Starting phenix.real_space_refine on Fri Jul 3 10:36:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7m3g_23654/07_2026/7m3g_23654.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m3g_23654/07_2026/7m3g_23654.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7m3g_23654/07_2026/7m3g_23654.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7m3g_23654/07_2026/7m3g_23654.cif" model { file = "/net/cci-nas-00/data/ceres_data/7m3g_23654/07_2026/7m3g_23654.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m3g_23654/07_2026/7m3g_23654.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7m3g_23654/07_2026/7m3g_23654.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m3g_23654/07_2026/7m3g_23654.map" } resolution = 2.5 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= 0.007 sd= 0.145 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: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 P 2 5.49 5 S 75 5.16 5 C 8616 2.51 5 N 2152 2.21 5 O 2449 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13298 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 6485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 821, 6485 Classifications: {'peptide': 821} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 31, 'TRANS': 789} Chain breaks: 3 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 3, 'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 6375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 6375 Classifications: {'peptide': 804} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 31, 'TRANS': 772} Chain breaks: 3 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="ACE C 1 " pdbres="DCY C 2 " Not linked: pdbres="DAR C 8 " pdbres="NH2 C 9 " Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Planarities with less than four sites: {'DCY:plan-1': 1, 'DAL:plan-1': 2, 'DAR:plan-2': 4} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="ACE D 1 " pdbres="DCY D 2 " Not linked: pdbres="DAR D 8 " pdbres="NH2 D 9 " Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Planarities with less than four sites: {'DCY:plan-1': 1, 'DAL:plan-1': 2, 'DAR:plan-2': 4} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 93 Unusual residues: {' CA': 3, 'H43': 1, 'NAG': 3, 'PO4': 1} Inner-chain residues flagged as termini: ['pdbres="TRP A 905 "'] Classifications: {'peptide': 1, 'undetermined': 8} Modifications used: {'COO': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 77 Unusual residues: {' CA': 1, 'H43': 1, 'NAG': 2, 'PO4': 1} Inner-chain residues flagged as termini: ['pdbres="TRP B 904 "'] Classifications: {'peptide': 1, 'undetermined': 5} Modifications used: {'COO': 1} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.59, per 1000 atoms: 0.19 Number of scatterers: 13298 At special positions: 0 Unit cell: (99.9, 92.13, 192.03, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 4 19.99 S 75 16.00 P 2 15.00 O 2449 8.00 N 2152 7.00 C 8616 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 101 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 561 " distance=2.04 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 395 " distance=2.02 Simple disulfide: pdb=" SG CYS A 542 " - pdb=" SG CYS A 562 " distance=2.03 Simple disulfide: pdb=" SG CYS A 546 " - pdb=" SG CYS A 565 " distance=2.04 Simple disulfide: pdb=" SG CYS A 568 " - pdb=" SG CYS A 582 " distance=2.03 Simple disulfide: pdb=" SG CYS A 585 " - pdb=" SG CYS A 598 " distance=2.04 Simple disulfide: pdb=" SG CYS A 677 " - pdb=" SG CYS A 765 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 101 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 561 " distance=2.04 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 395 " distance=2.02 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 449 " distance=2.04 Simple disulfide: pdb=" SG CYS B 542 " - pdb=" SG CYS B 562 " distance=2.04 Simple disulfide: pdb=" SG CYS B 546 " - pdb=" SG CYS B 565 " distance=2.04 Simple disulfide: pdb=" SG CYS B 568 " - pdb=" SG CYS B 582 " distance=2.03 Simple disulfide: pdb=" SG CYS B 585 " - pdb=" SG CYS B 598 " distance=2.03 Simple disulfide: pdb=" SG CYS B 677 " - pdb=" SG CYS B 765 " distance=2.03 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=4, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A 902 " - " ASN A 468 " " NAG A 903 " - " ASN A 488 " " NAG A 904 " - " ASN A 594 " " NAG B 902 " - " ASN B 468 " " NAG B 903 " - " ASN B 594 " " NAG E 1 " - " ASN A 261 " " NAG F 1 " - " ASN A 541 " " NAG G 1 " - " ASN B 261 " " NAG H 1 " - " ASN B 488 " " NAG I 1 " - " ASN B 541 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 411.8 milliseconds 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DCY C 2 " pdb=" CB DAL C 3 " pdb=" CB DAR C 4 " pdb=" CB DAR C 5 " pdb=" CB DAR C 6 " pdb=" CB DAL C 7 " pdb=" CB DAR C 8 " pdb=" CB DCY D 2 " pdb=" CB DAL D 3 " pdb=" CB DAR D 4 " pdb=" CB DAR D 5 " pdb=" CB DAR D 6 " pdb=" CB DAL D 7 " pdb=" CB DAR D 8 " Number of C-beta restraints generated: 3064 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 14 sheets defined 47.3% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 64 through 84 removed outlier: 3.535A pdb=" N PHE A 68 " --> pdb=" O ASN A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 115 removed outlier: 3.502A pdb=" N ALA A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 124 removed outlier: 3.605A pdb=" N ILE A 120 " --> pdb=" O ALA A 116 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP A 121 " --> pdb=" O GLN A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 158 removed outlier: 3.658A pdb=" N LEU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 176 removed outlier: 3.681A pdb=" N ASN A 176 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 204 Processing helix chain 'A' and resid 218 through 233 removed outlier: 3.810A pdb=" N GLY A 222 " --> pdb=" O TYR A 218 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 260 Processing helix chain 'A' and resid 272 through 287 Proline residue: A 278 - end of helix Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 329 through 335 Processing helix chain 'A' and resid 347 through 357 Processing helix chain 'A' and resid 400 through 404 removed outlier: 3.513A pdb=" N VAL A 404 " --> pdb=" O ILE A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 436 Processing helix chain 'A' and resid 456 through 466 removed outlier: 3.594A pdb=" N HIS A 466 " --> pdb=" O LYS A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 528 Processing helix chain 'A' and resid 610 through 637 Processing helix chain 'A' and resid 640 through 646 Processing helix chain 'A' and resid 649 through 664 Processing helix chain 'A' and resid 665 through 669 removed outlier: 3.700A pdb=" N PHE A 668 " --> pdb=" O SER A 665 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE A 669 " --> pdb=" O LEU A 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 665 through 669' Processing helix chain 'A' and resid 680 through 697 removed outlier: 4.144A pdb=" N PHE A 684 " --> pdb=" O ARG A 680 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL A 689 " --> pdb=" O GLY A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 746 removed outlier: 3.715A pdb=" N VAL A 728 " --> pdb=" O GLN A 724 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLN A 735 " --> pdb=" O CYS A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 794 removed outlier: 4.000A pdb=" N SER A 794 " --> pdb=" O PHE A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 821 removed outlier: 3.890A pdb=" N PHE A 806 " --> pdb=" O ASN A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 828 removed outlier: 3.510A pdb=" N SER A 827 " --> pdb=" O PRO A 823 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR A 828 " --> pdb=" O ALA A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 853 removed outlier: 3.506A pdb=" N ILE A 841 " --> pdb=" O GLU A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 863 removed outlier: 3.725A pdb=" N ILE A 859 " --> pdb=" O ASN A 855 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS A 863 " --> pdb=" O ILE A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 873 removed outlier: 3.700A pdb=" N VAL A 872 " --> pdb=" O THR A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 886 removed outlier: 3.757A pdb=" N VAL A 883 " --> pdb=" O HIS A 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 83 removed outlier: 3.748A pdb=" N MET B 74 " --> pdb=" O TRP B 70 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE B 75 " --> pdb=" O LEU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 115 removed outlier: 3.546A pdb=" N ALA B 107 " --> pdb=" O THR B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 124 removed outlier: 3.650A pdb=" N ILE B 120 " --> pdb=" O ALA B 116 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP B 121 " --> pdb=" O GLN B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 158 removed outlier: 3.781A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.544A pdb=" N LEU B 174 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN B 176 " --> pdb=" O LEU B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 204 removed outlier: 3.674A pdb=" N ALA B 198 " --> pdb=" O ALA B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 233 removed outlier: 3.715A pdb=" N GLY B 222 " --> pdb=" O TYR B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 261 Processing helix chain 'B' and resid 272 through 286 Proline residue: B 278 - end of helix Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 310 through 315 Processing helix chain 'B' and resid 329 through 336 Processing helix chain 'B' and resid 347 through 357 Processing helix chain 'B' and resid 400 through 404 removed outlier: 3.620A pdb=" N VAL B 404 " --> pdb=" O ILE B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 436 removed outlier: 3.536A pdb=" N ASN B 419 " --> pdb=" O ARG B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 455 removed outlier: 4.072A pdb=" N VAL B 455 " --> pdb=" O ILE B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 466 removed outlier: 3.589A pdb=" N HIS B 466 " --> pdb=" O LYS B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 528 Processing helix chain 'B' and resid 529 through 533 Processing helix chain 'B' and resid 610 through 637 Processing helix chain 'B' and resid 647 through 664 removed outlier: 3.799A pdb=" N TYR B 652 " --> pdb=" O ARG B 648 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B 653 " --> pdb=" O GLU B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 668 removed outlier: 3.785A pdb=" N PHE B 668 " --> pdb=" O SER B 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 665 through 668' Processing helix chain 'B' and resid 680 through 698 removed outlier: 4.038A pdb=" N PHE B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LYS B 698 " --> pdb=" O CYS B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 746 removed outlier: 4.156A pdb=" N CYS B 731 " --> pdb=" O LEU B 727 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLN B 735 " --> pdb=" O CYS B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 793 removed outlier: 3.936A pdb=" N LEU B 773 " --> pdb=" O SER B 769 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR B 780 " --> pdb=" O LEU B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 821 removed outlier: 4.059A pdb=" N PHE B 806 " --> pdb=" O ASN B 802 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 825 Processing helix chain 'B' and resid 831 through 854 removed outlier: 3.829A pdb=" N ALA B 835 " --> pdb=" O LYS B 831 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL B 836 " --> pdb=" O PHE B 832 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE B 841 " --> pdb=" O GLU B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 861 Processing helix chain 'D' and resid 2 through 7 removed outlier: 3.763A pdb=" N DAL D 7 " --> pdb=" O DAL D 3 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.299A pdb=" N ILE A 32 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ARG A 96 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU A 34 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N PHE A 98 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N GLY A 36 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ILE A 33 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N VAL A 142 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N GLY A 35 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N VAL A 165 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL A 141 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N GLN A 164 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 236 through 243 removed outlier: 8.151A pdb=" N VAL A 209 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N SER A 240 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR A 211 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU A 242 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA A 213 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL A 266 " --> pdb=" O TRP A 208 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE A 267 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE A 320 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N TYR A 489 " --> pdb=" O TYR A 510 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N TYR A 510 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE A 491 " --> pdb=" O VAL A 508 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 468 through 470 Processing sheet with id=AA4, first strand: chain 'A' and resid 550 through 554 Processing sheet with id=AA5, first strand: chain 'A' and resid 589 through 591 Processing sheet with id=AA6, first strand: chain 'A' and resid 602 through 604 Processing sheet with id=AA7, first strand: chain 'B' and resid 26 through 28 removed outlier: 6.442A pdb=" N ILE B 32 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ARG B 96 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU B 34 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N PHE B 98 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLY B 36 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ILE B 33 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N VAL B 142 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLY B 35 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N VAL B 165 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL B 141 " --> pdb=" O VAL B 165 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 41 through 44 removed outlier: 7.345A pdb=" N ARG B 62 " --> pdb=" O PHE B 42 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL B 44 " --> pdb=" O CYS B 60 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N CYS B 60 " --> pdb=" O VAL B 44 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 236 through 243 removed outlier: 8.043A pdb=" N VAL B 209 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N SER B 240 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR B 211 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LEU B 242 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ALA B 213 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N TRP B 208 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N VAL B 268 " --> pdb=" O TRP B 208 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLY B 210 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N PHE B 270 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE B 212 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE B 320 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TYR B 489 " --> pdb=" O TYR B 510 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TYR B 510 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE B 491 " --> pdb=" O VAL B 508 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 468 through 470 Processing sheet with id=AB2, first strand: chain 'B' and resid 550 through 554 Processing sheet with id=AB3, first strand: chain 'B' and resid 572 through 573 Processing sheet with id=AB4, first strand: chain 'B' and resid 589 through 591 Processing sheet with id=AB5, first strand: chain 'B' and resid 602 through 604 removed outlier: 6.616A pdb=" N GLU B 602 " --> pdb=" O ILE B 761 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ILE B 763 " --> pdb=" O GLU B 602 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLU B 604 " --> pdb=" O ILE B 763 " (cutoff:3.500A) removed outlier: 9.054A pdb=" N CYS B 765 " --> pdb=" O GLU B 604 " (cutoff:3.500A) 560 hydrogen bonds defined for protein. 1626 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: 1.59 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4043 1.34 - 1.46: 3424 1.46 - 1.58: 6061 1.58 - 1.71: 2 1.71 - 1.83: 89 Bond restraints: 13619 Sorted by residual: bond pdb=" C11 H43 A 901 " pdb=" N12 H43 A 901 " ideal model delta sigma weight residual 1.454 1.574 -0.120 2.00e-02 2.50e+03 3.63e+01 bond pdb=" C13 H43 A 901 " pdb=" N12 H43 A 901 " ideal model delta sigma weight residual 1.459 1.563 -0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" C11 H43 B 901 " pdb=" N12 H43 B 901 " ideal model delta sigma weight residual 1.454 1.553 -0.099 2.00e-02 2.50e+03 2.45e+01 bond pdb=" C8 H43 A 901 " pdb=" N9 H43 A 901 " ideal model delta sigma weight residual 1.367 1.465 -0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" C8 H43 B 901 " pdb=" N9 H43 B 901 " ideal model delta sigma weight residual 1.367 1.464 -0.097 2.00e-02 2.50e+03 2.34e+01 ... (remaining 13614 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 18063 2.83 - 5.67: 347 5.67 - 8.50: 54 8.50 - 11.34: 7 11.34 - 14.17: 1 Bond angle restraints: 18472 Sorted by residual: angle pdb=" CA PRO B 641 " pdb=" N PRO B 641 " pdb=" CD PRO B 641 " ideal model delta sigma weight residual 112.00 104.81 7.19 1.40e+00 5.10e-01 2.64e+01 angle pdb=" CB MET B 734 " pdb=" CG MET B 734 " pdb=" SD MET B 734 " ideal model delta sigma weight residual 112.70 126.87 -14.17 3.00e+00 1.11e-01 2.23e+01 angle pdb=" CA PRO B 748 " pdb=" N PRO B 748 " pdb=" CD PRO B 748 " ideal model delta sigma weight residual 112.00 105.43 6.57 1.40e+00 5.10e-01 2.20e+01 angle pdb=" CB ILE B 603 " pdb=" CG1 ILE B 603 " pdb=" CD1 ILE B 603 " ideal model delta sigma weight residual 113.80 123.60 -9.80 2.10e+00 2.27e-01 2.18e+01 angle pdb=" N GLU B 759 " pdb=" CA GLU B 759 " pdb=" C GLU B 759 " ideal model delta sigma weight residual 114.62 109.48 5.14 1.14e+00 7.69e-01 2.03e+01 ... (remaining 18467 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 6841 17.63 - 35.26: 743 35.26 - 52.88: 191 52.88 - 70.51: 39 70.51 - 88.14: 17 Dihedral angle restraints: 7831 sinusoidal: 3084 harmonic: 4747 Sorted by residual: dihedral pdb=" CB CYS A 677 " pdb=" SG CYS A 677 " pdb=" SG CYS A 765 " pdb=" CB CYS A 765 " ideal model delta sinusoidal sigma weight residual 93.00 178.24 -85.24 1 1.00e+01 1.00e-02 8.80e+01 dihedral pdb=" CB CYS A 585 " pdb=" SG CYS A 585 " pdb=" SG CYS A 598 " pdb=" CB CYS A 598 " ideal model delta sinusoidal sigma weight residual 93.00 167.99 -74.99 1 1.00e+01 1.00e-02 7.11e+01 dihedral pdb=" CA VAL B 142 " pdb=" C VAL B 142 " pdb=" N GLY B 143 " pdb=" CA GLY B 143 " ideal model delta harmonic sigma weight residual -180.00 -151.26 -28.74 0 5.00e+00 4.00e-02 3.30e+01 ... (remaining 7828 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1678 0.069 - 0.138: 368 0.138 - 0.207: 42 0.207 - 0.276: 3 0.276 - 0.345: 4 Chirality restraints: 2095 Sorted by residual: chirality pdb=" C13 H43 A 901 " pdb=" C14 H43 A 901 " pdb=" C24 H43 A 901 " pdb=" N12 H43 A 901 " both_signs ideal model delta sigma weight residual False -2.34 -2.68 0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CB ILE A 61 " pdb=" CA ILE A 61 " pdb=" CG1 ILE A 61 " pdb=" CG2 ILE A 61 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" C13 H43 B 901 " pdb=" C14 H43 B 901 " pdb=" C24 H43 B 901 " pdb=" N12 H43 B 901 " both_signs ideal model delta sigma weight residual False -2.34 -2.67 0.34 2.00e-01 2.50e+01 2.82e+00 ... (remaining 2092 not shown) Planarity restraints: 2328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 747 " -0.098 5.00e-02 4.00e+02 1.45e-01 3.38e+01 pdb=" N PRO B 748 " 0.251 5.00e-02 4.00e+02 pdb=" CA PRO B 748 " -0.080 5.00e-02 4.00e+02 pdb=" CD PRO B 748 " -0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 640 " -0.096 5.00e-02 4.00e+02 1.41e-01 3.20e+01 pdb=" N PRO B 641 " 0.244 5.00e-02 4.00e+02 pdb=" CA PRO B 641 " -0.077 5.00e-02 4.00e+02 pdb=" CD PRO B 641 " -0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 789 " 0.034 2.00e-02 2.50e+03 2.79e-02 1.36e+01 pdb=" CG PHE A 789 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 PHE A 789 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 789 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 789 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 789 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE A 789 " 0.006 2.00e-02 2.50e+03 ... (remaining 2325 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 79 2.61 - 3.18: 10247 3.18 - 3.75: 19479 3.75 - 4.33: 27735 4.33 - 4.90: 45487 Nonbonded interactions: 103027 Sorted by model distance: nonbonded pdb=" SG CYS B 482 " pdb=" SG DCY D 2 " model vdw 2.033 3.760 nonbonded pdb=" SG CYS A 482 " pdb=" SG DCY C 2 " model vdw 2.037 3.760 nonbonded pdb=" O ALA A 548 " pdb=" OG SER A 574 " model vdw 2.281 3.040 nonbonded pdb=" OD1 ASP A 480 " pdb=" N ASP A 484 " model vdw 2.290 3.120 nonbonded pdb=" OD2 ASP B 238 " pdb=" OG SER B 262 " model vdw 2.299 3.040 ... (remaining 103022 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 20 through 125 or resid 131 through 566 or (resid 567 and \ (name N or name CA or name C or name O or name CB )) or resid 568 through 704 or \ (resid 705 and (name N or name CA or name C or name O or name CB )) or resid 70 \ 6 through 862 or (resid 863 and (name N or name CA or name C or name O or name C \ B )) or resid 864 through 865 or (resid 866 and (name N or name CA or name C or \ name O or name CB )) or resid 867 through 870 or resid 903 through 906)) selection = (chain 'B' and (resid 20 through 48 or (resid 49 through 50 and (name N or name \ CA or name C or name O or name CB )) or resid 51 through 362 or resid 391 throug \ h 499 or (resid 500 and (name N or name CA or name C or name O or name CB )) or \ resid 501 through 555 or (resid 556 and (name N or name CA or name C or name O o \ r name CB )) or resid 557 through 725 or (resid 726 and (name N or name CA or na \ me C or name O or name CB )) or resid 727 through 870 or resid 902 through 905)) \ } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.920 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.020 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:6.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 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 : 0.007 0.120 13655 Z= 0.358 Angle : 0.985 14.174 18551 Z= 0.531 Chirality : 0.058 0.345 2095 Planarity : 0.008 0.145 2318 Dihedral : 16.312 88.139 4716 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.93 % Allowed : 18.54 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.18), residues: 1609 helix: -0.94 (0.17), residues: 686 sheet: -1.14 (0.32), residues: 223 loop : -1.70 (0.21), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 648 TYR 0.021 0.003 TYR A 421 PHE 0.063 0.003 PHE A 789 TRP 0.035 0.003 TRP B 675 HIS 0.006 0.002 HIS B 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00695 / 0.31 (13619) covalent geometry : angle 0.97388 / 0.53 (18472) SS BOND : bond 0.00574 / 0.28 ( 17) SS BOND : angle 1.80574 / 1.24 ( 34) hydrogen bonds : bond 0.15385 / 10.41 ( 560) hydrogen bonds : angle 5.43224 / 3.77 ( 1626) Misc. bond : bond 0.10019 / 5.01 ( 4) link_BETA1-4 : bond 0.00862 / 0.44 ( 5) link_BETA1-4 : angle 2.32195 / 1.27 ( 15) link_NAG-ASN : bond 0.00360 / 0.17 ( 10) link_NAG-ASN : angle 3.04998 / 1.87 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 163 time to evaluate : 0.496 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 170 average time/residue: 0.4223 time to fit residues: 80.1911 Evaluate side-chains 163 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 155 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 820 SER Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 697 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 0.0980 chunk 107 optimal weight: 0.1980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.1980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 1.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 117 GLN A 647 ASN A 673 GLN A 724 GLN A 753 ASN B 253 GLN B 583 ASN B 595 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.124944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.089401 restraints weight = 19585.085| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.61 r_work: 0.3006 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13655 Z= 0.123 Angle : 0.567 7.356 18551 Z= 0.299 Chirality : 0.044 0.179 2095 Planarity : 0.005 0.087 2318 Dihedral : 7.489 85.282 1798 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.79 % Allowed : 16.39 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.20), residues: 1609 helix: 0.66 (0.19), residues: 693 sheet: -1.02 (0.32), residues: 223 loop : -1.40 (0.22), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 69 TYR 0.017 0.001 TYR A 421 PHE 0.044 0.001 PHE A 789 TRP 0.014 0.001 TRP B 675 HIS 0.003 0.001 HIS A 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (13619) covalent geometry : angle 0.55537 / 0.30 (18472) SS BOND : bond 0.00313 / 0.16 ( 17) SS BOND : angle 1.04006 / 0.73 ( 34) hydrogen bonds : bond 0.05351 / 3.50 ( 560) hydrogen bonds : angle 4.30980 / 2.99 ( 1626) Misc. bond : bond 0.00080 / 0.04 ( 4) link_BETA1-4 : bond 0.00468 / 0.25 ( 5) link_BETA1-4 : angle 1.10076 / 0.64 ( 15) link_NAG-ASN : bond 0.00466 / 0.17 ( 10) link_NAG-ASN : angle 2.60978 / 1.52 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 168 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 499 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7165 (mp0) REVERT: A 673 GLN cc_start: 0.8193 (tt0) cc_final: 0.7946 (tt0) REVERT: B 399 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7388 (mp0) outliers start: 39 outliers final: 13 residues processed: 190 average time/residue: 0.3851 time to fit residues: 82.9946 Evaluate side-chains 176 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 161 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 691 CYS Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 253 GLN Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 594 ASN Chi-restraints excluded: chain B residue 660 CYS Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 849 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 119 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 160 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 117 GLN B 253 GLN B 463 HIS B 583 ASN B 722 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.122790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.086772 restraints weight = 19681.479| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.60 r_work: 0.2953 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13655 Z= 0.192 Angle : 0.627 7.642 18551 Z= 0.329 Chirality : 0.046 0.211 2095 Planarity : 0.005 0.070 2318 Dihedral : 6.953 85.910 1785 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.93 % Allowed : 17.18 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.20), residues: 1609 helix: 1.10 (0.20), residues: 695 sheet: -1.00 (0.33), residues: 223 loop : -1.33 (0.22), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 648 TYR 0.021 0.002 TYR A 421 PHE 0.026 0.002 PHE A 832 TRP 0.016 0.002 TRP A 299 HIS 0.005 0.001 HIS A 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.19 (13619) covalent geometry : angle 0.61409 / 0.33 (18472) SS BOND : bond 0.00474 / 0.23 ( 17) SS BOND : angle 1.31946 / 0.93 ( 34) hydrogen bonds : bond 0.06380 / 4.22 ( 560) hydrogen bonds : angle 4.25841 / 2.96 ( 1626) Misc. bond : bond 0.00028 / 0.01 ( 4) link_BETA1-4 : bond 0.00341 / 0.18 ( 5) link_BETA1-4 : angle 1.37657 / 0.83 ( 15) link_NAG-ASN : bond 0.00223 / 0.11 ( 10) link_NAG-ASN : angle 2.79007 / 1.65 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 168 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 499 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7260 (mp0) REVERT: A 793 LYS cc_start: 0.8899 (tppp) cc_final: 0.8453 (tppt) REVERT: B 270 PHE cc_start: 0.9242 (OUTLIER) cc_final: 0.8480 (m-80) REVERT: B 399 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.7462 (mp0) REVERT: B 441 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7028 (mpp-170) REVERT: B 507 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8348 (tm-30) outliers start: 41 outliers final: 21 residues processed: 191 average time/residue: 0.4171 time to fit residues: 89.9148 Evaluate side-chains 183 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 691 CYS Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 827 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 253 GLN Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 441 ARG Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 594 ASN Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 849 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 114 optimal weight: 0.9980 chunk 80 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 161 optimal weight: 0.9980 chunk 34 optimal weight: 0.0070 chunk 113 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 253 GLN B 253 GLN B 583 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.123227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.087492 restraints weight = 19648.627| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.59 r_work: 0.2968 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13655 Z= 0.153 Angle : 0.578 6.990 18551 Z= 0.304 Chirality : 0.045 0.191 2095 Planarity : 0.005 0.069 2318 Dihedral : 6.816 86.452 1785 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.22 % Allowed : 16.89 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.20), residues: 1609 helix: 1.33 (0.20), residues: 697 sheet: -0.98 (0.33), residues: 223 loop : -1.30 (0.22), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 648 TYR 0.019 0.002 TYR A 421 PHE 0.024 0.001 PHE B 729 TRP 0.017 0.002 TRP A 299 HIS 0.004 0.001 HIS A 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (13619) covalent geometry : angle 0.56726 / 0.30 (18472) SS BOND : bond 0.00384 / 0.19 ( 17) SS BOND : angle 1.12319 / 0.79 ( 34) hydrogen bonds : bond 0.05679 / 3.75 ( 560) hydrogen bonds : angle 4.16568 / 2.90 ( 1626) Misc. bond : bond 0.00022 / 0.01 ( 4) link_BETA1-4 : bond 0.00325 / 0.17 ( 5) link_BETA1-4 : angle 1.26373 / 0.75 ( 15) link_NAG-ASN : bond 0.00215 / 0.10 ( 10) link_NAG-ASN : angle 2.48292 / 1.48 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 161 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 ASP cc_start: 0.6951 (t0) cc_final: 0.6624 (m-30) REVERT: A 499 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7223 (mp0) REVERT: A 576 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7458 (pm20) REVERT: A 673 GLN cc_start: 0.8218 (tt0) cc_final: 0.8016 (tt0) REVERT: B 270 PHE cc_start: 0.9206 (OUTLIER) cc_final: 0.8426 (m-80) REVERT: B 399 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.7410 (mp0) REVERT: B 507 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8338 (tm-30) REVERT: B 517 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8690 (ttmm) outliers start: 45 outliers final: 23 residues processed: 186 average time/residue: 0.3849 time to fit residues: 81.4170 Evaluate side-chains 182 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 660 CYS Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 827 SER Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 594 ASN Chi-restraints excluded: chain B residue 675 TRP Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 849 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 133 optimal weight: 1.9990 chunk 44 optimal weight: 0.0570 chunk 138 optimal weight: 3.9990 chunk 144 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 152 optimal weight: 0.3980 chunk 70 optimal weight: 8.9990 chunk 24 optimal weight: 0.1980 chunk 56 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 253 GLN B 253 GLN B 583 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.124128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.089062 restraints weight = 19829.603| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.59 r_work: 0.2998 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13655 Z= 0.119 Angle : 0.539 8.537 18551 Z= 0.282 Chirality : 0.043 0.173 2095 Planarity : 0.004 0.066 2318 Dihedral : 6.592 86.529 1785 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.51 % Allowed : 17.25 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.21), residues: 1609 helix: 1.49 (0.20), residues: 708 sheet: -0.87 (0.33), residues: 223 loop : -1.25 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 648 TYR 0.017 0.001 TYR A 421 PHE 0.027 0.001 PHE B 729 TRP 0.017 0.001 TRP A 299 HIS 0.003 0.001 HIS A 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (13619) covalent geometry : angle 0.53083 / 0.28 (18472) SS BOND : bond 0.00290 / 0.14 ( 17) SS BOND : angle 0.91361 / 0.64 ( 34) hydrogen bonds : bond 0.04887 / 3.23 ( 560) hydrogen bonds : angle 4.01131 / 2.78 ( 1626) Misc. bond : bond 0.00017 / 0.01 ( 4) link_BETA1-4 : bond 0.00351 / 0.19 ( 5) link_BETA1-4 : angle 1.18495 / 0.69 ( 15) link_NAG-ASN : bond 0.00208 / 0.10 ( 10) link_NAG-ASN : angle 2.14159 / 1.28 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 157 time to evaluate : 0.516 Fit side-chains revert: symmetry clash REVERT: A 23 ASP cc_start: 0.6943 (t0) cc_final: 0.6615 (m-30) REVERT: A 253 GLN cc_start: 0.8459 (mt0) cc_final: 0.8239 (mm-40) REVERT: A 499 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7230 (mp0) REVERT: A 794 SER cc_start: 0.8633 (OUTLIER) cc_final: 0.8210 (p) REVERT: B 270 PHE cc_start: 0.9176 (OUTLIER) cc_final: 0.8414 (m-80) REVERT: B 399 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.7417 (mp0) REVERT: B 441 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.6926 (mpp-170) REVERT: B 507 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8320 (tm-30) outliers start: 49 outliers final: 23 residues processed: 190 average time/residue: 0.4186 time to fit residues: 90.3244 Evaluate side-chains 181 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 152 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 660 CYS Chi-restraints excluded: chain A residue 691 CYS Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 827 SER Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 441 ARG Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 660 CYS Chi-restraints excluded: chain B residue 675 TRP Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 845 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 10 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 253 GLN B 583 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.122366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.086341 restraints weight = 19461.197| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.59 r_work: 0.2946 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13655 Z= 0.218 Angle : 0.654 9.713 18551 Z= 0.338 Chirality : 0.048 0.258 2095 Planarity : 0.005 0.073 2318 Dihedral : 6.791 87.407 1785 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.65 % Allowed : 17.18 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.21), residues: 1609 helix: 1.37 (0.19), residues: 713 sheet: -1.00 (0.33), residues: 224 loop : -1.33 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 331 TYR 0.024 0.002 TYR A 421 PHE 0.026 0.002 PHE B 729 TRP 0.017 0.002 TRP A 299 HIS 0.006 0.001 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.22 (13619) covalent geometry : angle 0.63786 / 0.33 (18472) SS BOND : bond 0.00545 / 0.26 ( 17) SS BOND : angle 1.38481 / 0.98 ( 34) hydrogen bonds : bond 0.06494 / 4.29 ( 560) hydrogen bonds : angle 4.16754 / 2.90 ( 1626) Misc. bond : bond 0.00043 / 0.02 ( 4) link_BETA1-4 : bond 0.00317 / 0.16 ( 5) link_BETA1-4 : angle 1.38474 / 0.83 ( 15) link_NAG-ASN : bond 0.00226 / 0.11 ( 10) link_NAG-ASN : angle 3.27401 / 1.92 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 159 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 ASP cc_start: 0.6978 (t0) cc_final: 0.6648 (m-30) REVERT: A 249 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6674 (tp30) REVERT: A 253 GLN cc_start: 0.8529 (mt0) cc_final: 0.8257 (mm-40) REVERT: A 499 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7247 (mp0) REVERT: A 583 ASN cc_start: 0.8620 (OUTLIER) cc_final: 0.8356 (m110) REVERT: A 794 SER cc_start: 0.8738 (OUTLIER) cc_final: 0.8344 (p) REVERT: B 270 PHE cc_start: 0.9266 (OUTLIER) cc_final: 0.8453 (m-80) REVERT: B 399 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.7455 (mp0) REVERT: B 507 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8350 (tm-30) REVERT: B 517 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8698 (ttmm) REVERT: B 604 GLU cc_start: 0.8306 (tt0) cc_final: 0.8055 (tt0) outliers start: 51 outliers final: 30 residues processed: 193 average time/residue: 0.4233 time to fit residues: 92.3148 Evaluate side-chains 195 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 157 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 583 ASN Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 660 CYS Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 827 SER Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 253 GLN Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 441 ARG Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 675 TRP Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 849 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 17 optimal weight: 0.6980 chunk 137 optimal weight: 0.0470 chunk 26 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 overall best weight: 0.7484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 583 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.123042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.087712 restraints weight = 19578.413| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.74 r_work: 0.2944 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13655 Z= 0.160 Angle : 0.621 17.822 18551 Z= 0.317 Chirality : 0.047 0.523 2095 Planarity : 0.004 0.070 2318 Dihedral : 6.700 87.795 1785 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.22 % Allowed : 17.61 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.21), residues: 1609 helix: 1.44 (0.19), residues: 713 sheet: -0.87 (0.34), residues: 210 loop : -1.31 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 331 TYR 0.020 0.002 TYR A 421 PHE 0.030 0.002 PHE B 789 TRP 0.019 0.002 TRP A 299 HIS 0.004 0.001 HIS A 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (13619) covalent geometry : angle 0.58977 / 0.31 (18472) SS BOND : bond 0.00400 / 0.19 ( 17) SS BOND : angle 1.13203 / 0.79 ( 34) hydrogen bonds : bond 0.05749 / 3.81 ( 560) hydrogen bonds : angle 4.11071 / 2.86 ( 1626) Misc. bond : bond 0.00033 / 0.02 ( 4) link_BETA1-4 : bond 0.00299 / 0.16 ( 5) link_BETA1-4 : angle 1.29052 / 0.77 ( 15) link_NAG-ASN : bond 0.00264 / 0.11 ( 10) link_NAG-ASN : angle 4.68962 / 2.74 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 162 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 ASP cc_start: 0.7094 (t0) cc_final: 0.6684 (m-30) REVERT: A 249 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6647 (tp30) REVERT: A 253 GLN cc_start: 0.8448 (mt0) cc_final: 0.8141 (mm-40) REVERT: A 499 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7281 (mp0) REVERT: A 583 ASN cc_start: 0.8628 (OUTLIER) cc_final: 0.8368 (m110) REVERT: A 794 SER cc_start: 0.8757 (OUTLIER) cc_final: 0.8416 (p) REVERT: B 399 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.7434 (mp0) REVERT: B 507 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8396 (tm-30) REVERT: B 517 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8707 (ttmm) REVERT: B 604 GLU cc_start: 0.8268 (tt0) cc_final: 0.8061 (tt0) outliers start: 45 outliers final: 25 residues processed: 193 average time/residue: 0.4209 time to fit residues: 92.2188 Evaluate side-chains 186 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 583 ASN Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 660 CYS Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 827 SER Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 441 ARG Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 660 CYS Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 849 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 24 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 31 optimal weight: 0.0980 chunk 115 optimal weight: 1.9990 chunk 11 optimal weight: 0.0670 chunk 117 optimal weight: 0.6980 chunk 156 optimal weight: 3.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 253 GLN B 583 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.124123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.089019 restraints weight = 19495.247| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.75 r_work: 0.2968 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13655 Z= 0.125 Angle : 0.577 14.387 18551 Z= 0.295 Chirality : 0.044 0.306 2095 Planarity : 0.004 0.068 2318 Dihedral : 6.540 87.920 1785 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.79 % Allowed : 17.97 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.21), residues: 1609 helix: 1.65 (0.20), residues: 709 sheet: -0.77 (0.35), residues: 209 loop : -1.23 (0.22), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 648 TYR 0.018 0.001 TYR A 421 PHE 0.028 0.001 PHE B 729 TRP 0.019 0.001 TRP A 299 HIS 0.003 0.001 HIS A 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (13619) covalent geometry : angle 0.55380 / 0.29 (18472) SS BOND : bond 0.00298 / 0.15 ( 17) SS BOND : angle 0.93370 / 0.65 ( 34) hydrogen bonds : bond 0.04996 / 3.30 ( 560) hydrogen bonds : angle 3.99345 / 2.77 ( 1626) Misc. bond : bond 0.00023 / 0.01 ( 4) link_BETA1-4 : bond 0.00333 / 0.18 ( 5) link_BETA1-4 : angle 1.21305 / 0.71 ( 15) link_NAG-ASN : bond 0.00261 / 0.11 ( 10) link_NAG-ASN : angle 3.91640 / 2.24 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 159 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 ASP cc_start: 0.7120 (t0) cc_final: 0.6726 (m-30) REVERT: A 250 GLU cc_start: 0.8022 (pp20) cc_final: 0.7810 (mp0) REVERT: A 253 GLN cc_start: 0.8403 (mt0) cc_final: 0.8134 (mm-40) REVERT: A 499 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7235 (mp0) REVERT: A 583 ASN cc_start: 0.8592 (OUTLIER) cc_final: 0.8339 (m110) REVERT: A 794 SER cc_start: 0.8801 (OUTLIER) cc_final: 0.8499 (p) REVERT: B 270 PHE cc_start: 0.9114 (OUTLIER) cc_final: 0.8479 (m-80) REVERT: B 399 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.7484 (mp0) REVERT: B 507 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8384 (tm-30) REVERT: B 517 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8704 (ttmm) REVERT: B 604 GLU cc_start: 0.8256 (tt0) cc_final: 0.8033 (tt0) outliers start: 39 outliers final: 22 residues processed: 185 average time/residue: 0.3721 time to fit residues: 78.2703 Evaluate side-chains 181 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 152 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 583 ASN Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 660 CYS Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 827 SER Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 441 ARG Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 660 CYS Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 836 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 142 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 121 optimal weight: 0.0030 chunk 8 optimal weight: 0.3980 chunk 105 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 139 optimal weight: 0.8980 overall best weight: 0.8392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 253 GLN B 583 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.122889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.087119 restraints weight = 19550.977| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.58 r_work: 0.2963 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13655 Z= 0.173 Angle : 0.621 12.515 18551 Z= 0.318 Chirality : 0.046 0.263 2095 Planarity : 0.005 0.070 2318 Dihedral : 6.620 88.685 1785 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.58 % Allowed : 18.68 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.21), residues: 1609 helix: 1.56 (0.19), residues: 713 sheet: -0.85 (0.34), residues: 210 loop : -1.29 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 648 TYR 0.021 0.002 TYR A 421 PHE 0.029 0.002 PHE B 729 TRP 0.017 0.002 TRP A 299 HIS 0.005 0.001 HIS A 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.17 (13619) covalent geometry : angle 0.60085 / 0.31 (18472) SS BOND : bond 0.00437 / 0.21 ( 17) SS BOND : angle 1.14812 / 0.81 ( 34) hydrogen bonds : bond 0.05823 / 3.85 ( 560) hydrogen bonds : angle 4.05748 / 2.81 ( 1626) Misc. bond : bond 0.00036 / 0.02 ( 4) link_BETA1-4 : bond 0.00314 / 0.16 ( 5) link_BETA1-4 : angle 1.30833 / 0.78 ( 15) link_NAG-ASN : bond 0.00241 / 0.11 ( 10) link_NAG-ASN : angle 3.73055 / 2.13 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 150 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ASP cc_start: 0.6982 (t0) cc_final: 0.6641 (m-30) REVERT: A 250 GLU cc_start: 0.7976 (pp20) cc_final: 0.7736 (mp0) REVERT: A 253 GLN cc_start: 0.8379 (mt0) cc_final: 0.8128 (mm-40) REVERT: A 499 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7257 (mp0) REVERT: A 583 ASN cc_start: 0.8604 (OUTLIER) cc_final: 0.8350 (m110) REVERT: B 270 PHE cc_start: 0.9179 (OUTLIER) cc_final: 0.8471 (m-80) REVERT: B 399 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.7392 (mp0) REVERT: B 507 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8316 (tm-30) REVERT: B 517 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8689 (ttmm) REVERT: B 604 GLU cc_start: 0.8234 (tt0) cc_final: 0.8009 (tt0) outliers start: 36 outliers final: 26 residues processed: 175 average time/residue: 0.4131 time to fit residues: 82.1129 Evaluate side-chains 178 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 583 ASN Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 660 CYS Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 827 SER Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 253 GLN Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 441 ARG Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 660 CYS Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 836 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 139 optimal weight: 0.9990 chunk 130 optimal weight: 0.0980 chunk 35 optimal weight: 0.5980 chunk 148 optimal weight: 3.9990 chunk 76 optimal weight: 0.2980 chunk 119 optimal weight: 0.5980 chunk 49 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 156 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 253 GLN B 583 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.124100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.088501 restraints weight = 19622.643| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.59 r_work: 0.2993 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13655 Z= 0.123 Angle : 0.574 11.922 18551 Z= 0.294 Chirality : 0.044 0.220 2095 Planarity : 0.004 0.068 2318 Dihedral : 6.501 88.862 1785 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.08 % Allowed : 18.90 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.21), residues: 1609 helix: 1.73 (0.20), residues: 703 sheet: -0.77 (0.35), residues: 209 loop : -1.15 (0.22), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 648 TYR 0.018 0.001 TYR A 421 PHE 0.029 0.001 PHE B 729 TRP 0.019 0.001 TRP A 299 HIS 0.003 0.001 HIS A 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (13619) covalent geometry : angle 0.55616 / 0.29 (18472) SS BOND : bond 0.00294 / 0.15 ( 17) SS BOND : angle 0.91834 / 0.64 ( 34) hydrogen bonds : bond 0.04991 / 3.29 ( 560) hydrogen bonds : angle 3.96896 / 2.74 ( 1626) Misc. bond : bond 0.00024 / 0.01 ( 4) link_BETA1-4 : bond 0.00368 / 0.19 ( 5) link_BETA1-4 : angle 1.21370 / 0.71 ( 15) link_NAG-ASN : bond 0.00268 / 0.11 ( 10) link_NAG-ASN : angle 3.42156 / 1.93 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ASP cc_start: 0.6901 (t0) cc_final: 0.6574 (m-30) REVERT: A 253 GLN cc_start: 0.8341 (mt0) cc_final: 0.8072 (mm-40) REVERT: A 499 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7228 (mp0) REVERT: A 583 ASN cc_start: 0.8579 (OUTLIER) cc_final: 0.8312 (m110) REVERT: B 270 PHE cc_start: 0.9131 (OUTLIER) cc_final: 0.8429 (m-80) REVERT: B 399 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.7438 (mp0) REVERT: B 507 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8297 (tm-30) REVERT: B 517 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8689 (ttmm) REVERT: B 604 GLU cc_start: 0.8239 (tt0) cc_final: 0.8013 (tt0) outliers start: 29 outliers final: 23 residues processed: 171 average time/residue: 0.4142 time to fit residues: 80.4701 Evaluate side-chains 176 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 147 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 583 ASN Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 660 CYS Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 827 SER Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 441 ARG Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 789 PHE Chi-restraints excluded: chain B residue 836 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 145 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 127 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 140 optimal weight: 0.2980 chunk 74 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 583 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.123210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.087506 restraints weight = 19635.182| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.58 r_work: 0.2974 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13655 Z= 0.160 Angle : 0.602 11.118 18551 Z= 0.309 Chirality : 0.045 0.212 2095 Planarity : 0.004 0.069 2318 Dihedral : 6.537 89.308 1785 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.36 % Allowed : 18.68 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.21), residues: 1609 helix: 1.62 (0.19), residues: 715 sheet: -0.80 (0.34), residues: 222 loop : -1.23 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 331 TYR 0.020 0.002 TYR A 421 PHE 0.029 0.001 PHE B 729 TRP 0.017 0.002 TRP A 299 HIS 0.004 0.001 HIS A 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (13619) covalent geometry : angle 0.58530 / 0.31 (18472) SS BOND : bond 0.00395 / 0.19 ( 17) SS BOND : angle 1.07741 / 0.76 ( 34) hydrogen bonds : bond 0.05519 / 3.64 ( 560) hydrogen bonds : angle 3.99735 / 2.77 ( 1626) Misc. bond : bond 0.00032 / 0.02 ( 4) link_BETA1-4 : bond 0.00294 / 0.16 ( 5) link_BETA1-4 : angle 1.28345 / 0.76 ( 15) link_NAG-ASN : bond 0.00235 / 0.10 ( 10) link_NAG-ASN : angle 3.36672 / 1.90 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4997.08 seconds wall clock time: 85 minutes 45.11 seconds (5145.11 seconds total)