Starting phenix.real_space_refine on Tue Dec 31 17:45:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ayn_15717/12_2024/8ayn_15717.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ayn_15717/12_2024/8ayn_15717.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ayn_15717/12_2024/8ayn_15717.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ayn_15717/12_2024/8ayn_15717.map" model { file = "/net/cci-nas-00/data/ceres_data/8ayn_15717/12_2024/8ayn_15717.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ayn_15717/12_2024/8ayn_15717.cif" } resolution = 2.8 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= 0.000 sd= 0.004 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 P 8 5.49 5 S 84 5.16 5 C 10336 2.51 5 N 2484 2.21 5 O 2824 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 103 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 15748 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 3084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3084 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 391} Chain breaks: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 38 Chain: "I" Number of atoms: 1358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1358 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain breaks: 2 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 4, 'HIS:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 55 Chain: "J" Number of atoms: 1358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1358 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain breaks: 2 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 4, 'HIS:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 55 Chain: "D" Number of atoms: 3084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3084 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 391} Chain breaks: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 3088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3088 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 392} Chain breaks: 2 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 69 Chain: "A" Number of atoms: 3088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3088 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 392} Chain breaks: 2 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 69 Chain: "B" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 122 Unusual residues: {'OLC': 1, 'PLM': 1, 'POV': 1, 'ZK1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'OLR': 1, 'PLM': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'OLR': 1, 'PLM': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 122 Unusual residues: {'OLC': 1, 'PLM': 1, 'POV': 1, 'ZK1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 159 Unusual residues: {'OLC': 1, 'PLM': 4, 'POV': 1, 'ZK1': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Chain: "A" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 159 Unusual residues: {'OLC': 1, 'PLM': 4, 'POV': 1, 'ZK1': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Time building chain proxies: 10.28, per 1000 atoms: 0.65 Number of scatterers: 15748 At special positions: 0 Unit cell: (133.75, 108.07, 133.75, 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) S 84 16.00 P 8 15.00 F 12 9.00 O 2824 8.00 N 2484 7.00 C 10336 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS I 52 " - pdb=" SG CYS I 91 " distance=2.03 Simple disulfide: pdb=" SG CYS I 90 " - pdb=" SG CYS I 100 " distance=2.03 Simple disulfide: pdb=" SG CYS J 52 " - pdb=" SG CYS J 91 " distance=2.03 Simple disulfide: pdb=" SG CYS J 90 " - pdb=" SG CYS J 100 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 714 " - pdb=" SG CYS C 769 " distance=2.03 Simple disulfide: pdb=" SG CYS A 714 " - pdb=" SG CYS A 769 " 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 Time building additional restraints: 4.44 Conformation dependent library (CDL) restraints added in 2.2 seconds 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3640 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 22 sheets defined 56.3% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 462 through 469 Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.601A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 547 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 626 Processing helix chain 'B' and resid 635 through 642 removed outlier: 3.617A pdb=" N GLN B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 662 Processing helix chain 'B' and resid 664 through 677 Processing helix chain 'B' and resid 685 through 696 Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 742 through 757 removed outlier: 3.535A pdb=" N LEU B 748 " --> pdb=" O THR B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'B' and resid 788 through 818 removed outlier: 3.696A pdb=" N VAL B 792 " --> pdb=" O SER B 788 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N GLY B 794 " --> pdb=" O SER B 790 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL B 795 " --> pdb=" O ASN B 791 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 40 Processing helix chain 'I' and resid 116 through 128 removed outlier: 3.763A pdb=" N LEU I 120 " --> pdb=" O SER I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 128 through 150 removed outlier: 3.731A pdb=" N ARG I 149 " --> pdb=" O VAL I 145 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL I 150 " --> pdb=" O ALA I 146 " (cutoff:3.500A) Processing helix chain 'I' and resid 155 through 183 removed outlier: 3.812A pdb=" N LEU I 159 " --> pdb=" O ARG I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 233 removed outlier: 3.589A pdb=" N TYR I 206 " --> pdb=" O GLY I 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 40 Processing helix chain 'J' and resid 116 through 128 removed outlier: 3.763A pdb=" N LEU J 120 " --> pdb=" O SER J 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 128 through 150 removed outlier: 3.732A pdb=" N ARG J 149 " --> pdb=" O VAL J 145 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL J 150 " --> pdb=" O ALA J 146 " (cutoff:3.500A) Processing helix chain 'J' and resid 155 through 183 removed outlier: 3.814A pdb=" N LEU J 159 " --> pdb=" O ARG J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 233 removed outlier: 3.590A pdb=" N TYR J 206 " --> pdb=" O GLY J 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 437 removed outlier: 3.539A pdb=" N HIS D 435 " --> pdb=" O GLU D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 469 Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.605A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 547 Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 626 Processing helix chain 'D' and resid 636 through 642 removed outlier: 3.558A pdb=" N GLN D 642 " --> pdb=" O ASP D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 664 through 677 Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 706 through 714 removed outlier: 3.723A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 757 removed outlier: 3.591A pdb=" N LEU D 751 " --> pdb=" O ASN D 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 768 Processing helix chain 'D' and resid 788 through 791 Processing helix chain 'D' and resid 792 through 819 removed outlier: 3.604A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 415 removed outlier: 3.768A pdb=" N ASP C 415 " --> pdb=" O GLU C 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 412 through 415' Processing helix chain 'C' and resid 419 through 433 removed outlier: 3.553A pdb=" N GLU C 423 " --> pdb=" O GLY C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 465 Processing helix chain 'C' and resid 478 through 484 removed outlier: 3.738A pdb=" N VAL C 484 " --> pdb=" O VAL C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 515 removed outlier: 3.666A pdb=" N LEU C 514 " --> pdb=" O PHE C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 542 Processing helix chain 'C' and resid 543 through 547 Processing helix chain 'C' and resid 568 through 581 Processing helix chain 'C' and resid 591 through 625 Processing helix chain 'C' and resid 631 through 638 removed outlier: 3.608A pdb=" N GLN C 638 " --> pdb=" O ASP C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 657 Processing helix chain 'C' and resid 660 through 672 Processing helix chain 'C' and resid 681 through 693 removed outlier: 3.762A pdb=" N LYS C 693 " --> pdb=" O VAL C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 711 Processing helix chain 'C' and resid 738 through 752 Processing helix chain 'C' and resid 753 through 764 Processing helix chain 'C' and resid 788 through 812 removed outlier: 3.670A pdb=" N PHE C 792 " --> pdb=" O VAL C 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 415 removed outlier: 3.670A pdb=" N ASP A 415 " --> pdb=" O GLU A 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 412 through 415' Processing helix chain 'A' and resid 419 through 433 removed outlier: 3.639A pdb=" N GLU A 423 " --> pdb=" O GLY A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 465 Processing helix chain 'A' and resid 478 through 484 removed outlier: 3.750A pdb=" N VAL A 484 " --> pdb=" O VAL A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 515 removed outlier: 3.675A pdb=" N LEU A 514 " --> pdb=" O PHE A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 542 Processing helix chain 'A' and resid 543 through 547 Processing helix chain 'A' and resid 568 through 581 Processing helix chain 'A' and resid 591 through 625 Processing helix chain 'A' and resid 631 through 638 removed outlier: 3.604A pdb=" N GLN A 638 " --> pdb=" O ASP A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 657 Processing helix chain 'A' and resid 660 through 672 Processing helix chain 'A' and resid 681 through 693 removed outlier: 3.769A pdb=" N LYS A 693 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 711 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 753 through 764 Processing helix chain 'A' and resid 788 through 812 removed outlier: 3.666A pdb=" N PHE A 792 " --> pdb=" O VAL A 788 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 441 through 444 removed outlier: 6.092A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE B 474 " --> pdb=" O VAL B 396 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA3, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.809A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 701 through 705 removed outlier: 3.993A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 99 through 102 removed outlier: 4.231A pdb=" N VAL I 99 " --> pdb=" O CYS I 91 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS I 91 " --> pdb=" O VAL I 99 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU I 45 " --> pdb=" O SER I 84 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 99 through 102 removed outlier: 4.232A pdb=" N VAL J 99 " --> pdb=" O CYS J 91 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS J 91 " --> pdb=" O VAL J 99 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU J 45 " --> pdb=" O SER J 84 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 441 through 444 removed outlier: 5.924A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AA9, first strand: chain 'D' and resid 452 through 453 Processing sheet with id=AB1, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.771A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 646 through 648 removed outlier: 5.984A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 436 through 438 removed outlier: 3.551A pdb=" N VAL C 470 " --> pdb=" O ILE C 392 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL C 472 " --> pdb=" O THR C 394 " (cutoff:3.500A) removed outlier: 9.572A pdb=" N ALA C 471 " --> pdb=" O PRO C 733 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ALA C 473 " --> pdb=" O ALA C 731 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ALA C 731 " --> pdb=" O ALA C 473 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU C 475 " --> pdb=" O GLY C 729 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 436 through 438 removed outlier: 3.551A pdb=" N VAL C 470 " --> pdb=" O ILE C 392 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL C 472 " --> pdb=" O THR C 394 " (cutoff:3.500A) removed outlier: 9.572A pdb=" N ALA C 471 " --> pdb=" O PRO C 733 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ALA C 473 " --> pdb=" O ALA C 731 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ALA C 731 " --> pdb=" O ALA C 473 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU C 475 " --> pdb=" O GLY C 729 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU C 494 " --> pdb=" O LYS C 726 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N MET C 492 " --> pdb=" O TYR C 728 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 403 through 404 Processing sheet with id=AB6, first strand: chain 'C' and resid 448 through 449 removed outlier: 3.778A pdb=" N ALA C 448 " --> pdb=" O ASN C 457 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 642 through 644 removed outlier: 6.552A pdb=" N ALA C 642 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N LEU C 699 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N GLY C 644 " --> pdb=" O LEU C 699 " (cutoff:3.500A) removed outlier: 9.657A pdb=" N GLU C 701 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE C 498 " --> pdb=" O VAL C 719 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 436 through 438 Processing sheet with id=AB9, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AC1, first strand: chain 'A' and resid 448 through 449 removed outlier: 3.749A pdb=" N ALA A 448 " --> pdb=" O ASN A 457 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 485 through 487 Processing sheet with id=AC3, first strand: chain 'A' and resid 492 through 494 removed outlier: 3.931A pdb=" N MET A 492 " --> pdb=" O TYR A 728 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 494 " --> pdb=" O LYS A 726 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 642 through 644 removed outlier: 6.575A pdb=" N ALA A 642 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N LEU A 699 " --> pdb=" O ALA A 642 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLY A 644 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 9.682A pdb=" N GLU A 701 " --> pdb=" O GLY A 644 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE A 498 " --> pdb=" O VAL A 719 " (cutoff:3.500A) 883 hydrogen bonds defined for protein. 2577 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: 5.55 Time building geometry restraints manager: 5.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.34: 4735 1.34 - 1.50: 5004 1.50 - 1.65: 6179 1.65 - 1.81: 142 1.81 - 1.97: 6 Bond restraints: 16066 Sorted by residual: bond pdb=" C1 OLR I 503 " pdb=" C7 OLR I 503 " ideal model delta sigma weight residual 1.382 1.662 -0.280 2.00e-02 2.50e+03 1.95e+02 bond pdb=" C1 OLR J 503 " pdb=" C7 OLR J 503 " ideal model delta sigma weight residual 1.382 1.661 -0.279 2.00e-02 2.50e+03 1.94e+02 bond pdb=" C1 OLR J 503 " pdb=" S1 OLR J 503 " ideal model delta sigma weight residual 1.746 1.971 -0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C1 OLR I 503 " pdb=" S1 OLR I 503 " ideal model delta sigma weight residual 1.746 1.970 -0.224 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C2 OLR J 503 " pdb=" O1 OLR J 503 " ideal model delta sigma weight residual 1.205 1.397 -0.192 2.00e-02 2.50e+03 9.21e+01 ... (remaining 16061 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.34: 21497 5.34 - 10.68: 133 10.68 - 16.02: 12 16.02 - 21.36: 5 21.36 - 26.70: 15 Bond angle restraints: 21662 Sorted by residual: angle pdb=" C35 POV A 907 " pdb=" C36 POV A 907 " pdb=" C37 POV A 907 " ideal model delta sigma weight residual 113.93 140.63 -26.70 3.00e+00 1.11e-01 7.92e+01 angle pdb=" C35 POV C 907 " pdb=" C36 POV C 907 " pdb=" C37 POV C 907 " ideal model delta sigma weight residual 113.93 140.52 -26.59 3.00e+00 1.11e-01 7.85e+01 angle pdb=" CAR ZK1 D 901 " pdb=" CAS ZK1 D 901 " pdb=" CAZ ZK1 D 901 " ideal model delta sigma weight residual 119.91 144.30 -24.39 3.00e+00 1.11e-01 6.61e+01 angle pdb=" CAJ ZK1 D 901 " pdb=" CAS ZK1 D 901 " pdb=" CAZ ZK1 D 901 " ideal model delta sigma weight residual 120.43 96.40 24.03 3.00e+00 1.11e-01 6.42e+01 angle pdb=" CAI ZK1 D 901 " pdb=" CAR ZK1 D 901 " pdb=" NAX ZK1 D 901 " ideal model delta sigma weight residual 120.86 97.28 23.58 3.00e+00 1.11e-01 6.18e+01 ... (remaining 21657 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.77: 9242 32.77 - 65.54: 265 65.54 - 98.31: 38 98.31 - 131.08: 4 131.08 - 163.85: 7 Dihedral angle restraints: 9556 sinusoidal: 3838 harmonic: 5718 Sorted by residual: dihedral pdb=" CB CYS D 718 " pdb=" SG CYS D 718 " pdb=" SG CYS D 773 " pdb=" CB CYS D 773 " ideal model delta sinusoidal sigma weight residual 93.00 135.84 -42.84 1 1.00e+01 1.00e-02 2.56e+01 dihedral pdb=" O20 OLC D 902 " pdb=" C21 OLC D 902 " pdb=" C22 OLC D 902 " pdb=" O23 OLC D 902 " ideal model delta sinusoidal sigma weight residual 302.77 138.92 163.85 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C29 POV B 904 " pdb="C210 POV B 904 " pdb="C211 POV B 904 " pdb="C212 POV B 904 " ideal model delta sinusoidal sigma weight residual 112.25 -84.78 -162.97 1 3.00e+01 1.11e-03 2.09e+01 ... (remaining 9553 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1926 0.059 - 0.119: 443 0.119 - 0.178: 22 0.178 - 0.238: 9 0.238 - 0.297: 4 Chirality restraints: 2404 Sorted by residual: chirality pdb=" C8 OLR J 503 " pdb=" C10 OLR J 503 " pdb=" C6 OLR J 503 " pdb=" C9 OLR J 503 " both_signs ideal model delta sigma weight residual False -2.44 -2.73 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" C8 OLR I 503 " pdb=" C10 OLR I 503 " pdb=" C6 OLR I 503 " pdb=" C9 OLR I 503 " both_signs ideal model delta sigma weight residual False -2.44 -2.73 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CG LEU A 573 " pdb=" CB LEU A 573 " pdb=" CD1 LEU A 573 " pdb=" CD2 LEU A 573 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 2401 not shown) Planarity restraints: 2632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 736 " -0.071 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO D 737 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO D 737 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO D 737 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 399 " -0.034 5.00e-02 4.00e+02 5.06e-02 4.09e+00 pdb=" N PRO C 400 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 400 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 400 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 399 " -0.033 5.00e-02 4.00e+02 5.01e-02 4.01e+00 pdb=" N PRO A 400 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 400 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 400 " -0.024 5.00e-02 4.00e+02 ... (remaining 2629 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 124 2.58 - 3.16: 13537 3.16 - 3.74: 23248 3.74 - 4.32: 33889 4.32 - 4.90: 57340 Nonbonded interactions: 128138 Sorted by model distance: nonbonded pdb=" O PHE A 654 " pdb=" OG SER A 658 " model vdw 2.003 3.040 nonbonded pdb=" O PHE C 654 " pdb=" OG SER C 658 " model vdw 2.018 3.040 nonbonded pdb=" OG1 THR I 41 " pdb=" OG SER I 204 " model vdw 2.043 3.040 nonbonded pdb=" OG1 THR J 41 " pdb=" OG SER J 204 " model vdw 2.044 3.040 nonbonded pdb=" NH2 ARG B 715 " pdb=" O LYS B 770 " model vdw 2.064 3.120 ... (remaining 128133 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 393 through 398 or resid 400 through 403 or resid 405 thro \ ugh 406 or (resid 407 and (name N or name CA or name C or name O or name CB )) o \ r resid 412 through 414 or resid 416 through 422 or resid 424 through 431 or res \ id 433 or resid 436 or resid 438 or resid 440 through 441 or resid 443 through 4 \ 49 or (resid 450 and (name N or name CA or name C or name O or name CB )) or res \ id 452 through 453 or (resid 454 and (name N or name CA or name C or name O or n \ ame CB )) or resid 456 through 466 or resid 468 through 469 or resid 471 or resi \ d 473 through 546 or resid 567 through 581 or resid 583 through 635 or resid 637 \ through 646 or resid 649 through 663 or resid 665 through 670 or resid 672 thro \ ugh 682 or resid 684 through 685 or resid 688 through 692 or (resid 693 and (nam \ e N or name CA or name C or name O or name CB )) or resid 694 through 736 or res \ id 738 or resid 741 through 756 or (resid 757 and (name N or name CA or name C o \ r name O or name CB )) or resid 758 through 759 or resid 761 through 770 or (res \ id 772 through 773 and (name N or name CA or name C or name O or name CB )) or r \ esid 779 through 795 or resid 797 through 815 or resid 901 through 903)) selection = (chain 'B' and (resid 397 through 402 or resid 404 through 407 or resid 409 thro \ ugh 411 or resid 416 through 418 or resid 420 through 426 or resid 428 through 4 \ 35 or resid 437 or resid 440 or resid 442 or resid 444 through 445 or (resid 447 \ and (name N or name CA or name C or name O or name CB )) or resid 448 through 4 \ 54 or resid 456 through 458 or resid 460 through 470 or resid 472 through 473 or \ resid 475 or resid 477 through 508 or (resid 509 and (name N or name CA or name \ C or name O or name CB )) or resid 510 or (resid 511 and (name N or name CA or \ name C or name O or name CB )) or resid 512 through 585 or resid 587 through 637 \ or (resid 638 and (name N or name CA or name C or name O or name CB )) or resid \ 639 or resid 641 through 650 or resid 653 through 655 or (resid 656 and (name N \ or name CA or name C or name O or name CB )) or resid 657 through 660 or (resid \ 661 and (name N or name CA or name C or name O or name CB )) or resid 662 or (r \ esid 663 and (name N or name CA or name C or name O or name CB )) or resid 664 t \ hrough 667 or resid 669 or (resid 670 and (name N or name CA or name C or name O \ or name CB )) or resid 671 through 673 or (resid 674 and (name N or name CA or \ name C or name O or name CB )) or resid 676 through 686 or resid 688 through 689 \ or resid 692 through 698 or (resid 699 and (name N or name CA or name C or name \ O or name CB )) or resid 700 through 704 or (resid 705 and (name N or name CA o \ r name C or name O or name CB )) or resid 706 through 715 or (resid 716 and (nam \ e N or name CA or name C or name O or name CB )) or resid 717 through 740 or res \ id 742 or resid 745 through 763 or resid 765 through 774 or resid 776 through 77 \ 7 or resid 783 through 799 or resid 801 through 817 or (resid 818 through 819 an \ d (name N or name CA or name C or name O or name CB )) or resid 901 through 903) \ ) selection = (chain 'C' and (resid 393 through 398 or resid 400 through 403 or resid 405 thro \ ugh 406 or (resid 407 and (name N or name CA or name C or name O or name CB )) o \ r resid 412 through 414 or resid 416 through 422 or resid 424 through 431 or res \ id 433 or resid 436 or resid 438 or resid 440 through 441 or resid 443 through 4 \ 49 or (resid 450 and (name N or name CA or name C or name O or name CB )) or res \ id 452 through 453 or (resid 454 and (name N or name CA or name C or name O or n \ ame CB )) or resid 456 through 466 or resid 468 through 469 or resid 471 or resi \ d 473 through 546 or resid 567 through 581 or resid 583 through 635 or resid 637 \ through 646 or resid 649 through 663 or resid 665 through 670 or resid 672 thro \ ugh 682 or resid 684 through 685 or resid 688 through 692 or (resid 693 and (nam \ e N or name CA or name C or name O or name CB )) or resid 694 through 736 or res \ id 738 or resid 741 through 756 or (resid 757 and (name N or name CA or name C o \ r name O or name CB )) or resid 758 through 759 or resid 761 through 770 or (res \ id 772 through 773 and (name N or name CA or name C or name O or name CB )) or r \ esid 779 through 795 or resid 797 through 815 or resid 901 through 903)) selection = (chain 'D' and (resid 397 through 402 or resid 404 through 407 or resid 409 thro \ ugh 411 or resid 416 through 418 or resid 420 through 426 or resid 428 through 4 \ 35 or resid 437 or resid 440 or resid 442 or resid 444 through 445 or (resid 447 \ and (name N or name CA or name C or name O or name CB )) or resid 448 through 4 \ 54 or resid 456 through 458 or resid 460 through 470 or resid 472 through 473 or \ resid 475 or resid 477 through 508 or (resid 509 and (name N or name CA or name \ C or name O or name CB )) or resid 510 or (resid 511 and (name N or name CA or \ name C or name O or name CB )) or resid 512 through 585 or resid 587 through 637 \ or (resid 638 and (name N or name CA or name C or name O or name CB )) or resid \ 639 or resid 641 through 650 or resid 653 through 655 or (resid 656 and (name N \ or name CA or name C or name O or name CB )) or resid 657 through 660 or (resid \ 661 and (name N or name CA or name C or name O or name CB )) or resid 662 or (r \ esid 663 and (name N or name CA or name C or name O or name CB )) or resid 664 t \ hrough 667 or resid 669 or (resid 670 and (name N or name CA or name C or name O \ or name CB )) or resid 671 through 673 or (resid 674 and (name N or name CA or \ name C or name O or name CB )) or resid 676 through 686 or resid 688 through 689 \ or resid 692 through 698 or (resid 699 and (name N or name CA or name C or name \ O or name CB )) or resid 700 through 704 or (resid 705 and (name N or name CA o \ r name C or name O or name CB )) or resid 706 through 715 or (resid 716 and (nam \ e N or name CA or name C or name O or name CB )) or resid 717 through 740 or res \ id 742 or resid 745 through 763 or resid 765 through 774 or resid 776 through 77 \ 7 or resid 783 through 799 or resid 801 through 817 or (resid 818 through 819 an \ d (name N or name CA or name C or name O or name CB )) or resid 901 through 903) \ ) } ncs_group { reference = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.710 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 38.510 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.280 16066 Z= 0.740 Angle : 1.214 26.695 21662 Z= 0.478 Chirality : 0.048 0.297 2404 Planarity : 0.004 0.104 2632 Dihedral : 16.279 163.853 5892 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 0.76 (0.19), residues: 1966 helix: 1.88 (0.16), residues: 1056 sheet: -1.72 (0.37), residues: 178 loop : -0.95 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 667 HIS 0.008 0.002 HIS I 83 PHE 0.016 0.002 PHE I 205 TYR 0.015 0.002 TYR D 647 ARG 0.016 0.001 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 1.836 Fit side-chains REVERT: B 634 GLU cc_start: 0.7131 (pt0) cc_final: 0.6918 (pp20) REVERT: B 674 MET cc_start: 0.6113 (mtp) cc_final: 0.5896 (mtp) REVERT: A 389 ARG cc_start: 0.7045 (ptt90) cc_final: 0.6736 (ptt90) REVERT: A 436 TYR cc_start: 0.8197 (p90) cc_final: 0.7948 (p90) REVERT: A 459 MET cc_start: 0.7558 (mtm) cc_final: 0.7335 (mtm) REVERT: A 803 MET cc_start: 0.7859 (mtm) cc_final: 0.7647 (mtm) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 1.5552 time to fit residues: 389.4052 Evaluate side-chains 167 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 1.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 0.7980 chunk 148 optimal weight: 0.6980 chunk 82 optimal weight: 0.1980 chunk 50 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 153 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 93 optimal weight: 0.3980 chunk 114 optimal weight: 0.5980 chunk 177 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 435 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16066 Z= 0.168 Angle : 0.515 6.074 21662 Z= 0.267 Chirality : 0.039 0.132 2404 Planarity : 0.004 0.044 2632 Dihedral : 14.067 163.281 2708 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.05 % Allowed : 7.76 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 1.39 (0.20), residues: 1966 helix: 2.39 (0.16), residues: 1096 sheet: -1.88 (0.36), residues: 186 loop : -0.69 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 762 HIS 0.007 0.002 HIS J 83 PHE 0.012 0.001 PHE A 580 TYR 0.018 0.001 TYR A 434 ARG 0.005 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 189 time to evaluate : 1.733 Fit side-chains REVERT: B 674 MET cc_start: 0.6042 (mtp) cc_final: 0.5778 (mtm) REVERT: D 449 LYS cc_start: 0.5301 (ptmt) cc_final: 0.4855 (pttt) REVERT: D 721 MET cc_start: 0.8727 (ptp) cc_final: 0.8486 (ptp) REVERT: C 492 MET cc_start: 0.9232 (ttm) cc_final: 0.8898 (ttm) REVERT: A 389 ARG cc_start: 0.7238 (ptt90) cc_final: 0.6986 (ptt90) REVERT: A 459 MET cc_start: 0.7641 (mtm) cc_final: 0.7274 (mtm) REVERT: A 752 GLN cc_start: 0.7166 (mt0) cc_final: 0.6946 (mt0) outliers start: 16 outliers final: 5 residues processed: 198 average time/residue: 1.3144 time to fit residues: 288.9712 Evaluate side-chains 166 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 161 time to evaluate : 1.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 662 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 121 optimal weight: 0.1980 chunk 49 optimal weight: 0.6980 chunk 178 optimal weight: 0.5980 chunk 192 optimal weight: 0.0670 chunk 158 optimal weight: 5.9990 chunk 176 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 overall best weight: 0.5120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16066 Z= 0.159 Angle : 0.477 6.070 21662 Z= 0.248 Chirality : 0.038 0.159 2404 Planarity : 0.004 0.037 2632 Dihedral : 12.878 156.271 2708 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.58 % Allowed : 9.67 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 1.51 (0.20), residues: 1966 helix: 2.50 (0.16), residues: 1096 sheet: -1.45 (0.37), residues: 168 loop : -0.83 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 578 HIS 0.005 0.001 HIS I 83 PHE 0.010 0.001 PHE A 580 TYR 0.027 0.001 TYR A 434 ARG 0.004 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 184 time to evaluate : 1.762 Fit side-chains REVERT: B 629 MET cc_start: 0.7312 (mpp) cc_final: 0.6983 (mtt) REVERT: B 674 MET cc_start: 0.6211 (mtp) cc_final: 0.5988 (mtm) REVERT: D 449 LYS cc_start: 0.4891 (ptmt) cc_final: 0.4564 (pttt) REVERT: D 549 TYR cc_start: 0.7306 (t80) cc_final: 0.6978 (t80) REVERT: D 762 LEU cc_start: 0.7862 (mt) cc_final: 0.7659 (mp) REVERT: C 438 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8373 (tp) REVERT: C 459 MET cc_start: 0.7728 (mtm) cc_final: 0.7375 (mtm) REVERT: C 492 MET cc_start: 0.9247 (ttm) cc_final: 0.8941 (ttm) REVERT: C 748 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7580 (ttpp) REVERT: A 389 ARG cc_start: 0.7171 (ptt90) cc_final: 0.6932 (ptt90) outliers start: 24 outliers final: 9 residues processed: 196 average time/residue: 1.3329 time to fit residues: 289.1050 Evaluate side-chains 173 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 162 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain D residue 594 ARG Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 748 LYS Chi-restraints excluded: chain A residue 662 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 0.9980 chunk 134 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 119 optimal weight: 5.9990 chunk 178 optimal weight: 3.9990 chunk 189 optimal weight: 0.0670 chunk 93 optimal weight: 0.8980 chunk 169 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 752 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16066 Z= 0.179 Angle : 0.486 6.201 21662 Z= 0.253 Chirality : 0.039 0.136 2404 Planarity : 0.004 0.038 2632 Dihedral : 12.245 141.771 2708 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.91 % Allowed : 11.64 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 1.47 (0.19), residues: 1966 helix: 2.44 (0.16), residues: 1094 sheet: -1.34 (0.39), residues: 154 loop : -0.83 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 766 HIS 0.004 0.001 HIS I 83 PHE 0.011 0.001 PHE A 810 TYR 0.011 0.001 TYR I 206 ARG 0.003 0.000 ARG A 656 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 182 time to evaluate : 1.864 Fit side-chains REVERT: B 586 ARG cc_start: 0.7264 (OUTLIER) cc_final: 0.6462 (mmp-170) REVERT: B 629 MET cc_start: 0.7245 (mpp) cc_final: 0.6867 (mtt) REVERT: B 661 ARG cc_start: 0.7628 (mtm180) cc_final: 0.7306 (ptt90) REVERT: D 449 LYS cc_start: 0.5299 (ptmt) cc_final: 0.4745 (pttt) REVERT: C 438 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8336 (tp) REVERT: C 748 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7651 (ttpp) REVERT: A 389 ARG cc_start: 0.7190 (ptt90) cc_final: 0.6747 (ptt90) REVERT: A 656 ARG cc_start: 0.7010 (OUTLIER) cc_final: 0.6572 (mtm-85) outliers start: 29 outliers final: 10 residues processed: 200 average time/residue: 1.2468 time to fit residues: 277.5901 Evaluate side-chains 177 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 163 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 586 ARG Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 594 ARG Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 748 LYS Chi-restraints excluded: chain A residue 656 ARG Chi-restraints excluded: chain A residue 662 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 2.9990 chunk 107 optimal weight: 0.4980 chunk 2 optimal weight: 8.9990 chunk 141 optimal weight: 6.9990 chunk 78 optimal weight: 8.9990 chunk 161 optimal weight: 0.9990 chunk 130 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 47 optimal weight: 0.0050 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 752 GLN A 752 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16066 Z= 0.206 Angle : 0.498 6.655 21662 Z= 0.259 Chirality : 0.039 0.133 2404 Planarity : 0.004 0.039 2632 Dihedral : 12.024 122.564 2708 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.97 % Allowed : 13.42 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 1.40 (0.19), residues: 1966 helix: 2.38 (0.16), residues: 1094 sheet: -1.24 (0.41), residues: 130 loop : -0.92 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 667 HIS 0.004 0.001 HIS J 83 PHE 0.012 0.001 PHE I 130 TYR 0.022 0.001 TYR A 434 ARG 0.003 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 186 time to evaluate : 1.826 Fit side-chains REVERT: B 586 ARG cc_start: 0.7284 (OUTLIER) cc_final: 0.6479 (mmp-170) REVERT: B 629 MET cc_start: 0.7221 (mpp) cc_final: 0.6852 (mtt) REVERT: B 661 ARG cc_start: 0.7754 (mtm180) cc_final: 0.7450 (ptt90) REVERT: B 674 MET cc_start: 0.6986 (mtp) cc_final: 0.6714 (mtm) REVERT: I 48 ARG cc_start: 0.7533 (mtt-85) cc_final: 0.7238 (mtt90) REVERT: J 48 ARG cc_start: 0.7560 (mtt-85) cc_final: 0.7264 (mtt90) REVERT: D 449 LYS cc_start: 0.5444 (ptmt) cc_final: 0.4908 (pttt) REVERT: D 629 MET cc_start: 0.7507 (mpp) cc_final: 0.7131 (mtt) REVERT: D 747 ASN cc_start: 0.8271 (t0) cc_final: 0.7814 (t0) REVERT: D 762 LEU cc_start: 0.7862 (mt) cc_final: 0.7508 (mt) REVERT: C 438 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8364 (tp) REVERT: C 748 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7626 (ttpp) REVERT: A 717 MET cc_start: 0.7612 (ptm) cc_final: 0.7361 (ptm) outliers start: 30 outliers final: 14 residues processed: 205 average time/residue: 1.2905 time to fit residues: 293.8976 Evaluate side-chains 190 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 173 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain B residue 586 ARG Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 594 ARG Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 748 LYS Chi-restraints excluded: chain A residue 662 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 0.5980 chunk 170 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 189 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 435 HIS C 752 GLN A 752 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16066 Z= 0.319 Angle : 0.570 7.835 21662 Z= 0.297 Chirality : 0.042 0.176 2404 Planarity : 0.004 0.043 2632 Dihedral : 12.648 109.587 2708 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.11 % Allowed : 14.01 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 1.01 (0.19), residues: 1966 helix: 2.03 (0.16), residues: 1090 sheet: -1.59 (0.35), residues: 186 loop : -0.90 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 667 HIS 0.004 0.001 HIS I 198 PHE 0.019 0.002 PHE I 130 TYR 0.019 0.002 TYR A 434 ARG 0.005 0.001 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 170 time to evaluate : 1.519 Fit side-chains REVERT: B 586 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.6445 (mmp-170) REVERT: B 629 MET cc_start: 0.7185 (mpp) cc_final: 0.6861 (mtt) REVERT: B 674 MET cc_start: 0.6879 (mtp) cc_final: 0.6655 (mtm) REVERT: B 695 LYS cc_start: 0.6413 (mtmm) cc_final: 0.6055 (pttt) REVERT: D 449 LYS cc_start: 0.5468 (ptmt) cc_final: 0.5108 (pttt) REVERT: D 747 ASN cc_start: 0.8325 (t0) cc_final: 0.7888 (t0) REVERT: C 438 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8409 (tp) REVERT: C 748 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7690 (ttpp) outliers start: 32 outliers final: 14 residues processed: 195 average time/residue: 1.2680 time to fit residues: 274.5692 Evaluate side-chains 178 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain B residue 586 ARG Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 594 ARG Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 748 LYS Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 682 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 138 optimal weight: 0.4980 chunk 107 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 188 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 752 GLN A 752 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16066 Z= 0.233 Angle : 0.517 7.141 21662 Z= 0.269 Chirality : 0.040 0.131 2404 Planarity : 0.004 0.042 2632 Dihedral : 11.883 102.998 2708 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.91 % Allowed : 14.80 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 1.15 (0.19), residues: 1966 helix: 2.14 (0.16), residues: 1092 sheet: -1.51 (0.36), residues: 182 loop : -0.83 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 766 HIS 0.004 0.001 HIS I 198 PHE 0.012 0.001 PHE J 130 TYR 0.018 0.001 TYR A 434 ARG 0.005 0.000 ARG A 467 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 1.878 Fit side-chains REVERT: B 586 ARG cc_start: 0.7276 (OUTLIER) cc_final: 0.6395 (mmp-170) REVERT: B 629 MET cc_start: 0.7165 (mpp) cc_final: 0.6692 (mtt) REVERT: B 674 MET cc_start: 0.6871 (mtp) cc_final: 0.6647 (mtm) REVERT: B 695 LYS cc_start: 0.6427 (mtmm) cc_final: 0.6069 (pttt) REVERT: I 48 ARG cc_start: 0.7515 (mtt-85) cc_final: 0.7298 (mtt90) REVERT: J 48 ARG cc_start: 0.7581 (mtt-85) cc_final: 0.7332 (mtt90) REVERT: D 449 LYS cc_start: 0.5377 (ptmt) cc_final: 0.5010 (pttt) REVERT: C 438 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8303 (tp) REVERT: A 717 MET cc_start: 0.7565 (ptm) cc_final: 0.7111 (ptp) outliers start: 29 outliers final: 14 residues processed: 199 average time/residue: 1.2339 time to fit residues: 273.5829 Evaluate side-chains 184 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 168 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain B residue 586 ARG Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 594 ARG Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 499 MET Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 662 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 112 optimal weight: 20.0000 chunk 56 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 36 optimal weight: 20.0000 chunk 120 optimal weight: 0.9980 chunk 128 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 148 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 752 GLN A 752 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16066 Z= 0.252 Angle : 0.532 8.152 21662 Z= 0.276 Chirality : 0.040 0.144 2404 Planarity : 0.004 0.042 2632 Dihedral : 11.738 100.776 2708 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.84 % Allowed : 15.33 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 1.10 (0.19), residues: 1966 helix: 2.10 (0.16), residues: 1090 sheet: -1.49 (0.36), residues: 182 loop : -0.86 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 766 HIS 0.004 0.001 HIS I 198 PHE 0.013 0.002 PHE I 130 TYR 0.017 0.002 TYR A 434 ARG 0.006 0.000 ARG A 467 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 173 time to evaluate : 1.852 Fit side-chains REVERT: B 586 ARG cc_start: 0.7287 (OUTLIER) cc_final: 0.6407 (mmp-170) REVERT: B 629 MET cc_start: 0.7093 (mpp) cc_final: 0.6592 (mtt) REVERT: B 674 MET cc_start: 0.6880 (mtp) cc_final: 0.6653 (mtm) REVERT: B 695 LYS cc_start: 0.6638 (mtmm) cc_final: 0.6247 (pttt) REVERT: I 48 ARG cc_start: 0.7512 (mtt-85) cc_final: 0.7273 (mtt90) REVERT: J 48 ARG cc_start: 0.7593 (mtt-85) cc_final: 0.7350 (mtt90) REVERT: D 449 LYS cc_start: 0.5785 (ptmt) cc_final: 0.5145 (pttt) REVERT: D 629 MET cc_start: 0.7426 (mpp) cc_final: 0.7149 (mtp) REVERT: D 721 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8424 (ptp) REVERT: D 747 ASN cc_start: 0.8274 (t0) cc_final: 0.7852 (t0) REVERT: D 762 LEU cc_start: 0.7847 (mt) cc_final: 0.7527 (mt) REVERT: C 438 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8317 (tp) REVERT: C 748 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7614 (ttpp) outliers start: 28 outliers final: 16 residues processed: 194 average time/residue: 1.2616 time to fit residues: 274.1159 Evaluate side-chains 189 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 169 time to evaluate : 2.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain B residue 586 ARG Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 594 ARG Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 748 LYS Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 682 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 2.9990 chunk 180 optimal weight: 4.9990 chunk 165 optimal weight: 0.9990 chunk 176 optimal weight: 0.5980 chunk 105 optimal weight: 0.7980 chunk 76 optimal weight: 10.0000 chunk 138 optimal weight: 0.4980 chunk 54 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 175 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 752 GLN A 752 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16066 Z= 0.185 Angle : 0.489 7.547 21662 Z= 0.254 Chirality : 0.039 0.129 2404 Planarity : 0.004 0.041 2632 Dihedral : 11.013 96.668 2708 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.64 % Allowed : 15.59 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 1.31 (0.19), residues: 1966 helix: 2.30 (0.16), residues: 1094 sheet: -1.41 (0.36), residues: 182 loop : -0.84 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 766 HIS 0.004 0.001 HIS I 83 PHE 0.012 0.001 PHE A 810 TYR 0.017 0.001 TYR A 434 ARG 0.005 0.000 ARG A 467 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 168 time to evaluate : 1.930 Fit side-chains REVERT: B 586 ARG cc_start: 0.7279 (OUTLIER) cc_final: 0.6401 (mmp-170) REVERT: B 629 MET cc_start: 0.7144 (mpp) cc_final: 0.6761 (mtt) REVERT: B 674 MET cc_start: 0.6944 (mtp) cc_final: 0.6688 (mtm) REVERT: B 695 LYS cc_start: 0.6662 (mtmm) cc_final: 0.6289 (pttt) REVERT: I 48 ARG cc_start: 0.7505 (mtt-85) cc_final: 0.7233 (mtt90) REVERT: J 48 ARG cc_start: 0.7520 (mtt-85) cc_final: 0.7258 (mtt90) REVERT: D 449 LYS cc_start: 0.5489 (ptmt) cc_final: 0.4853 (pttt) REVERT: D 629 MET cc_start: 0.7392 (mpp) cc_final: 0.7130 (mtp) REVERT: C 438 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8314 (tp) REVERT: C 748 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7589 (ttpp) outliers start: 25 outliers final: 16 residues processed: 189 average time/residue: 1.2749 time to fit residues: 268.1986 Evaluate side-chains 185 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain B residue 586 ARG Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 594 ARG Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 748 LYS Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 682 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 2.9990 chunk 186 optimal weight: 0.4980 chunk 113 optimal weight: 2.9990 chunk 88 optimal weight: 0.4980 chunk 129 optimal weight: 0.8980 chunk 195 optimal weight: 2.9990 chunk 179 optimal weight: 4.9990 chunk 155 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 752 GLN A 752 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16066 Z= 0.197 Angle : 0.504 9.791 21662 Z= 0.260 Chirality : 0.039 0.136 2404 Planarity : 0.004 0.041 2632 Dihedral : 10.923 95.590 2708 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.58 % Allowed : 16.12 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 1.29 (0.19), residues: 1966 helix: 2.28 (0.16), residues: 1094 sheet: -1.41 (0.36), residues: 182 loop : -0.86 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 766 HIS 0.004 0.001 HIS I 83 PHE 0.013 0.001 PHE A 810 TYR 0.017 0.001 TYR A 434 ARG 0.003 0.000 ARG A 467 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 1.959 Fit side-chains REVERT: B 586 ARG cc_start: 0.7266 (OUTLIER) cc_final: 0.6386 (mmp-170) REVERT: B 629 MET cc_start: 0.7133 (mpp) cc_final: 0.6754 (mtt) REVERT: B 674 MET cc_start: 0.6734 (mtp) cc_final: 0.6426 (mtm) REVERT: B 695 LYS cc_start: 0.6695 (mtmm) cc_final: 0.6454 (pttt) REVERT: I 48 ARG cc_start: 0.7506 (mtt-85) cc_final: 0.7225 (mtt90) REVERT: J 48 ARG cc_start: 0.7502 (mtt-85) cc_final: 0.7227 (mtt90) REVERT: D 449 LYS cc_start: 0.5316 (ptmt) cc_final: 0.4900 (pttt) REVERT: D 629 MET cc_start: 0.7397 (mpp) cc_final: 0.7039 (mtt) REVERT: C 438 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8311 (tp) REVERT: C 748 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7577 (ttpp) REVERT: A 717 MET cc_start: 0.7533 (ptm) cc_final: 0.7300 (ptp) outliers start: 24 outliers final: 19 residues processed: 186 average time/residue: 1.2566 time to fit residues: 260.2539 Evaluate side-chains 184 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 1.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 586 ARG Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 594 ARG Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 748 LYS Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 499 MET Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 682 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 47 optimal weight: 20.0000 chunk 143 optimal weight: 0.0020 chunk 22 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 159 optimal weight: 0.6980 chunk 19 optimal weight: 0.4980 chunk 28 optimal weight: 4.9990 overall best weight: 1.2392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 752 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.173243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.112625 restraints weight = 16766.242| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.05 r_work: 0.2933 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16066 Z= 0.272 Angle : 0.543 7.984 21662 Z= 0.282 Chirality : 0.041 0.149 2404 Planarity : 0.004 0.042 2632 Dihedral : 11.497 101.416 2708 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.78 % Allowed : 16.18 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 1.09 (0.19), residues: 1966 helix: 2.11 (0.16), residues: 1090 sheet: -1.46 (0.36), residues: 182 loop : -0.91 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 766 HIS 0.004 0.001 HIS J 198 PHE 0.016 0.002 PHE I 130 TYR 0.020 0.002 TYR A 434 ARG 0.009 0.000 ARG A 467 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5205.12 seconds wall clock time: 94 minutes 13.75 seconds (5653.75 seconds total)