Starting phenix.real_space_refine on Sun May 18 00:26:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ayn_15717/05_2025/8ayn_15717.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ayn_15717/05_2025/8ayn_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_15717/05_2025/8ayn_15717.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ayn_15717/05_2025/8ayn_15717.map" model { file = "/net/cci-nas-00/data/ceres_data/8ayn_15717/05_2025/8ayn_15717.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ayn_15717/05_2025/8ayn_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-5687/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: 9.51, per 1000 atoms: 0.60 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: 4.25 Conformation dependent library (CDL) restraints added in 2.0 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: 1.52 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: 4.25 Time building geometry restraints manager: 4.81 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: 0.05 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: 1.820 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: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 34.720 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.760 ------------------------------------------------------------------------------- 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 16074 Z= 0.517 Angle : 1.214 26.695 21678 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 Details of bonding type rmsd hydrogen bonds : bond 0.11437 ( 879) hydrogen bonds : angle 4.92758 ( 2577) SS BOND : bond 0.00290 ( 8) SS BOND : angle 2.04939 ( 16) covalent geometry : bond 0.01172 (16066) covalent geometry : angle 1.21351 (21662) *********************** 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 : 1.846 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: 1.4810 time to fit residues: 372.0314 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 : 1.766 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.179216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.119690 restraints weight = 16244.243| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.95 r_work: 0.3000 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 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 16074 Z= 0.118 Angle : 0.515 6.074 21678 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 Details of bonding type rmsd hydrogen bonds : bond 0.04027 ( 879) hydrogen bonds : angle 3.78606 ( 2577) SS BOND : bond 0.00243 ( 8) SS BOND : angle 0.79679 ( 16) covalent geometry : bond 0.00254 (16066) covalent geometry : angle 0.51471 (21662) *********************** 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 : 1.626 Fit side-chains REVERT: B 591 ILE cc_start: 0.8654 (pt) cc_final: 0.8386 (pp) REVERT: B 634 GLU cc_start: 0.7525 (pt0) cc_final: 0.7258 (pt0) REVERT: B 640 SER cc_start: 0.7838 (t) cc_final: 0.7629 (m) REVERT: D 400 ILE cc_start: 0.7138 (OUTLIER) cc_final: 0.6870 (tt) REVERT: D 449 LYS cc_start: 0.5058 (ptmt) cc_final: 0.4500 (pttt) REVERT: D 721 MET cc_start: 0.8546 (ptp) cc_final: 0.8241 (ptp) REVERT: D 765 LYS cc_start: 0.6726 (tmtt) cc_final: 0.6487 (tmmm) REVERT: C 492 MET cc_start: 0.9447 (ttm) cc_final: 0.9107 (ttm) REVERT: A 389 ARG cc_start: 0.7239 (ptt90) cc_final: 0.6995 (ptt90) REVERT: A 459 MET cc_start: 0.7057 (mtm) cc_final: 0.6679 (mtm) REVERT: A 590 ARG cc_start: 0.8379 (mtp-110) cc_final: 0.8177 (mtp180) REVERT: A 630 GLU cc_start: 0.7061 (tm-30) cc_final: 0.6802 (tp30) REVERT: A 717 MET cc_start: 0.7196 (ttp) cc_final: 0.6849 (ptm) REVERT: A 752 GLN cc_start: 0.7029 (mt0) cc_final: 0.6777 (mt0) outliers start: 16 outliers final: 5 residues processed: 198 average time/residue: 1.1860 time to fit residues: 260.8576 Evaluate side-chains 170 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 164 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain D residue 400 ILE 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 83 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 177 optimal weight: 0.9980 chunk 145 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 137 optimal weight: 0.6980 chunk 113 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 435 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.174571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.114370 restraints weight = 16371.730| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.14 r_work: 0.2884 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16074 Z= 0.159 Angle : 0.535 7.459 21678 Z= 0.279 Chirality : 0.040 0.159 2404 Planarity : 0.004 0.041 2632 Dihedral : 13.725 165.462 2708 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % 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: 1.21 (0.19), residues: 1966 helix: 2.19 (0.16), residues: 1096 sheet: -1.64 (0.36), residues: 180 loop : -0.77 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 574 HIS 0.005 0.001 HIS J 83 PHE 0.014 0.002 PHE I 130 TYR 0.024 0.002 TYR A 434 ARG 0.004 0.000 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.04750 ( 879) hydrogen bonds : angle 3.90821 ( 2577) SS BOND : bond 0.00323 ( 8) SS BOND : angle 0.81704 ( 16) covalent geometry : bond 0.00379 (16066) covalent geometry : angle 0.53438 (21662) *********************** 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 212 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 188 time to evaluate : 1.712 Fit side-chains REVERT: B 591 ILE cc_start: 0.8619 (pt) cc_final: 0.8385 (pp) REVERT: B 629 MET cc_start: 0.7616 (mpp) cc_final: 0.7330 (mtt) REVERT: B 634 GLU cc_start: 0.7632 (pt0) cc_final: 0.6856 (pp20) REVERT: D 449 LYS cc_start: 0.5082 (ptmt) cc_final: 0.4582 (pttt) REVERT: D 591 ILE cc_start: 0.8627 (pt) cc_final: 0.8383 (pp) REVERT: C 438 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8317 (tp) REVERT: A 389 ARG cc_start: 0.7101 (ptt90) cc_final: 0.6861 (ptt90) REVERT: A 630 GLU cc_start: 0.7517 (tm-30) cc_final: 0.7265 (tm-30) REVERT: A 656 ARG cc_start: 0.6692 (OUTLIER) cc_final: 0.6205 (mtm-85) outliers start: 24 outliers final: 15 residues processed: 203 average time/residue: 1.2668 time to fit residues: 285.7609 Evaluate side-chains 185 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 168 time to evaluate : 1.705 ------------------------------------------------------------------------------- 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 721 MET Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain D residue 400 ILE 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 682 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 656 ARG Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 682 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 31 optimal weight: 3.9990 chunk 160 optimal weight: 0.0670 chunk 182 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 30 optimal weight: 0.4980 chunk 64 optimal weight: 0.3980 chunk 14 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 87 optimal weight: 0.0070 chunk 142 optimal weight: 5.9990 overall best weight: 0.7938 ------------------------------------------------------------------------------- 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 = 0.3956 r_free = 0.3956 target = 0.174992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.105774 restraints weight = 16468.357| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.02 r_work: 0.2936 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16074 Z= 0.129 Angle : 0.493 6.436 21678 Z= 0.258 Chirality : 0.039 0.139 2404 Planarity : 0.004 0.041 2632 Dihedral : 13.215 173.608 2708 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.58 % Allowed : 11.97 % 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: 1.30 (0.19), residues: 1966 helix: 2.28 (0.16), residues: 1094 sheet: -1.54 (0.38), residues: 156 loop : -0.84 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 574 HIS 0.005 0.001 HIS I 83 PHE 0.011 0.001 PHE I 130 TYR 0.018 0.001 TYR A 434 ARG 0.006 0.000 ARG A 467 Details of bonding type rmsd hydrogen bonds : bond 0.04269 ( 879) hydrogen bonds : angle 3.74253 ( 2577) SS BOND : bond 0.00263 ( 8) SS BOND : angle 0.59928 ( 16) covalent geometry : bond 0.00298 (16066) covalent geometry : angle 0.49309 (21662) *********************** 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 213 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 189 time to evaluate : 2.029 Fit side-chains REVERT: B 586 ARG cc_start: 0.7722 (mmm160) cc_final: 0.6948 (mtp180) REVERT: B 629 MET cc_start: 0.7633 (mpp) cc_final: 0.7339 (mtt) REVERT: B 634 GLU cc_start: 0.7740 (pt0) cc_final: 0.7046 (pp20) REVERT: B 661 ARG cc_start: 0.7720 (mtm180) cc_final: 0.7349 (ptt90) REVERT: D 400 ILE cc_start: 0.7122 (mm) cc_final: 0.6852 (mt) REVERT: D 449 LYS cc_start: 0.5204 (ptmt) cc_final: 0.4698 (pttt) REVERT: D 683 VAL cc_start: 0.6890 (m) cc_final: 0.6626 (t) REVERT: D 768 TYR cc_start: 0.6341 (m-10) cc_final: 0.6108 (m-10) REVERT: C 438 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8340 (tp) REVERT: C 748 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7446 (ttpp) REVERT: A 467 ARG cc_start: 0.6991 (mtm-85) cc_final: 0.6735 (mtm-85) REVERT: A 501 LYS cc_start: 0.6831 (tptt) cc_final: 0.6576 (tptt) outliers start: 24 outliers final: 12 residues processed: 204 average time/residue: 1.1540 time to fit residues: 262.6205 Evaluate side-chains 182 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 168 time to evaluate : 1.597 ------------------------------------------------------------------------------- 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 721 MET 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 168 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 167 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 173 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.172299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.112523 restraints weight = 16683.340| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.10 r_work: 0.2900 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16074 Z= 0.206 Angle : 0.580 8.328 21678 Z= 0.302 Chirality : 0.042 0.194 2404 Planarity : 0.004 0.045 2632 Dihedral : 13.798 169.178 2708 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.17 % Allowed : 13.55 % Favored : 84.28 % 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: 0.90 (0.19), residues: 1966 helix: 1.93 (0.16), residues: 1090 sheet: -1.68 (0.35), residues: 180 loop : -0.91 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 574 HIS 0.005 0.001 HIS J 198 PHE 0.018 0.002 PHE J 130 TYR 0.019 0.002 TYR A 434 ARG 0.006 0.001 ARG A 467 Details of bonding type rmsd hydrogen bonds : bond 0.05278 ( 879) hydrogen bonds : angle 3.99488 ( 2577) SS BOND : bond 0.00492 ( 8) SS BOND : angle 1.05520 ( 16) covalent geometry : bond 0.00504 (16066) covalent geometry : angle 0.57909 (21662) *********************** 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 212 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 179 time to evaluate : 1.613 Fit side-chains REVERT: B 629 MET cc_start: 0.7509 (mpp) cc_final: 0.7263 (mtt) REVERT: B 634 GLU cc_start: 0.7872 (pt0) cc_final: 0.7041 (pp20) REVERT: D 449 LYS cc_start: 0.5037 (ptmt) cc_final: 0.4542 (pttt) REVERT: D 708 MET cc_start: 0.7516 (OUTLIER) cc_final: 0.7265 (tpt) REVERT: D 747 ASN cc_start: 0.7992 (t0) cc_final: 0.7519 (t0) REVERT: C 438 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8362 (tp) REVERT: C 748 LYS cc_start: 0.7683 (OUTLIER) cc_final: 0.7391 (ttpp) REVERT: A 467 ARG cc_start: 0.6793 (mtm-85) cc_final: 0.6570 (mtm-85) outliers start: 33 outliers final: 16 residues processed: 202 average time/residue: 1.1768 time to fit residues: 264.7496 Evaluate side-chains 183 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 1.630 ------------------------------------------------------------------------------- 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 721 MET Chi-restraints excluded: chain B residue 736 THR 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 683 VAL 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 682 THR Chi-restraints excluded: chain C residue 748 LYS Chi-restraints excluded: chain C residue 803 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 50 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 187 optimal weight: 0.9990 chunk 158 optimal weight: 0.4980 chunk 1 optimal weight: 8.9990 chunk 65 optimal weight: 7.9990 chunk 194 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 145 optimal weight: 0.6980 chunk 154 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.174881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.114735 restraints weight = 16687.763| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.03 r_work: 0.2944 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16074 Z= 0.124 Angle : 0.494 7.483 21678 Z= 0.258 Chirality : 0.039 0.130 2404 Planarity : 0.004 0.042 2632 Dihedral : 12.542 126.989 2708 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.11 % Allowed : 14.54 % Favored : 83.36 % 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: 1.17 (0.19), residues: 1966 helix: 2.19 (0.16), residues: 1094 sheet: -1.63 (0.35), residues: 180 loop : -0.87 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 667 HIS 0.004 0.001 HIS J 83 PHE 0.017 0.001 PHE D 682 TYR 0.018 0.001 TYR A 434 ARG 0.004 0.000 ARG A 467 Details of bonding type rmsd hydrogen bonds : bond 0.04219 ( 879) hydrogen bonds : angle 3.72337 ( 2577) SS BOND : bond 0.00308 ( 8) SS BOND : angle 0.66535 ( 16) covalent geometry : bond 0.00287 (16066) covalent geometry : angle 0.49406 (21662) *********************** 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 212 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 180 time to evaluate : 1.647 Fit side-chains REVERT: B 586 ARG cc_start: 0.7634 (mmm160) cc_final: 0.6791 (mtp180) REVERT: B 629 MET cc_start: 0.7577 (mpp) cc_final: 0.7334 (mtt) REVERT: B 634 GLU cc_start: 0.7876 (pt0) cc_final: 0.7077 (pp20) REVERT: B 661 ARG cc_start: 0.7610 (mtm180) cc_final: 0.7216 (mtm180) REVERT: B 695 LYS cc_start: 0.6301 (mtmm) cc_final: 0.5674 (pttt) REVERT: I 48 ARG cc_start: 0.7248 (mtt-85) cc_final: 0.6844 (mtt90) REVERT: J 48 ARG cc_start: 0.7267 (mtt-85) cc_final: 0.6855 (mtt90) REVERT: D 449 LYS cc_start: 0.5129 (ptmt) cc_final: 0.4676 (pttt) REVERT: D 545 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7528 (ttt-90) REVERT: D 683 VAL cc_start: 0.6710 (m) cc_final: 0.6445 (t) REVERT: D 708 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.7252 (tpt) REVERT: D 762 LEU cc_start: 0.7181 (mt) cc_final: 0.6871 (mt) REVERT: C 438 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8211 (tp) REVERT: C 748 LYS cc_start: 0.7597 (OUTLIER) cc_final: 0.7163 (ttpp) REVERT: A 467 ARG cc_start: 0.6777 (mtm-85) cc_final: 0.6510 (mtm-85) REVERT: A 769 CYS cc_start: 0.7342 (OUTLIER) cc_final: 0.6633 (m) outliers start: 32 outliers final: 14 residues processed: 204 average time/residue: 1.1285 time to fit residues: 256.6828 Evaluate side-chains 188 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 1.567 ------------------------------------------------------------------------------- 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 721 MET Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 545 ARG 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 484 VAL Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 769 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 91 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 142 optimal weight: 6.9990 chunk 162 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 149 optimal weight: 5.9990 chunk 171 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 105 optimal weight: 0.1980 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.172608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.112809 restraints weight = 16839.677| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.12 r_work: 0.2900 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16074 Z= 0.184 Angle : 0.557 8.263 21678 Z= 0.289 Chirality : 0.041 0.187 2404 Planarity : 0.004 0.044 2632 Dihedral : 12.422 109.575 2708 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.37 % Allowed : 14.41 % Favored : 83.22 % 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: 0.99 (0.19), residues: 1966 helix: 2.00 (0.16), residues: 1090 sheet: -1.58 (0.36), residues: 182 loop : -0.87 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 574 HIS 0.004 0.001 HIS I 198 PHE 0.016 0.002 PHE J 130 TYR 0.016 0.002 TYR D 405 ARG 0.005 0.000 ARG A 656 Details of bonding type rmsd hydrogen bonds : bond 0.04985 ( 879) hydrogen bonds : angle 3.90473 ( 2577) SS BOND : bond 0.00395 ( 8) SS BOND : angle 1.05379 ( 16) covalent geometry : bond 0.00449 (16066) covalent geometry : angle 0.55691 (21662) *********************** 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 209 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 173 time to evaluate : 1.727 Fit side-chains REVERT: B 586 ARG cc_start: 0.7680 (mmm160) cc_final: 0.6782 (mtp180) REVERT: B 629 MET cc_start: 0.7500 (OUTLIER) cc_final: 0.7252 (mtt) REVERT: B 634 GLU cc_start: 0.7839 (pt0) cc_final: 0.7041 (pp20) REVERT: B 695 LYS cc_start: 0.6338 (mtmm) cc_final: 0.5686 (pttt) REVERT: D 545 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7529 (ttt-90) REVERT: D 629 MET cc_start: 0.7791 (mpp) cc_final: 0.7474 (mtt) REVERT: D 708 MET cc_start: 0.7539 (OUTLIER) cc_final: 0.7315 (tpt) REVERT: D 747 ASN cc_start: 0.7952 (t0) cc_final: 0.7489 (t0) REVERT: C 748 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7253 (ttpp) REVERT: A 467 ARG cc_start: 0.6646 (mtm-85) cc_final: 0.6203 (ttm110) REVERT: A 769 CYS cc_start: 0.7253 (OUTLIER) cc_final: 0.6601 (m) outliers start: 36 outliers final: 15 residues processed: 201 average time/residue: 1.1161 time to fit residues: 251.4116 Evaluate side-chains 190 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 1.828 ------------------------------------------------------------------------------- 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 629 MET Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 545 ARG Chi-restraints excluded: chain D residue 594 ARG Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 708 MET 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 Chi-restraints excluded: chain A residue 769 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 155 optimal weight: 0.6980 chunk 144 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 chunk 156 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 chunk 166 optimal weight: 0.9990 chunk 162 optimal weight: 0.0040 chunk 121 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 overall best weight: 0.6796 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.175058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.115096 restraints weight = 16764.427| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.15 r_work: 0.2958 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16074 Z= 0.120 Angle : 0.497 8.992 21678 Z= 0.257 Chirality : 0.039 0.131 2404 Planarity : 0.004 0.042 2632 Dihedral : 11.482 104.045 2708 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.11 % Allowed : 14.93 % Favored : 82.96 % 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: 1.24 (0.19), residues: 1966 helix: 2.24 (0.16), residues: 1094 sheet: -1.51 (0.36), residues: 182 loop : -0.86 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 766 HIS 0.004 0.001 HIS I 83 PHE 0.012 0.001 PHE D 682 TYR 0.015 0.001 TYR D 405 ARG 0.005 0.000 ARG A 656 Details of bonding type rmsd hydrogen bonds : bond 0.04123 ( 879) hydrogen bonds : angle 3.68524 ( 2577) SS BOND : bond 0.00192 ( 8) SS BOND : angle 0.71729 ( 16) covalent geometry : bond 0.00275 (16066) covalent geometry : angle 0.49645 (21662) *********************** 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 212 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 180 time to evaluate : 1.779 Fit side-chains REVERT: B 586 ARG cc_start: 0.7608 (mmm160) cc_final: 0.6783 (mtp180) REVERT: B 629 MET cc_start: 0.7499 (mpp) cc_final: 0.7251 (mtt) REVERT: B 634 GLU cc_start: 0.7867 (pt0) cc_final: 0.7065 (pp20) REVERT: B 657 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7416 (mm-30) REVERT: B 695 LYS cc_start: 0.6373 (mtmm) cc_final: 0.5736 (pttt) REVERT: I 48 ARG cc_start: 0.7202 (mtt-85) cc_final: 0.6805 (mtt90) REVERT: J 48 ARG cc_start: 0.7182 (mtt-85) cc_final: 0.6784 (mtt90) REVERT: D 449 LYS cc_start: 0.4943 (ptmt) cc_final: 0.4548 (pttt) REVERT: D 509 LYS cc_start: 0.7280 (tptt) cc_final: 0.6749 (ttmm) REVERT: D 545 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7415 (ttt-90) REVERT: D 629 MET cc_start: 0.7767 (mpp) cc_final: 0.7465 (mtt) REVERT: D 683 VAL cc_start: 0.6687 (m) cc_final: 0.6383 (t) REVERT: D 708 MET cc_start: 0.7443 (OUTLIER) cc_final: 0.7134 (tpt) REVERT: C 748 LYS cc_start: 0.7551 (OUTLIER) cc_final: 0.7135 (ttpp) REVERT: C 769 CYS cc_start: 0.7216 (OUTLIER) cc_final: 0.6617 (m) REVERT: C 803 MET cc_start: 0.8190 (mtm) cc_final: 0.7954 (mmm) REVERT: A 467 ARG cc_start: 0.6741 (mtm-85) cc_final: 0.6251 (ttm110) REVERT: A 769 CYS cc_start: 0.7232 (OUTLIER) cc_final: 0.6605 (m) outliers start: 32 outliers final: 15 residues processed: 203 average time/residue: 1.2069 time to fit residues: 272.4259 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 : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 545 ARG Chi-restraints excluded: chain D residue 594 ARG Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 708 MET 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 C residue 769 CYS 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 Chi-restraints excluded: chain A residue 769 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 128 optimal weight: 1.9990 chunk 164 optimal weight: 0.7980 chunk 130 optimal weight: 0.6980 chunk 141 optimal weight: 3.9990 chunk 122 optimal weight: 0.0970 chunk 98 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 4 optimal weight: 0.1980 chunk 177 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.176237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.112245 restraints weight = 16766.197| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.37 r_work: 0.2907 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16074 Z= 0.110 Angle : 0.481 9.179 21678 Z= 0.249 Chirality : 0.038 0.135 2404 Planarity : 0.003 0.040 2632 Dihedral : 10.773 96.403 2708 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.78 % Allowed : 15.66 % Favored : 82.57 % 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 (0.19), residues: 1966 helix: 2.40 (0.16), residues: 1094 sheet: -1.21 (0.39), residues: 156 loop : -0.96 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 766 HIS 0.004 0.001 HIS I 83 PHE 0.012 0.001 PHE D 682 TYR 0.013 0.001 TYR D 405 ARG 0.004 0.000 ARG A 656 Details of bonding type rmsd hydrogen bonds : bond 0.03872 ( 879) hydrogen bonds : angle 3.58073 ( 2577) SS BOND : bond 0.00174 ( 8) SS BOND : angle 0.53621 ( 16) covalent geometry : bond 0.00247 (16066) covalent geometry : angle 0.48083 (21662) *********************** 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 210 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 183 time to evaluate : 1.690 Fit side-chains REVERT: B 509 LYS cc_start: 0.7590 (tptt) cc_final: 0.7061 (ttmm) REVERT: B 586 ARG cc_start: 0.7604 (mmm160) cc_final: 0.7057 (mtp180) REVERT: B 629 MET cc_start: 0.7467 (mpp) cc_final: 0.7139 (mtt) REVERT: B 634 GLU cc_start: 0.7806 (pt0) cc_final: 0.7168 (pp20) REVERT: B 695 LYS cc_start: 0.6481 (mtmm) cc_final: 0.5957 (pttt) REVERT: D 434 LYS cc_start: 0.6333 (tmtt) cc_final: 0.5879 (ttpp) REVERT: D 629 MET cc_start: 0.7923 (mpp) cc_final: 0.7687 (mtp) REVERT: D 683 VAL cc_start: 0.6799 (m) cc_final: 0.6541 (t) REVERT: D 708 MET cc_start: 0.7439 (OUTLIER) cc_final: 0.7141 (tpt) REVERT: C 748 LYS cc_start: 0.7764 (OUTLIER) cc_final: 0.7298 (ttpp) REVERT: C 769 CYS cc_start: 0.7075 (OUTLIER) cc_final: 0.6603 (m) REVERT: C 803 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.8171 (mmm) REVERT: A 467 ARG cc_start: 0.6827 (mtm-85) cc_final: 0.6288 (ttm110) REVERT: A 769 CYS cc_start: 0.7222 (OUTLIER) cc_final: 0.6658 (m) outliers start: 27 outliers final: 19 residues processed: 204 average time/residue: 1.1675 time to fit residues: 266.0779 Evaluate side-chains 194 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 543 VAL 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 445 VAL Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 594 ARG Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain C residue 470 VAL 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 748 LYS Chi-restraints excluded: chain C residue 769 CYS Chi-restraints excluded: chain C residue 803 MET 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 Chi-restraints excluded: chain A residue 769 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 2 optimal weight: 9.9990 chunk 167 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.172987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.113426 restraints weight = 16937.900| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.21 r_work: 0.2908 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16074 Z= 0.181 Angle : 0.562 9.426 21678 Z= 0.291 Chirality : 0.041 0.175 2404 Planarity : 0.004 0.043 2632 Dihedral : 11.615 103.175 2708 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.71 % Allowed : 16.51 % Favored : 81.78 % 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: 1.05 (0.19), residues: 1966 helix: 2.08 (0.16), residues: 1090 sheet: -1.53 (0.36), residues: 182 loop : -0.91 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 766 HIS 0.004 0.001 HIS J 198 PHE 0.015 0.002 PHE A 810 TYR 0.013 0.002 TYR B 405 ARG 0.004 0.000 ARG A 656 Details of bonding type rmsd hydrogen bonds : bond 0.04924 ( 879) hydrogen bonds : angle 3.85753 ( 2577) SS BOND : bond 0.00352 ( 8) SS BOND : angle 0.96923 ( 16) covalent geometry : bond 0.00440 (16066) covalent geometry : angle 0.56146 (21662) ********************** 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 200 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 174 time to evaluate : 1.955 Fit side-chains REVERT: B 509 LYS cc_start: 0.7495 (tptt) cc_final: 0.6965 (ttmm) REVERT: B 586 ARG cc_start: 0.7632 (mmm160) cc_final: 0.6803 (mtp180) REVERT: B 629 MET cc_start: 0.7473 (mpp) cc_final: 0.7164 (mtt) REVERT: B 634 GLU cc_start: 0.7850 (pt0) cc_final: 0.7041 (pp20) REVERT: B 695 LYS cc_start: 0.6574 (mtmm) cc_final: 0.6079 (pttt) REVERT: D 708 MET cc_start: 0.7536 (OUTLIER) cc_final: 0.7302 (tpt) REVERT: D 747 ASN cc_start: 0.7891 (t0) cc_final: 0.7419 (t0) REVERT: D 766 TRP cc_start: 0.6574 (m100) cc_final: 0.6339 (m100) REVERT: C 748 LYS cc_start: 0.7725 (OUTLIER) cc_final: 0.7443 (ttpp) REVERT: C 769 CYS cc_start: 0.7187 (OUTLIER) cc_final: 0.6576 (m) REVERT: A 467 ARG cc_start: 0.6713 (mtm-85) cc_final: 0.6265 (ttm110) REVERT: A 769 CYS cc_start: 0.7241 (OUTLIER) cc_final: 0.6568 (m) outliers start: 26 outliers final: 17 residues processed: 195 average time/residue: 1.2189 time to fit residues: 268.3892 Evaluate side-chains 188 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 167 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 736 THR 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 633 ILE Chi-restraints excluded: chain D residue 708 MET 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 748 LYS Chi-restraints excluded: chain C residue 769 CYS 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 Chi-restraints excluded: chain A residue 769 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 74 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 187 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.173288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.113814 restraints weight = 16814.825| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.18 r_work: 0.2915 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16074 Z= 0.172 Angle : 0.550 8.416 21678 Z= 0.286 Chirality : 0.041 0.156 2404 Planarity : 0.004 0.044 2632 Dihedral : 11.555 106.863 2708 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.78 % Allowed : 16.71 % Favored : 81.51 % 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: 2.04 (0.16), residues: 1090 sheet: -1.54 (0.36), residues: 182 loop : -0.92 (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 J 198 PHE 0.014 0.002 PHE A 810 TYR 0.014 0.002 TYR D 405 ARG 0.005 0.000 ARG A 656 Details of bonding type rmsd hydrogen bonds : bond 0.04756 ( 879) hydrogen bonds : angle 3.84531 ( 2577) SS BOND : bond 0.00310 ( 8) SS BOND : angle 0.85456 ( 16) covalent geometry : bond 0.00418 (16066) covalent geometry : angle 0.54933 (21662) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12686.50 seconds wall clock time: 218 minutes 16.83 seconds (13096.83 seconds total)