 882 ILE cc_start: 0.7560 (OUTLIER) cc_final: 0.7298 (pt) REVERT: A 1003 GLU cc_start: 0.7079 (pm20) cc_final: 0.6872 (pm20) REVERT: A 1004 ASP cc_start: 0.6832 (m-30) cc_final: 0.6243 (m-30) REVERT: B 429 MET cc_start: 0.6909 (ppp) cc_final: 0.6329 (ppp) REVERT: B 523 ASP cc_start: 0.6465 (m-30) cc_final: 0.6230 (m-30) REVERT: B 568 LEU cc_start: 0.0836 (OUTLIER) cc_final: 0.0593 (pt) REVERT: B 719 LEU cc_start: 0.8054 (mt) cc_final: 0.7818 (mp) REVERT: B 777 PHE cc_start: 0.7708 (OUTLIER) cc_final: 0.7404 (m-10) REVERT: B 962 GLU cc_start: 0.8303 (mm-30) cc_final: 0.8094 (mm-30) REVERT: B 1005 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8348 (mt0) REVERT: B 1039 PHE cc_start: 0.8927 (t80) cc_final: 0.8307 (t80) REVERT: B 1044 GLN cc_start: 0.8635 (tm-30) cc_final: 0.8214 (mm110) REVERT: C 246 MET cc_start: 0.6501 (ppp) cc_final: 0.5860 (ppp) REVERT: C 341 PHE cc_start: 0.9028 (OUTLIER) cc_final: 0.6889 (t80) REVERT: C 350 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7710 (tm-30) REVERT: C 664 LEU cc_start: 0.9034 (tp) cc_final: 0.8737 (tp) REVERT: C 699 ILE cc_start: 0.7591 (OUTLIER) cc_final: 0.7208 (pt) REVERT: C 728 THR cc_start: 0.9518 (OUTLIER) cc_final: 0.9167 (m) REVERT: C 823 LYS cc_start: 0.7886 (mttt) cc_final: 0.7662 (tppt) REVERT: C 824 LYS cc_start: 0.8476 (mttt) cc_final: 0.8236 (tmtt) REVERT: C 861 GLN cc_start: 0.8679 (tm-30) cc_final: 0.8137 (mm-40) REVERT: D 375 TYR cc_start: 0.6967 (OUTLIER) cc_final: 0.6638 (t80) REVERT: D 429 MET cc_start: 0.7617 (ppp) cc_final: 0.7248 (ppp) REVERT: D 470 MET cc_start: 0.8654 (mmm) cc_final: 0.8342 (mmp) REVERT: D 508 ASP cc_start: 0.7143 (OUTLIER) cc_final: 0.6320 (m-30) REVERT: D 882 ILE cc_start: 0.7610 (OUTLIER) cc_final: 0.7248 (pt) REVERT: D 911 THR cc_start: 0.9526 (OUTLIER) cc_final: 0.9130 (m) REVERT: D 1006 LYS cc_start: 0.8028 (ttmt) cc_final: 0.7298 (tppt) REVERT: D 1041 ARG cc_start: 0.8558 (tpp80) cc_final: 0.7787 (mtt-85) REVERT: D 1043 GLU cc_start: 0.6062 (mm-30) cc_final: 0.5722 (mm-30) REVERT: D 1044 GLN cc_start: 0.8714 (tm-30) cc_final: 0.8319 (mm110) outliers start: 89 outliers final: 68 residues processed: 478 average time/residue: 0.1381 time to fit residues: 108.7348 Evaluate side-chains 486 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 405 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 418 PHE Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain A residue 521 SER Chi-restraints excluded: chain A residue 524 PHE Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 803 TYR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 851 SER Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 883 PHE Chi-restraints excluded: chain A residue 926 MET Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 936 ASN Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 418 PHE Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 482 HIS Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 754 ILE Chi-restraints excluded: chain B residue 777 PHE Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 803 TYR Chi-restraints excluded: chain B residue 834 MET Chi-restraints excluded: chain B residue 874 ILE Chi-restraints excluded: chain B residue 883 PHE Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 999 PHE Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1009 HIS Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 299 HIS Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 621 CYS Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 666 LEU Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain C residue 728 THR Chi-restraints excluded: chain C residue 744 VAL Chi-restraints excluded: chain C residue 816 PHE Chi-restraints excluded: chain D residue 371 PHE Chi-restraints excluded: chain D residue 375 TYR Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 418 PHE Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 471 LYS Chi-restraints excluded: chain D residue 508 ASP Chi-restraints excluded: chain D residue 521 SER Chi-restraints excluded: chain D residue 753 LYS Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 797 VAL Chi-restraints excluded: chain D residue 803 TYR Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain D residue 874 ILE Chi-restraints excluded: chain D residue 882 ILE Chi-restraints excluded: chain D residue 883 PHE Chi-restraints excluded: chain D residue 911 THR Chi-restraints excluded: chain D residue 927 VAL Chi-restraints excluded: chain D residue 937 VAL Chi-restraints excluded: chain D residue 999 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 154 optimal weight: 10.0000 chunk 128 optimal weight: 0.8980 chunk 211 optimal weight: 0.7980 chunk 152 optimal weight: 0.8980 chunk 250 optimal weight: 0.2980 chunk 8 optimal weight: 10.0000 chunk 238 optimal weight: 10.0000 chunk 258 optimal weight: 0.8980 chunk 189 optimal weight: 0.7980 chunk 83 optimal weight: 10.0000 chunk 249 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 936 ASN B 461 ASN ** B1048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.165801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.137699 restraints weight = 32590.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.140608 restraints weight = 22841.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.141671 restraints weight = 15104.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.141911 restraints weight = 12016.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.142333 restraints weight = 11580.766| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.6659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23649 Z= 0.166 Angle : 0.918 16.902 32237 Z= 0.457 Chirality : 0.047 0.255 3775 Planarity : 0.005 0.052 3968 Dihedral : 8.878 108.245 3506 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.83 % Allowed : 9.85 % Favored : 89.32 % Rotamer: Outliers : 4.68 % Allowed : 25.26 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 6.43 % Twisted Proline : 0.00 % Twisted General : 0.49 % 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: -1.71 (0.17), residues: 2528 helix: -0.13 (0.13), residues: 1703 sheet: None (None), residues: 0 loop : -3.29 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 800 TYR 0.018 0.001 TYR B 840 PHE 0.021 0.002 PHE B1039 TRP 0.026 0.002 TRP A 480 HIS 0.003 0.001 HIS C 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.17 (23645) covalent geometry : angle 0.91808 / 0.46 (32229) SS BOND : bond 0.00177 / 0.09 ( 4) SS BOND : angle 0.31661 / 0.15 ( 8) hydrogen bonds : bond 0.03322 / 1.99 ( 994) hydrogen bonds : angle 3.82416 / 2.37 ( 2856) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3736.73 seconds wall clock time: 65 minutes 24.35 seconds (3924.35 seconds total)