Starting phenix.real_space_refine on Thu Jul 31 17:53:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m3g_23654/07_2025/7m3g_23654.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m3g_23654/07_2025/7m3g_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7m3g_23654/07_2025/7m3g_23654.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m3g_23654/07_2025/7m3g_23654.map" model { file = "/net/cci-nas-00/data/ceres_data/7m3g_23654/07_2025/7m3g_23654.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m3g_23654/07_2025/7m3g_23654.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 3} 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: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} 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} Modifications used: {'PEPT-D': 7} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} 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} Modifications used: {'PEPT-D': 7} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 8.91, per 1000 atoms: 0.67 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=19, 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 482 " - pdb=" SG DCY C 2 " distance=2.04 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 482 " - pdb=" SG DCY D 2 " distance=2.03 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=0, 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 " Time building additional restraints: 3.72 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.41 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: 4.60 Time building geometry restraints manager: 4.09 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: 4047 1.34 - 1.46: 3424 1.46 - 1.58: 6061 1.58 - 1.71: 2 1.71 - 1.83: 89 Bond restraints: 13623 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 13618 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 18091 2.83 - 5.67: 335 5.67 - 8.50: 48 8.50 - 11.34: 7 11.34 - 14.17: 1 Bond angle restraints: 18482 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 18477 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 7931 35.99 - 71.98: 244 71.98 - 107.98: 18 107.98 - 143.97: 1 143.97 - 179.96: 4 Dihedral angle restraints: 8198 sinusoidal: 3451 harmonic: 4747 Sorted by residual: dihedral pdb=" CD DAR D 4 " pdb=" NE DAR D 4 " pdb=" CZ DAR D 4 " pdb=" NH1 DAR D 4 " ideal model delta sinusoidal sigma weight residual 0.00 179.96 -179.96 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CD DAR C 8 " pdb=" NE DAR C 8 " pdb=" CZ DAR C 8 " pdb=" NH1 DAR C 8 " ideal model delta sinusoidal sigma weight residual 0.00 -179.93 179.93 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CD DAR D 5 " pdb=" NE DAR D 5 " pdb=" CZ DAR D 5 " pdb=" NH1 DAR D 5 " ideal model delta sinusoidal sigma weight residual 0.00 -179.70 179.70 1 1.00e+01 1.00e-02 1.92e+02 ... (remaining 8195 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: 2332 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 2329 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3499 2.80 - 3.33: 11058 3.33 - 3.85: 21208 3.85 - 4.38: 24712 4.38 - 4.90: 42544 Nonbonded interactions: 103021 Sorted by model distance: 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 nonbonded pdb=" OD2 ASP A 238 " pdb=" OG SER A 262 " model vdw 2.312 3.040 nonbonded pdb=" O GLY A 613 " pdb=" OG1 THR A 617 " model vdw 2.322 3.040 ... (remaining 103016 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: 2.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 32.910 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 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 13657 Z= 0.314 Angle : 0.972 14.174 18565 Z= 0.530 Chirality : 0.058 0.345 2095 Planarity : 0.008 0.145 2322 Dihedral : 17.275 179.960 5077 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 2.21 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.035 0.003 TRP B 675 HIS 0.006 0.002 HIS B 338 PHE 0.063 0.003 PHE A 789 TYR 0.021 0.003 TYR A 421 ARG 0.011 0.001 ARG A 648 Details of bonding type rmsd link_NAG-ASN : bond 0.00360 ( 10) link_NAG-ASN : angle 3.04998 ( 30) link_BETA1-4 : bond 0.00862 ( 5) link_BETA1-4 : angle 2.32195 ( 15) hydrogen bonds : bond 0.15385 ( 560) hydrogen bonds : angle 5.43224 ( 1626) SS BOND : bond 0.00561 ( 19) SS BOND : angle 1.94525 ( 38) covalent geometry : bond 0.00695 (13623) covalent geometry : angle 0.96053 (18482) *********************** 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 : 1.349 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 170 average time/residue: 1.0151 time to fit residues: 193.3809 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 : 1.551 ------------------------------------------------------------------------------- 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 136 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 65 optimal weight: 0.0980 chunk 126 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 94 optimal weight: 0.5980 chunk 147 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3711 r_free = 0.3711 target = 0.123886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.088059 restraints weight = 19449.519| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.59 r_work: 0.2977 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13657 Z= 0.155 Angle : 0.617 9.226 18565 Z= 0.324 Chirality : 0.045 0.189 2095 Planarity : 0.005 0.088 2322 Dihedral : 11.581 179.422 2159 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.15 % Allowed : 16.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.20), residues: 1609 helix: 0.58 (0.19), residues: 694 sheet: -1.05 (0.32), residues: 223 loop : -1.47 (0.22), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 299 HIS 0.004 0.001 HIS A 463 PHE 0.044 0.002 PHE A 789 TYR 0.019 0.002 TYR A 421 ARG 0.005 0.000 ARG B 69 Details of bonding type rmsd link_NAG-ASN : bond 0.00305 ( 10) link_NAG-ASN : angle 3.11711 ( 30) link_BETA1-4 : bond 0.00417 ( 5) link_BETA1-4 : angle 1.28129 ( 15) hydrogen bonds : bond 0.06120 ( 560) hydrogen bonds : angle 4.38415 ( 1626) SS BOND : bond 0.00386 ( 19) SS BOND : angle 1.32189 ( 38) covalent geometry : bond 0.00356 (13623) covalent geometry : angle 0.60092 (18482) *********************** 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 214 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 170 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 499 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7205 (mp0) REVERT: B 399 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.7436 (mp0) outliers start: 44 outliers final: 16 residues processed: 193 average time/residue: 0.8706 time to fit residues: 190.5092 Evaluate side-chains 180 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 1.429 ------------------------------------------------------------------------------- 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 197 MET 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 605 PHE 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 702 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 849 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 17 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 111 optimal weight: 0.0040 chunk 13 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 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 = 0.3711 r_free = 0.3711 target = 0.123787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.087979 restraints weight = 19575.541| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.60 r_work: 0.2979 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13657 Z= 0.147 Angle : 0.586 6.898 18565 Z= 0.308 Chirality : 0.045 0.200 2095 Planarity : 0.005 0.070 2322 Dihedral : 10.737 179.982 2146 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.15 % Allowed : 16.89 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.20), residues: 1609 helix: 1.12 (0.20), residues: 695 sheet: -0.98 (0.33), residues: 223 loop : -1.35 (0.22), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 299 HIS 0.004 0.001 HIS A 463 PHE 0.024 0.001 PHE A 832 TYR 0.019 0.002 TYR A 421 ARG 0.004 0.000 ARG A 648 Details of bonding type rmsd link_NAG-ASN : bond 0.00246 ( 10) link_NAG-ASN : angle 2.74024 ( 30) link_BETA1-4 : bond 0.00340 ( 5) link_BETA1-4 : angle 1.38963 ( 15) hydrogen bonds : bond 0.05721 ( 560) hydrogen bonds : angle 4.20239 ( 1626) SS BOND : bond 0.00360 ( 19) SS BOND : angle 1.17498 ( 38) covalent geometry : bond 0.00338 (13623) covalent geometry : angle 0.57294 (18482) *********************** 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 214 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 170 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 499 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7208 (mp0) REVERT: A 575 ASP cc_start: 0.8282 (p0) cc_final: 0.7811 (p0) REVERT: A 576 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7570 (pm20) REVERT: A 793 LYS cc_start: 0.8900 (tppp) cc_final: 0.8411 (tppt) REVERT: B 270 PHE cc_start: 0.9189 (OUTLIER) cc_final: 0.8475 (m-80) REVERT: B 399 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.7422 (mp0) REVERT: B 441 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7034 (mpp-170) REVERT: B 507 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8325 (tm-30) REVERT: B 771 MET cc_start: 0.3803 (mmt) cc_final: 0.3500 (ptt) outliers start: 44 outliers final: 20 residues processed: 192 average time/residue: 0.8616 time to fit residues: 188.5632 Evaluate side-chains 187 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 1.294 ------------------------------------------------------------------------------- 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 197 MET 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 576 GLU Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 743 LEU 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 560 THR Chi-restraints excluded: chain B residue 594 ASN Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 737 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 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 33 optimal weight: 0.9980 chunk 48 optimal weight: 0.0370 chunk 156 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 39 optimal weight: 0.0870 chunk 129 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 158 optimal weight: 1.9990 overall best weight: 0.6236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3710 r_free = 0.3710 target = 0.123640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.088012 restraints weight = 19423.515| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.58 r_work: 0.2979 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13657 Z= 0.142 Angle : 0.570 8.629 18565 Z= 0.298 Chirality : 0.045 0.200 2095 Planarity : 0.005 0.069 2322 Dihedral : 10.474 179.909 2146 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 2.75 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.21), residues: 1609 helix: 1.37 (0.20), residues: 702 sheet: -0.92 (0.33), residues: 223 loop : -1.36 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 299 HIS 0.004 0.001 HIS A 463 PHE 0.025 0.001 PHE B 729 TYR 0.019 0.002 TYR A 421 ARG 0.003 0.000 ARG A 648 Details of bonding type rmsd link_NAG-ASN : bond 0.00224 ( 10) link_NAG-ASN : angle 2.50543 ( 30) link_BETA1-4 : bond 0.00324 ( 5) link_BETA1-4 : angle 1.37262 ( 15) hydrogen bonds : bond 0.05461 ( 560) hydrogen bonds : angle 4.12389 ( 1626) SS BOND : bond 0.00347 ( 19) SS BOND : angle 1.11355 ( 38) covalent geometry : bond 0.00327 (13623) covalent geometry : angle 0.55883 (18482) *********************** 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 204 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 159 time to evaluate : 1.534 Fit side-chains REVERT: A 253 GLN cc_start: 0.8416 (mt0) cc_final: 0.8173 (mm-40) REVERT: A 499 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7201 (mp0) REVERT: A 575 ASP cc_start: 0.8249 (p0) cc_final: 0.7703 (p0) REVERT: A 576 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7420 (pm20) REVERT: B 270 PHE cc_start: 0.9208 (OUTLIER) cc_final: 0.8462 (m-80) REVERT: B 399 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7376 (mp0) REVERT: B 441 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.6952 (mpp-170) REVERT: B 507 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8305 (tm-30) REVERT: B 517 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8688 (ttmm) outliers start: 45 outliers final: 21 residues processed: 189 average time/residue: 0.8761 time to fit residues: 187.6051 Evaluate side-chains 180 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 1.361 ------------------------------------------------------------------------------- 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 570 ASP Chi-restraints excluded: chain A residue 576 GLU 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 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 560 THR Chi-restraints excluded: chain B residue 675 TRP Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 760 ILE 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 29 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 73 optimal weight: 0.0770 chunk 92 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 143 optimal weight: 0.0570 chunk 96 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3703 r_free = 0.3703 target = 0.123181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.087321 restraints weight = 19532.866| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.59 r_work: 0.2967 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13657 Z= 0.172 Angle : 0.638 18.268 18565 Z= 0.329 Chirality : 0.049 0.727 2095 Planarity : 0.005 0.070 2322 Dihedral : 10.443 179.659 2146 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.08 % Allowed : 16.61 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.21), residues: 1609 helix: 1.34 (0.20), residues: 713 sheet: -0.93 (0.33), residues: 223 loop : -1.41 (0.22), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 299 HIS 0.005 0.001 HIS A 595 PHE 0.025 0.002 PHE B 729 TYR 0.021 0.002 TYR A 421 ARG 0.003 0.000 ARG A 331 Details of bonding type rmsd link_NAG-ASN : bond 0.00807 ( 10) link_NAG-ASN : angle 4.90060 ( 30) link_BETA1-4 : bond 0.00339 ( 5) link_BETA1-4 : angle 1.41487 ( 15) hydrogen bonds : bond 0.05819 ( 560) hydrogen bonds : angle 4.13489 ( 1626) SS BOND : bond 0.00413 ( 19) SS BOND : angle 1.23148 ( 38) covalent geometry : bond 0.00406 (13623) covalent geometry : angle 0.60460 (18482) *********************** 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 217 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 160 time to evaluate : 1.482 Fit side-chains revert: symmetry clash REVERT: A 23 ASP cc_start: 0.7078 (t0) cc_final: 0.6677 (m-30) REVERT: A 253 GLN cc_start: 0.8411 (mt0) cc_final: 0.8138 (mm-40) REVERT: A 499 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7203 (mp0) REVERT: A 576 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7432 (pm20) REVERT: A 583 ASN cc_start: 0.8605 (OUTLIER) cc_final: 0.8360 (m110) REVERT: A 794 SER cc_start: 0.8650 (OUTLIER) cc_final: 0.8225 (p) REVERT: B 270 PHE cc_start: 0.9218 (OUTLIER) cc_final: 0.8495 (m-80) REVERT: B 399 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.7416 (mp0) REVERT: B 507 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8329 (tm-30) REVERT: B 517 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8699 (ttmm) outliers start: 57 outliers final: 29 residues processed: 199 average time/residue: 0.9041 time to fit residues: 203.6963 Evaluate side-chains 194 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 157 time to evaluate : 1.344 ------------------------------------------------------------------------------- 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 583 ASN 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 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 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 660 CYS Chi-restraints excluded: chain B residue 675 TRP Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 737 VAL 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 849 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 126 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 146 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 24 optimal weight: 0.0870 chunk 80 optimal weight: 3.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 583 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.122697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.087415 restraints weight = 19766.801| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.56 r_work: 0.2962 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13657 Z= 0.181 Angle : 0.644 13.953 18565 Z= 0.330 Chirality : 0.048 0.495 2095 Planarity : 0.005 0.071 2322 Dihedral : 10.438 179.530 2146 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.72 % Allowed : 17.04 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.21), residues: 1609 helix: 1.34 (0.19), residues: 715 sheet: -0.96 (0.33), residues: 224 loop : -1.41 (0.22), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 299 HIS 0.007 0.001 HIS A 595 PHE 0.026 0.002 PHE B 729 TYR 0.021 0.002 TYR A 421 ARG 0.003 0.000 ARG A 331 Details of bonding type rmsd link_NAG-ASN : bond 0.00738 ( 10) link_NAG-ASN : angle 4.88833 ( 30) link_BETA1-4 : bond 0.00327 ( 5) link_BETA1-4 : angle 1.42395 ( 15) hydrogen bonds : bond 0.05951 ( 560) hydrogen bonds : angle 4.14517 ( 1626) SS BOND : bond 0.00433 ( 19) SS BOND : angle 1.27060 ( 38) covalent geometry : bond 0.00432 (13623) covalent geometry : angle 0.61072 (18482) *********************** 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 214 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 162 time to evaluate : 1.595 Fit side-chains revert: symmetry clash REVERT: A 23 ASP cc_start: 0.7069 (t0) cc_final: 0.6689 (m-30) REVERT: A 249 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.6630 (tp30) REVERT: A 253 GLN cc_start: 0.8432 (mt0) cc_final: 0.8131 (mm-40) REVERT: A 499 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7222 (mp0) REVERT: A 576 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7372 (pm20) REVERT: A 583 ASN cc_start: 0.8618 (OUTLIER) cc_final: 0.8362 (m110) REVERT: A 794 SER cc_start: 0.8709 (OUTLIER) cc_final: 0.8303 (p) REVERT: B 270 PHE cc_start: 0.9232 (OUTLIER) cc_final: 0.8453 (m-80) REVERT: B 399 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7437 (mp0) REVERT: B 507 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8326 (tm-30) REVERT: B 517 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8704 (ttmm) REVERT: B 604 GLU cc_start: 0.8314 (tt0) cc_final: 0.8102 (tt0) outliers start: 52 outliers final: 27 residues processed: 197 average time/residue: 0.9031 time to fit residues: 201.3664 Evaluate side-chains 192 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 156 time to evaluate : 1.367 ------------------------------------------------------------------------------- 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 576 GLU 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 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 517 LYS Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 640 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 770 LEU Chi-restraints excluded: chain B residue 836 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 125 optimal weight: 2.9990 chunk 109 optimal weight: 0.4980 chunk 97 optimal weight: 0.9980 chunk 148 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 0.0050 chunk 155 optimal weight: 0.0570 chunk 140 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 70 optimal weight: 0.0980 overall best weight: 0.2912 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3729 r_free = 0.3729 target = 0.124918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.089414 restraints weight = 19668.719| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.60 r_work: 0.3009 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13657 Z= 0.111 Angle : 0.577 16.431 18565 Z= 0.290 Chirality : 0.046 0.568 2095 Planarity : 0.004 0.065 2322 Dihedral : 10.406 179.836 2146 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.86 % Allowed : 17.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.21), residues: 1609 helix: 1.64 (0.20), residues: 706 sheet: -0.85 (0.33), residues: 223 loop : -1.25 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 299 HIS 0.004 0.001 HIS A 595 PHE 0.028 0.001 PHE B 729 TYR 0.016 0.001 TYR A 421 ARG 0.002 0.000 ARG A 648 Details of bonding type rmsd link_NAG-ASN : bond 0.00686 ( 10) link_NAG-ASN : angle 4.97729 ( 30) link_BETA1-4 : bond 0.00339 ( 5) link_BETA1-4 : angle 1.31283 ( 15) hydrogen bonds : bond 0.04653 ( 560) hydrogen bonds : angle 3.97607 ( 1626) SS BOND : bond 0.00232 ( 19) SS BOND : angle 0.90318 ( 38) covalent geometry : bond 0.00235 (13623) covalent geometry : angle 0.53906 (18482) *********************** 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 195 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 155 time to evaluate : 1.338 Fit side-chains REVERT: A 23 ASP cc_start: 0.7105 (t0) cc_final: 0.6722 (m-30) REVERT: A 253 GLN cc_start: 0.8415 (mt0) cc_final: 0.8135 (mm-40) REVERT: A 499 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7174 (mp0) REVERT: A 576 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7327 (pm20) REVERT: A 794 SER cc_start: 0.8707 (OUTLIER) cc_final: 0.8346 (p) REVERT: B 270 PHE cc_start: 0.9167 (OUTLIER) cc_final: 0.8408 (m-80) REVERT: B 399 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.7445 (mp0) REVERT: B 507 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8293 (tm-30) outliers start: 40 outliers final: 21 residues processed: 182 average time/residue: 0.8930 time to fit residues: 183.6791 Evaluate side-chains 178 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 576 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 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 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 519 GLU 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 737 VAL Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 836 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 78 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 107 optimal weight: 0.2980 chunk 6 optimal weight: 0.0050 chunk 14 optimal weight: 0.3980 chunk 143 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 HIS 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 = 0.3723 r_free = 0.3723 target = 0.124510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.088818 restraints weight = 19669.008| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.60 r_work: 0.2998 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13657 Z= 0.125 Angle : 0.582 13.659 18565 Z= 0.294 Chirality : 0.045 0.488 2095 Planarity : 0.004 0.067 2322 Dihedral : 10.295 179.735 2146 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.93 % Allowed : 17.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.21), residues: 1609 helix: 1.72 (0.20), residues: 709 sheet: -0.66 (0.35), residues: 205 loop : -1.18 (0.22), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 299 HIS 0.004 0.001 HIS A 463 PHE 0.028 0.001 PHE B 729 TYR 0.018 0.001 TYR A 421 ARG 0.002 0.000 ARG A 648 Details of bonding type rmsd link_NAG-ASN : bond 0.00426 ( 10) link_NAG-ASN : angle 4.44269 ( 30) link_BETA1-4 : bond 0.00333 ( 5) link_BETA1-4 : angle 1.31094 ( 15) hydrogen bonds : bond 0.04951 ( 560) hydrogen bonds : angle 3.94475 ( 1626) SS BOND : bond 0.00291 ( 19) SS BOND : angle 0.96306 ( 38) covalent geometry : bond 0.00281 (13623) covalent geometry : angle 0.55247 (18482) *********************** 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 200 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 159 time to evaluate : 1.375 Fit side-chains revert: symmetry clash REVERT: A 23 ASP cc_start: 0.6920 (t0) cc_final: 0.6611 (m-30) REVERT: A 253 GLN cc_start: 0.8424 (mt0) cc_final: 0.8140 (mm-40) REVERT: A 499 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7233 (mp0) REVERT: A 576 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7308 (pm20) REVERT: A 794 SER cc_start: 0.8831 (OUTLIER) cc_final: 0.8580 (p) REVERT: B 270 PHE cc_start: 0.9192 (OUTLIER) cc_final: 0.8420 (m-80) REVERT: B 399 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7440 (mp0) REVERT: B 507 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8288 (tm-30) REVERT: B 517 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8699 (ttmm) REVERT: B 604 GLU cc_start: 0.8223 (tt0) cc_final: 0.7976 (tt0) outliers start: 41 outliers final: 23 residues processed: 184 average time/residue: 0.9178 time to fit residues: 190.6147 Evaluate side-chains 181 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 1.304 ------------------------------------------------------------------------------- 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 540 SER Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 612 PHE 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 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 660 CYS Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 737 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 Chi-restraints excluded: chain B residue 849 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 152 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 76 optimal weight: 8.9990 chunk 151 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3699 r_free = 0.3699 target = 0.122903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.086966 restraints weight = 19482.157| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.59 r_work: 0.2961 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 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 : 0.005 0.039 13657 Z= 0.193 Angle : 0.649 12.965 18565 Z= 0.331 Chirality : 0.048 0.444 2095 Planarity : 0.005 0.069 2322 Dihedral : 10.417 179.416 2146 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.79 % Allowed : 18.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.21), residues: 1609 helix: 1.55 (0.19), residues: 713 sheet: -0.79 (0.35), residues: 210 loop : -1.29 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 675 HIS 0.005 0.001 HIS A 463 PHE 0.038 0.002 PHE B 789 TYR 0.022 0.002 TYR A 421 ARG 0.003 0.000 ARG A 331 Details of bonding type rmsd link_NAG-ASN : bond 0.00331 ( 10) link_NAG-ASN : angle 4.36421 ( 30) link_BETA1-4 : bond 0.00347 ( 5) link_BETA1-4 : angle 1.41160 ( 15) hydrogen bonds : bond 0.06063 ( 560) hydrogen bonds : angle 4.06877 ( 1626) SS BOND : bond 0.00466 ( 19) SS BOND : angle 1.29572 ( 38) covalent geometry : bond 0.00465 (13623) covalent geometry : angle 0.62198 (18482) *********************** 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 190 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 151 time to evaluate : 1.401 Fit side-chains revert: symmetry clash REVERT: A 23 ASP cc_start: 0.6996 (t0) cc_final: 0.6645 (m-30) REVERT: A 253 GLN cc_start: 0.8456 (mt0) cc_final: 0.8184 (mm-40) REVERT: A 499 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7241 (mp0) REVERT: A 576 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7456 (pm20) REVERT: A 583 ASN cc_start: 0.8574 (OUTLIER) cc_final: 0.8345 (m110) REVERT: B 184 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.9065 (mt) REVERT: B 270 PHE cc_start: 0.9247 (OUTLIER) cc_final: 0.8492 (m-80) REVERT: B 399 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.7414 (mp0) REVERT: B 507 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8331 (tm-30) REVERT: B 517 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8709 (ttmm) REVERT: B 604 GLU cc_start: 0.8237 (tt0) cc_final: 0.8030 (tt0) REVERT: B 811 MET cc_start: 0.8963 (mmm) cc_final: 0.8714 (mmm) outliers start: 39 outliers final: 22 residues processed: 176 average time/residue: 0.9626 time to fit residues: 191.7804 Evaluate side-chains 178 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 1.389 ------------------------------------------------------------------------------- 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 540 SER Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 583 ASN Chi-restraints excluded: chain A residue 612 PHE 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 827 SER Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 184 LEU 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 695 ILE 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 849 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 38 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 6 optimal weight: 0.0040 chunk 61 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 144 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 154 optimal weight: 0.6980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 HIS 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 = 0.124277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.088562 restraints weight = 19455.314| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.60 r_work: 0.2993 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13657 Z= 0.131 Angle : 0.587 12.642 18565 Z= 0.299 Chirality : 0.045 0.405 2095 Planarity : 0.004 0.067 2322 Dihedral : 10.328 179.541 2146 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.58 % Allowed : 18.11 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.21), residues: 1609 helix: 1.68 (0.20), residues: 709 sheet: -0.72 (0.35), residues: 209 loop : -1.23 (0.22), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 299 HIS 0.003 0.001 HIS A 463 PHE 0.032 0.001 PHE B 789 TYR 0.018 0.001 TYR A 421 ARG 0.002 0.000 ARG A 648 Details of bonding type rmsd link_NAG-ASN : bond 0.00338 ( 10) link_NAG-ASN : angle 4.06220 ( 30) link_BETA1-4 : bond 0.00402 ( 5) link_BETA1-4 : angle 1.32726 ( 15) hydrogen bonds : bond 0.05081 ( 560) hydrogen bonds : angle 3.97676 ( 1626) SS BOND : bond 0.00301 ( 19) SS BOND : angle 1.00393 ( 38) covalent geometry : bond 0.00298 (13623) covalent geometry : angle 0.56212 (18482) ********************** 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 186 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 150 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 ASP cc_start: 0.6894 (t0) cc_final: 0.6582 (m-30) REVERT: A 253 GLN cc_start: 0.8443 (mt0) cc_final: 0.8172 (mm-40) REVERT: A 499 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7218 (mp0) REVERT: A 576 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7429 (pm20) REVERT: B 184 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.9044 (mt) REVERT: B 399 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7446 (mp0) REVERT: B 507 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8278 (tm-30) REVERT: B 517 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8706 (ttmm) REVERT: B 604 GLU cc_start: 0.8234 (tt0) cc_final: 0.8011 (tt0) outliers start: 36 outliers final: 24 residues processed: 172 average time/residue: 0.8832 time to fit residues: 172.3741 Evaluate side-chains 178 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 1.366 ------------------------------------------------------------------------------- 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 540 SER Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 592 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 827 SER Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 184 LEU 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 642 ILE Chi-restraints excluded: chain B residue 695 ILE 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 65 optimal weight: 0.0010 chunk 161 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 85 optimal weight: 0.3980 chunk 52 optimal weight: 5.9990 chunk 55 optimal weight: 0.0070 chunk 51 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.4204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 HIS B 583 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.124926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.089409 restraints weight = 19510.183| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.60 r_work: 0.3010 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13657 Z= 0.117 Angle : 0.570 11.922 18565 Z= 0.289 Chirality : 0.044 0.349 2095 Planarity : 0.004 0.065 2322 Dihedral : 10.184 179.658 2146 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.58 % Allowed : 18.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.21), residues: 1609 helix: 1.72 (0.19), residues: 719 sheet: -0.70 (0.35), residues: 205 loop : -1.22 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 675 HIS 0.003 0.001 HIS A 463 PHE 0.032 0.001 PHE B 789 TYR 0.016 0.001 TYR A 421 ARG 0.002 0.000 ARG A 648 Details of bonding type rmsd link_NAG-ASN : bond 0.00330 ( 10) link_NAG-ASN : angle 3.73558 ( 30) link_BETA1-4 : bond 0.00356 ( 5) link_BETA1-4 : angle 1.28775 ( 15) hydrogen bonds : bond 0.04662 ( 560) hydrogen bonds : angle 3.89406 ( 1626) SS BOND : bond 0.00266 ( 19) SS BOND : angle 0.91731 ( 38) covalent geometry : bond 0.00261 (13623) covalent geometry : angle 0.54848 (18482) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11461.79 seconds wall clock time: 195 minutes 18.83 seconds (11718.83 seconds total)