Starting phenix.real_space_refine on Fri Aug 1 00:08:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vov_43392/07_2025/8vov_43392.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vov_43392/07_2025/8vov_43392.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vov_43392/07_2025/8vov_43392.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vov_43392/07_2025/8vov_43392.map" model { file = "/net/cci-nas-00/data/ceres_data/8vov_43392/07_2025/8vov_43392.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vov_43392/07_2025/8vov_43392.cif" } resolution = 3.6 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 78 5.16 5 C 8826 2.51 5 N 2454 2.21 5 O 2628 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13998 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2281 Classifications: {'peptide': 289} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 272} Chain breaks: 2 Chain: "B" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2281 Classifications: {'peptide': 289} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 272} Chain breaks: 2 Chain: "C" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2281 Classifications: {'peptide': 289} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 272} Chain breaks: 2 Chain: "D" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2281 Classifications: {'peptide': 289} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 272} Chain breaks: 2 Chain: "E" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2281 Classifications: {'peptide': 289} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 272} Chain breaks: 2 Chain: "F" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2281 Classifications: {'peptide': 289} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 272} Chain breaks: 2 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {'A1AC1': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {'A1AC1': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {'A1AC1': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {'A1AC1': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {'A1AC1': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {'A1AC1': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.98, per 1000 atoms: 0.64 Number of scatterers: 13998 At special positions: 0 Unit cell: (156.285, 152.145, 63.135, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 78 16.00 P 12 15.00 O 2628 8.00 N 2454 7.00 C 8826 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 4.23 Conformation dependent library (CDL) restraints added in 2.0 seconds 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3216 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 6 sheets defined 59.9% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 482 through 499 removed outlier: 4.071A pdb=" N TYR A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.966A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 536 Processing helix chain 'A' and resid 543 through 553 removed outlier: 3.652A pdb=" N LEU A 547 " --> pdb=" O LYS A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 569 removed outlier: 4.189A pdb=" N GLU A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA A 569 " --> pdb=" O LYS A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 586 Processing helix chain 'A' and resid 600 through 610 Processing helix chain 'A' and resid 630 through 635 removed outlier: 3.556A pdb=" N ARG A 635 " --> pdb=" O ALA A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 661 Processing helix chain 'A' and resid 671 through 679 removed outlier: 3.607A pdb=" N THR A 679 " --> pdb=" O LEU A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 709 Processing helix chain 'A' and resid 732 through 741 removed outlier: 3.871A pdb=" N PHE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 767 removed outlier: 3.656A pdb=" N GLY A 767 " --> pdb=" O GLN A 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 482 through 499 removed outlier: 3.966A pdb=" N TYR B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 499 through 507 removed outlier: 3.908A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 536 Processing helix chain 'B' and resid 543 through 553 removed outlier: 3.544A pdb=" N LEU B 547 " --> pdb=" O LYS B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 569 removed outlier: 4.230A pdb=" N GLU B 561 " --> pdb=" O ALA B 557 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA B 569 " --> pdb=" O LYS B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 586 Processing helix chain 'B' and resid 600 through 610 Processing helix chain 'B' and resid 630 through 635 removed outlier: 3.544A pdb=" N ARG B 635 " --> pdb=" O ALA B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 661 Processing helix chain 'B' and resid 671 through 679 removed outlier: 3.636A pdb=" N THR B 679 " --> pdb=" O LEU B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 709 removed outlier: 3.541A pdb=" N ARG B 709 " --> pdb=" O SER B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 741 removed outlier: 3.918A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG B 741 " --> pdb=" O GLU B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 767 removed outlier: 3.538A pdb=" N GLY B 767 " --> pdb=" O GLN B 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 482 through 499 removed outlier: 3.893A pdb=" N TYR C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 499 through 507 removed outlier: 3.996A pdb=" N PHE C 503 " --> pdb=" O HIS C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 536 Processing helix chain 'C' and resid 543 through 553 removed outlier: 3.539A pdb=" N LEU C 547 " --> pdb=" O LYS C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 569 removed outlier: 4.164A pdb=" N GLU C 561 " --> pdb=" O ALA C 557 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA C 569 " --> pdb=" O LYS C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 586 Processing helix chain 'C' and resid 600 through 611 Processing helix chain 'C' and resid 630 through 635 removed outlier: 3.565A pdb=" N ARG C 635 " --> pdb=" O ALA C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 661 Processing helix chain 'C' and resid 671 through 679 Processing helix chain 'C' and resid 683 through 709 removed outlier: 3.529A pdb=" N ARG C 709 " --> pdb=" O SER C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 741 removed outlier: 3.758A pdb=" N PHE C 736 " --> pdb=" O ARG C 732 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 767 removed outlier: 3.658A pdb=" N GLY C 767 " --> pdb=" O GLN C 763 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 479 Processing helix chain 'D' and resid 482 through 499 removed outlier: 4.011A pdb=" N TYR D 495 " --> pdb=" O GLU D 491 " (cutoff:3.500A) Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 499 through 507 removed outlier: 3.912A pdb=" N PHE D 503 " --> pdb=" O HIS D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 536 Processing helix chain 'D' and resid 543 through 553 removed outlier: 3.548A pdb=" N LEU D 547 " --> pdb=" O LYS D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 569 removed outlier: 4.301A pdb=" N GLU D 561 " --> pdb=" O ALA D 557 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA D 569 " --> pdb=" O LYS D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 586 Processing helix chain 'D' and resid 600 through 610 Processing helix chain 'D' and resid 630 through 635 Processing helix chain 'D' and resid 649 through 661 Processing helix chain 'D' and resid 671 through 679 removed outlier: 3.554A pdb=" N THR D 679 " --> pdb=" O LEU D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 709 Processing helix chain 'D' and resid 732 through 741 removed outlier: 3.885A pdb=" N PHE D 736 " --> pdb=" O ARG D 732 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG D 741 " --> pdb=" O GLU D 737 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 767 Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 482 through 499 removed outlier: 4.145A pdb=" N TYR E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 499 through 507 removed outlier: 4.001A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 536 Processing helix chain 'E' and resid 543 through 553 removed outlier: 3.598A pdb=" N LEU E 547 " --> pdb=" O LYS E 543 " (cutoff:3.500A) Processing helix chain 'E' and resid 557 through 569 removed outlier: 4.177A pdb=" N GLU E 561 " --> pdb=" O ALA E 557 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA E 569 " --> pdb=" O LYS E 565 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 586 Processing helix chain 'E' and resid 600 through 610 Processing helix chain 'E' and resid 630 through 635 removed outlier: 3.592A pdb=" N ARG E 635 " --> pdb=" O ALA E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 661 Processing helix chain 'E' and resid 671 through 678 Processing helix chain 'E' and resid 683 through 709 removed outlier: 3.520A pdb=" N ARG E 709 " --> pdb=" O SER E 705 " (cutoff:3.500A) Processing helix chain 'E' and resid 732 through 741 removed outlier: 3.678A pdb=" N PHE E 736 " --> pdb=" O ARG E 732 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG E 741 " --> pdb=" O GLU E 737 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 767 removed outlier: 3.595A pdb=" N GLY E 767 " --> pdb=" O GLN E 763 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 482 through 499 removed outlier: 4.159A pdb=" N TYR F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 499 through 507 removed outlier: 3.949A pdb=" N PHE F 503 " --> pdb=" O HIS F 499 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 536 Processing helix chain 'F' and resid 543 through 553 removed outlier: 3.593A pdb=" N LEU F 547 " --> pdb=" O LYS F 543 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 569 removed outlier: 4.208A pdb=" N GLU F 561 " --> pdb=" O ALA F 557 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA F 569 " --> pdb=" O LYS F 565 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 586 Processing helix chain 'F' and resid 600 through 610 Processing helix chain 'F' and resid 630 through 635 Processing helix chain 'F' and resid 649 through 661 Processing helix chain 'F' and resid 671 through 679 removed outlier: 3.630A pdb=" N THR F 679 " --> pdb=" O LEU F 675 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 709 removed outlier: 3.534A pdb=" N ARG F 709 " --> pdb=" O SER F 705 " (cutoff:3.500A) Processing helix chain 'F' and resid 732 through 741 removed outlier: 3.797A pdb=" N PHE F 736 " --> pdb=" O ARG F 732 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG F 741 " --> pdb=" O GLU F 737 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 767 Processing sheet with id=AA1, first strand: chain 'A' and resid 538 through 542 removed outlier: 6.794A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N ILE A 643 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU A 515 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 538 through 542 removed outlier: 6.883A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 538 through 542 removed outlier: 6.935A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N GLY C 513 " --> pdb=" O GLN C 641 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N ILE C 643 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU C 515 " --> pdb=" O ILE C 643 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 538 through 542 removed outlier: 6.848A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N ILE D 643 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU D 515 " --> pdb=" O ILE D 643 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 538 through 542 removed outlier: 6.911A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 538 through 542 removed outlier: 6.890A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) 674 hydrogen bonds defined for protein. 1938 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: 4.87 Time building geometry restraints manager: 4.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2400 1.31 - 1.44: 3504 1.44 - 1.56: 8202 1.56 - 1.69: 30 1.69 - 1.81: 126 Bond restraints: 14262 Sorted by residual: bond pdb=" C14 A1AC1 F 901 " pdb=" C19 A1AC1 F 901 " ideal model delta sigma weight residual 1.384 1.676 -0.292 2.00e-02 2.50e+03 2.13e+02 bond pdb=" C14 A1AC1 A 901 " pdb=" C19 A1AC1 A 901 " ideal model delta sigma weight residual 1.384 1.675 -0.291 2.00e-02 2.50e+03 2.12e+02 bond pdb=" C14 A1AC1 D 901 " pdb=" C19 A1AC1 D 901 " ideal model delta sigma weight residual 1.384 1.675 -0.291 2.00e-02 2.50e+03 2.12e+02 bond pdb=" C14 A1AC1 C 901 " pdb=" C19 A1AC1 C 901 " ideal model delta sigma weight residual 1.384 1.675 -0.291 2.00e-02 2.50e+03 2.11e+02 bond pdb=" C14 A1AC1 E 901 " pdb=" C19 A1AC1 E 901 " ideal model delta sigma weight residual 1.384 1.673 -0.289 2.00e-02 2.50e+03 2.09e+02 ... (remaining 14257 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.35: 19086 4.35 - 8.69: 104 8.69 - 13.04: 22 13.04 - 17.39: 6 17.39 - 21.74: 6 Bond angle restraints: 19224 Sorted by residual: angle pdb=" C14 A1AC1 A 901 " pdb=" C15 A1AC1 A 901 " pdb=" N2 A1AC1 A 901 " ideal model delta sigma weight residual 102.74 124.48 -21.74 3.00e+00 1.11e-01 5.25e+01 angle pdb=" C14 A1AC1 D 901 " pdb=" C15 A1AC1 D 901 " pdb=" N2 A1AC1 D 901 " ideal model delta sigma weight residual 102.74 124.40 -21.66 3.00e+00 1.11e-01 5.21e+01 angle pdb=" C14 A1AC1 F 901 " pdb=" C15 A1AC1 F 901 " pdb=" N2 A1AC1 F 901 " ideal model delta sigma weight residual 102.74 124.39 -21.65 3.00e+00 1.11e-01 5.21e+01 angle pdb=" C14 A1AC1 C 901 " pdb=" C15 A1AC1 C 901 " pdb=" N2 A1AC1 C 901 " ideal model delta sigma weight residual 102.74 124.30 -21.56 3.00e+00 1.11e-01 5.17e+01 angle pdb=" C14 A1AC1 E 901 " pdb=" C15 A1AC1 E 901 " pdb=" N2 A1AC1 E 901 " ideal model delta sigma weight residual 102.74 124.24 -21.50 3.00e+00 1.11e-01 5.14e+01 ... (remaining 19219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.73: 8173 28.73 - 57.46: 476 57.46 - 86.19: 54 86.19 - 114.92: 9 114.92 - 143.65: 12 Dihedral angle restraints: 8724 sinusoidal: 3768 harmonic: 4956 Sorted by residual: dihedral pdb=" C5' ADP C 900 " pdb=" O5' ADP C 900 " pdb=" PA ADP C 900 " pdb=" O2A ADP C 900 " ideal model delta sinusoidal sigma weight residual -60.00 83.65 -143.65 1 2.00e+01 2.50e-03 4.33e+01 dihedral pdb=" C5' ADP A 900 " pdb=" O5' ADP A 900 " pdb=" PA ADP A 900 " pdb=" O2A ADP A 900 " ideal model delta sinusoidal sigma weight residual -60.00 82.71 -142.70 1 2.00e+01 2.50e-03 4.31e+01 dihedral pdb=" C5' ADP F 900 " pdb=" O5' ADP F 900 " pdb=" PA ADP F 900 " pdb=" O2A ADP F 900 " ideal model delta sinusoidal sigma weight residual -60.00 81.94 -141.94 1 2.00e+01 2.50e-03 4.29e+01 ... (remaining 8721 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1797 0.055 - 0.111: 212 0.111 - 0.166: 55 0.166 - 0.221: 0 0.221 - 0.277: 6 Chirality restraints: 2070 Sorted by residual: chirality pdb=" C11 A1AC1 E 901 " pdb=" C10 A1AC1 E 901 " pdb=" C20 A1AC1 E 901 " pdb=" N2 A1AC1 E 901 " both_signs ideal model delta sigma weight residual False -2.35 -2.62 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C11 A1AC1 A 901 " pdb=" C10 A1AC1 A 901 " pdb=" C20 A1AC1 A 901 " pdb=" N2 A1AC1 A 901 " both_signs ideal model delta sigma weight residual False -2.35 -2.62 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C11 A1AC1 C 901 " pdb=" C10 A1AC1 C 901 " pdb=" C20 A1AC1 C 901 " pdb=" N2 A1AC1 C 901 " both_signs ideal model delta sigma weight residual False -2.35 -2.62 0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 2067 not shown) Planarity restraints: 2502 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 A1AC1 A 901 " 0.131 2.00e-02 2.50e+03 6.28e-02 1.08e+02 pdb=" C12 A1AC1 A 901 " -0.038 2.00e-02 2.50e+03 pdb=" C13 A1AC1 A 901 " -0.014 2.00e-02 2.50e+03 pdb=" C14 A1AC1 A 901 " -0.004 2.00e-02 2.50e+03 pdb=" C15 A1AC1 A 901 " -0.021 2.00e-02 2.50e+03 pdb=" C16 A1AC1 A 901 " -0.001 2.00e-02 2.50e+03 pdb=" C17 A1AC1 A 901 " 0.017 2.00e-02 2.50e+03 pdb=" C18 A1AC1 A 901 " 0.025 2.00e-02 2.50e+03 pdb=" C19 A1AC1 A 901 " 0.018 2.00e-02 2.50e+03 pdb=" N2 A1AC1 A 901 " -0.147 2.00e-02 2.50e+03 pdb=" O2 A1AC1 A 901 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 A1AC1 B 901 " -0.003 2.00e-02 2.50e+03 5.95e-02 9.72e+01 pdb=" C12 A1AC1 B 901 " -0.010 2.00e-02 2.50e+03 pdb=" C13 A1AC1 B 901 " -0.011 2.00e-02 2.50e+03 pdb=" C14 A1AC1 B 901 " 0.038 2.00e-02 2.50e+03 pdb=" C15 A1AC1 B 901 " 0.058 2.00e-02 2.50e+03 pdb=" C16 A1AC1 B 901 " -0.044 2.00e-02 2.50e+03 pdb=" C17 A1AC1 B 901 " -0.034 2.00e-02 2.50e+03 pdb=" C18 A1AC1 B 901 " 0.005 2.00e-02 2.50e+03 pdb=" C19 A1AC1 B 901 " 0.044 2.00e-02 2.50e+03 pdb=" N2 A1AC1 B 901 " -0.140 2.00e-02 2.50e+03 pdb=" O2 A1AC1 B 901 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 A1AC1 E 901 " 0.097 2.00e-02 2.50e+03 5.91e-02 9.60e+01 pdb=" C12 A1AC1 E 901 " -0.031 2.00e-02 2.50e+03 pdb=" C13 A1AC1 E 901 " -0.015 2.00e-02 2.50e+03 pdb=" C14 A1AC1 E 901 " 0.008 2.00e-02 2.50e+03 pdb=" C15 A1AC1 E 901 " 0.002 2.00e-02 2.50e+03 pdb=" C16 A1AC1 E 901 " -0.015 2.00e-02 2.50e+03 pdb=" C17 A1AC1 E 901 " 0.003 2.00e-02 2.50e+03 pdb=" C18 A1AC1 E 901 " 0.021 2.00e-02 2.50e+03 pdb=" C19 A1AC1 E 901 " 0.027 2.00e-02 2.50e+03 pdb=" N2 A1AC1 E 901 " -0.153 2.00e-02 2.50e+03 pdb=" O2 A1AC1 E 901 " 0.055 2.00e-02 2.50e+03 ... (remaining 2499 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 77 2.57 - 3.15: 11449 3.15 - 3.73: 20530 3.73 - 4.32: 26358 4.32 - 4.90: 46180 Nonbonded interactions: 104594 Sorted by model distance: nonbonded pdb=" OG SER A 683 " pdb=" OD1 ASP A 686 " model vdw 1.985 3.040 nonbonded pdb=" OG SER D 683 " pdb=" OD2 ASP D 686 " model vdw 2.064 3.040 nonbonded pdb=" OG SER C 683 " pdb=" OD2 ASP C 686 " model vdw 2.072 3.040 nonbonded pdb=" NE2 GLN C 494 " pdb=" OE2 GLU C 534 " model vdw 2.116 3.120 nonbonded pdb=" N GLU D 466 " pdb=" OE1 GLU D 466 " model vdw 2.142 3.120 ... (remaining 104589 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 19.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 36.560 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 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 0.292 14262 Z= 0.570 Angle : 0.877 21.735 19224 Z= 0.348 Chirality : 0.043 0.277 2070 Planarity : 0.004 0.063 2502 Dihedral : 18.129 143.649 5508 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.07 % Allowed : 17.28 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.83 (0.22), residues: 1698 helix: 2.41 (0.18), residues: 906 sheet: -0.67 (0.34), residues: 186 loop : 0.05 (0.27), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 476 HIS 0.003 0.001 HIS C 499 PHE 0.010 0.001 PHE F 516 TYR 0.006 0.001 TYR E 517 ARG 0.002 0.000 ARG B 753 Details of bonding type rmsd hydrogen bonds : bond 0.15869 ( 674) hydrogen bonds : angle 4.78040 ( 1938) covalent geometry : bond 0.01157 (14262) covalent geometry : angle 0.87670 (19224) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 165 time to evaluate : 1.679 Fit side-chains REVERT: C 560 ARG cc_start: 0.7646 (ttm-80) cc_final: 0.7254 (mtp85) REVERT: C 740 MET cc_start: 0.8705 (mmm) cc_final: 0.8463 (tpt) REVERT: E 522 CYS cc_start: 0.8348 (m) cc_final: 0.8045 (m) REVERT: E 742 PHE cc_start: 0.8850 (m-80) cc_final: 0.8311 (m-10) outliers start: 1 outliers final: 1 residues processed: 166 average time/residue: 0.2788 time to fit residues: 67.3039 Evaluate side-chains 154 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 153 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 527 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 70 optimal weight: 0.1980 chunk 43 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 chunk 131 optimal weight: 0.3980 chunk 50 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 152 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.130267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.102619 restraints weight = 20201.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.105745 restraints weight = 12707.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.107938 restraints weight = 9388.052| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.0842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14262 Z= 0.156 Angle : 0.590 6.836 19224 Z= 0.281 Chirality : 0.042 0.130 2070 Planarity : 0.004 0.050 2502 Dihedral : 13.243 134.573 2012 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.50 % Allowed : 16.60 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.85 (0.21), residues: 1698 helix: 2.23 (0.18), residues: 930 sheet: -0.08 (0.35), residues: 186 loop : 0.09 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 476 HIS 0.002 0.001 HIS F 499 PHE 0.012 0.001 PHE D 771 TYR 0.012 0.001 TYR B 495 ARG 0.003 0.000 ARG E 744 Details of bonding type rmsd hydrogen bonds : bond 0.04940 ( 674) hydrogen bonds : angle 3.72623 ( 1938) covalent geometry : bond 0.00379 (14262) covalent geometry : angle 0.58995 (19224) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 1.628 Fit side-chains REVERT: E 522 CYS cc_start: 0.8443 (m) cc_final: 0.8064 (m) REVERT: E 742 PHE cc_start: 0.8914 (m-80) cc_final: 0.8196 (m-10) outliers start: 22 outliers final: 6 residues processed: 181 average time/residue: 0.3984 time to fit residues: 105.5192 Evaluate side-chains 159 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 153 time to evaluate : 2.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 527 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 96 optimal weight: 8.9990 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 45 optimal weight: 0.3980 chunk 20 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 165 optimal weight: 10.0000 chunk 146 optimal weight: 0.7980 chunk 8 optimal weight: 0.0270 chunk 40 optimal weight: 7.9990 overall best weight: 0.5840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.132276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.103768 restraints weight = 20248.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.107283 restraints weight = 12134.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.109660 restraints weight = 8697.188| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14262 Z= 0.112 Angle : 0.546 7.668 19224 Z= 0.256 Chirality : 0.041 0.152 2070 Planarity : 0.004 0.051 2502 Dihedral : 12.170 125.478 2012 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.23 % Allowed : 16.12 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.90 (0.21), residues: 1698 helix: 2.26 (0.18), residues: 930 sheet: 0.24 (0.36), residues: 186 loop : 0.02 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 476 HIS 0.001 0.000 HIS F 499 PHE 0.014 0.001 PHE B 742 TYR 0.009 0.001 TYR D 495 ARG 0.002 0.000 ARG E 653 Details of bonding type rmsd hydrogen bonds : bond 0.03934 ( 674) hydrogen bonds : angle 3.30830 ( 1938) covalent geometry : bond 0.00253 (14262) covalent geometry : angle 0.54616 (19224) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 2.714 Fit side-chains REVERT: B 580 ASP cc_start: 0.8812 (p0) cc_final: 0.8594 (p0) REVERT: B 740 MET cc_start: 0.9024 (tpp) cc_final: 0.8771 (mmm) REVERT: C 756 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7921 (mm-30) REVERT: D 550 MET cc_start: 0.8951 (mtp) cc_final: 0.8702 (mtp) REVERT: E 475 THR cc_start: 0.8699 (OUTLIER) cc_final: 0.8488 (p) REVERT: E 522 CYS cc_start: 0.8300 (m) cc_final: 0.7837 (m) REVERT: E 742 PHE cc_start: 0.8873 (m-80) cc_final: 0.8046 (m-10) REVERT: F 756 GLU cc_start: 0.8255 (mm-30) cc_final: 0.8014 (mm-30) outliers start: 18 outliers final: 9 residues processed: 177 average time/residue: 0.3173 time to fit residues: 86.0898 Evaluate side-chains 160 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 150 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain E residue 564 ASP Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 527 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 154 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 80 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 23 optimal weight: 8.9990 chunk 75 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.127639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.099860 restraints weight = 20380.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.102987 restraints weight = 12905.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.105100 restraints weight = 9521.762| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 14262 Z= 0.248 Angle : 0.633 8.882 19224 Z= 0.300 Chirality : 0.045 0.138 2070 Planarity : 0.004 0.055 2502 Dihedral : 11.976 129.266 2012 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.12 % Allowed : 17.49 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.60 (0.21), residues: 1698 helix: 2.01 (0.18), residues: 930 sheet: 0.03 (0.35), residues: 192 loop : -0.07 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 476 HIS 0.005 0.002 HIS F 499 PHE 0.016 0.002 PHE F 516 TYR 0.012 0.002 TYR B 495 ARG 0.002 0.000 ARG D 733 Details of bonding type rmsd hydrogen bonds : bond 0.04949 ( 674) hydrogen bonds : angle 3.56967 ( 1938) covalent geometry : bond 0.00626 (14262) covalent geometry : angle 0.63276 (19224) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 2.390 Fit side-chains REVERT: A 550 MET cc_start: 0.9138 (mtm) cc_final: 0.8819 (mtp) REVERT: B 484 ASP cc_start: 0.7265 (m-30) cc_final: 0.7053 (t0) REVERT: B 550 MET cc_start: 0.9281 (OUTLIER) cc_final: 0.8853 (mtp) REVERT: B 580 ASP cc_start: 0.8948 (p0) cc_final: 0.8733 (p0) REVERT: E 522 CYS cc_start: 0.8534 (m) cc_final: 0.8185 (m) REVERT: E 742 PHE cc_start: 0.8928 (m-80) cc_final: 0.8059 (m-10) REVERT: F 488 GLU cc_start: 0.7870 (tp30) cc_final: 0.7612 (tp30) REVERT: F 756 GLU cc_start: 0.8248 (mm-30) cc_final: 0.8003 (mm-30) outliers start: 31 outliers final: 19 residues processed: 169 average time/residue: 0.2622 time to fit residues: 66.5318 Evaluate side-chains 164 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 703 ILE Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain E residue 564 ASP Chi-restraints excluded: chain E residue 703 ILE Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 489 LEU Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 527 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 167 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 159 optimal weight: 8.9990 chunk 151 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 76 optimal weight: 0.0060 chunk 122 optimal weight: 0.9980 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.130631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.102511 restraints weight = 20441.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.105792 restraints weight = 12799.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.108005 restraints weight = 9392.459| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14262 Z= 0.112 Angle : 0.544 8.522 19224 Z= 0.252 Chirality : 0.041 0.124 2070 Planarity : 0.004 0.054 2502 Dihedral : 11.337 129.814 2012 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.50 % Allowed : 18.10 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.66 (0.21), residues: 1698 helix: 2.07 (0.18), residues: 930 sheet: 0.23 (0.36), residues: 174 loop : -0.13 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 476 HIS 0.001 0.000 HIS F 499 PHE 0.009 0.001 PHE C 539 TYR 0.008 0.001 TYR B 495 ARG 0.004 0.000 ARG E 662 Details of bonding type rmsd hydrogen bonds : bond 0.03898 ( 674) hydrogen bonds : angle 3.24838 ( 1938) covalent geometry : bond 0.00259 (14262) covalent geometry : angle 0.54377 (19224) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 1.544 Fit side-chains REVERT: B 580 ASP cc_start: 0.8912 (p0) cc_final: 0.8698 (p0) REVERT: B 742 PHE cc_start: 0.8995 (m-10) cc_final: 0.8789 (m-10) REVERT: C 756 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7927 (mm-30) REVERT: E 475 THR cc_start: 0.8719 (OUTLIER) cc_final: 0.8486 (p) REVERT: E 522 CYS cc_start: 0.8379 (m) cc_final: 0.7942 (m) REVERT: E 742 PHE cc_start: 0.8919 (m-80) cc_final: 0.8040 (m-10) REVERT: F 488 GLU cc_start: 0.7836 (tp30) cc_final: 0.7553 (tp30) REVERT: F 512 LYS cc_start: 0.8308 (tppt) cc_final: 0.7952 (ttpt) REVERT: F 756 GLU cc_start: 0.8224 (mm-30) cc_final: 0.8024 (mm-30) outliers start: 22 outliers final: 12 residues processed: 170 average time/residue: 0.2520 time to fit residues: 63.1602 Evaluate side-chains 163 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain E residue 564 ASP Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain F residue 762 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 146 optimal weight: 1.9990 chunk 156 optimal weight: 4.9990 chunk 124 optimal weight: 0.0670 chunk 101 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 5 optimal weight: 0.1980 chunk 50 optimal weight: 6.9990 chunk 128 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.134659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.110340 restraints weight = 19604.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.113106 restraints weight = 15998.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.114643 restraints weight = 11218.066| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14262 Z= 0.103 Angle : 0.526 8.466 19224 Z= 0.242 Chirality : 0.040 0.126 2070 Planarity : 0.004 0.053 2502 Dihedral : 10.830 134.751 2012 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.71 % Allowed : 17.76 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.79 (0.21), residues: 1698 helix: 2.18 (0.18), residues: 930 sheet: 0.20 (0.34), residues: 186 loop : -0.04 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 476 HIS 0.001 0.000 HIS F 499 PHE 0.013 0.001 PHE A 742 TYR 0.032 0.001 TYR F 517 ARG 0.002 0.000 ARG E 487 Details of bonding type rmsd hydrogen bonds : bond 0.03443 ( 674) hydrogen bonds : angle 3.08800 ( 1938) covalent geometry : bond 0.00237 (14262) covalent geometry : angle 0.52627 (19224) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 164 time to evaluate : 1.942 Fit side-chains REVERT: B 580 ASP cc_start: 0.8777 (p0) cc_final: 0.8570 (p0) REVERT: C 560 ARG cc_start: 0.7526 (ttm-80) cc_final: 0.7078 (mtp85) REVERT: E 512 LYS cc_start: 0.8521 (tppt) cc_final: 0.8064 (ttpt) REVERT: E 522 CYS cc_start: 0.8014 (m) cc_final: 0.7611 (m) REVERT: E 742 PHE cc_start: 0.8937 (m-80) cc_final: 0.8126 (m-10) REVERT: F 512 LYS cc_start: 0.8196 (tppt) cc_final: 0.7959 (ttpt) REVERT: F 668 LYS cc_start: 0.7824 (mmmt) cc_final: 0.6833 (tttt) outliers start: 25 outliers final: 17 residues processed: 181 average time/residue: 0.3122 time to fit residues: 83.2932 Evaluate side-chains 168 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 2.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain E residue 564 ASP Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain F residue 762 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 61 optimal weight: 0.0010 chunk 76 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.142381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.114466 restraints weight = 20231.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.117958 restraints weight = 12466.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.120321 restraints weight = 9080.348| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14262 Z= 0.107 Angle : 0.537 8.938 19224 Z= 0.245 Chirality : 0.041 0.124 2070 Planarity : 0.004 0.053 2502 Dihedral : 10.697 134.470 2012 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.78 % Allowed : 18.17 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.84 (0.21), residues: 1698 helix: 2.21 (0.18), residues: 930 sheet: 0.17 (0.32), residues: 204 loop : 0.02 (0.28), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 476 HIS 0.003 0.001 HIS D 499 PHE 0.020 0.001 PHE A 771 TYR 0.030 0.001 TYR F 517 ARG 0.003 0.000 ARG A 711 Details of bonding type rmsd hydrogen bonds : bond 0.03374 ( 674) hydrogen bonds : angle 3.07450 ( 1938) covalent geometry : bond 0.00253 (14262) covalent geometry : angle 0.53743 (19224) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 158 time to evaluate : 2.459 Fit side-chains REVERT: A 669 ASP cc_start: 0.7298 (t70) cc_final: 0.6638 (t70) REVERT: B 580 ASP cc_start: 0.8846 (p0) cc_final: 0.8621 (p0) REVERT: C 560 ARG cc_start: 0.7602 (ttm-80) cc_final: 0.7128 (mtp85) REVERT: D 550 MET cc_start: 0.9074 (mtp) cc_final: 0.8800 (mtp) REVERT: E 512 LYS cc_start: 0.8506 (tppt) cc_final: 0.7994 (ttpt) REVERT: E 522 CYS cc_start: 0.8126 (m) cc_final: 0.7653 (m) REVERT: E 742 PHE cc_start: 0.8888 (m-80) cc_final: 0.8029 (m-10) REVERT: F 488 GLU cc_start: 0.7648 (tp30) cc_final: 0.7420 (tt0) REVERT: F 512 LYS cc_start: 0.8255 (tppt) cc_final: 0.7969 (ttpt) REVERT: F 669 ASP cc_start: 0.7644 (t70) cc_final: 0.6923 (t70) outliers start: 26 outliers final: 18 residues processed: 175 average time/residue: 0.5242 time to fit residues: 137.1553 Evaluate side-chains 174 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 3.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain C residue 550 MET Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain E residue 564 ASP Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain F residue 647 LEU Chi-restraints excluded: chain F residue 762 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 110 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 14 optimal weight: 0.4980 chunk 83 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 129 optimal weight: 0.8980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.139008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.110896 restraints weight = 20265.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.114295 restraints weight = 12680.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.116599 restraints weight = 9284.162| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 14262 Z= 0.189 Angle : 0.583 9.536 19224 Z= 0.270 Chirality : 0.043 0.131 2070 Planarity : 0.004 0.054 2502 Dihedral : 11.083 139.303 2012 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.05 % Allowed : 17.90 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.69 (0.21), residues: 1698 helix: 2.15 (0.18), residues: 924 sheet: 0.15 (0.33), residues: 192 loop : -0.17 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 476 HIS 0.005 0.001 HIS D 499 PHE 0.016 0.002 PHE A 771 TYR 0.031 0.001 TYR F 517 ARG 0.002 0.000 ARG D 653 Details of bonding type rmsd hydrogen bonds : bond 0.04140 ( 674) hydrogen bonds : angle 3.26247 ( 1938) covalent geometry : bond 0.00472 (14262) covalent geometry : angle 0.58280 (19224) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 1.835 Fit side-chains REVERT: A 669 ASP cc_start: 0.7345 (t70) cc_final: 0.6810 (t70) REVERT: B 580 ASP cc_start: 0.8910 (p0) cc_final: 0.8689 (p0) REVERT: E 512 LYS cc_start: 0.8557 (tppt) cc_final: 0.8000 (ttpt) REVERT: E 522 CYS cc_start: 0.8340 (m) cc_final: 0.7900 (m) REVERT: E 742 PHE cc_start: 0.8908 (m-80) cc_final: 0.8034 (m-10) REVERT: F 488 GLU cc_start: 0.7796 (tp30) cc_final: 0.7506 (tt0) REVERT: F 512 LYS cc_start: 0.8358 (tppt) cc_final: 0.8020 (ttpt) REVERT: F 669 ASP cc_start: 0.7739 (t70) cc_final: 0.6922 (t70) outliers start: 30 outliers final: 22 residues processed: 172 average time/residue: 0.3623 time to fit residues: 93.3322 Evaluate side-chains 171 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 703 ILE Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain E residue 564 ASP Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain F residue 647 LEU Chi-restraints excluded: chain F residue 762 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 138 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 161 optimal weight: 0.7980 chunk 128 optimal weight: 0.0270 chunk 1 optimal weight: 2.9990 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.141245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.113259 restraints weight = 20111.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.116745 restraints weight = 12488.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.119077 restraints weight = 9118.625| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14262 Z= 0.121 Angle : 0.554 9.235 19224 Z= 0.256 Chirality : 0.042 0.185 2070 Planarity : 0.004 0.053 2502 Dihedral : 10.931 137.233 2012 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.71 % Allowed : 18.37 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.75 (0.21), residues: 1698 helix: 2.13 (0.18), residues: 930 sheet: 0.19 (0.33), residues: 192 loop : -0.04 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 476 HIS 0.002 0.001 HIS D 499 PHE 0.019 0.001 PHE A 771 TYR 0.031 0.001 TYR F 517 ARG 0.002 0.000 ARG E 487 Details of bonding type rmsd hydrogen bonds : bond 0.03658 ( 674) hydrogen bonds : angle 3.12834 ( 1938) covalent geometry : bond 0.00291 (14262) covalent geometry : angle 0.55422 (19224) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 1.755 Fit side-chains REVERT: A 669 ASP cc_start: 0.7303 (t70) cc_final: 0.6736 (t70) REVERT: B 580 ASP cc_start: 0.8886 (p0) cc_final: 0.8621 (p0) REVERT: D 550 MET cc_start: 0.9156 (mtp) cc_final: 0.8854 (mtp) REVERT: E 487 ARG cc_start: 0.7485 (tmm-80) cc_final: 0.7276 (tmm-80) REVERT: E 512 LYS cc_start: 0.8512 (tppt) cc_final: 0.7977 (ttpt) REVERT: E 522 CYS cc_start: 0.8202 (m) cc_final: 0.7720 (m) REVERT: E 742 PHE cc_start: 0.8895 (m-80) cc_final: 0.8032 (m-10) REVERT: F 512 LYS cc_start: 0.8311 (tppt) cc_final: 0.7983 (ttpt) REVERT: F 669 ASP cc_start: 0.7674 (t70) cc_final: 0.6821 (t70) outliers start: 25 outliers final: 20 residues processed: 173 average time/residue: 0.2595 time to fit residues: 66.4770 Evaluate side-chains 173 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain E residue 564 ASP Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain F residue 762 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 33 optimal weight: 0.0000 chunk 126 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 124 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 161 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.142260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.114224 restraints weight = 20234.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.117759 restraints weight = 12527.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.120114 restraints weight = 9115.488| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14262 Z= 0.112 Angle : 0.541 9.211 19224 Z= 0.249 Chirality : 0.041 0.127 2070 Planarity : 0.004 0.053 2502 Dihedral : 10.570 134.330 2012 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.50 % Allowed : 18.72 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.81 (0.21), residues: 1698 helix: 2.18 (0.18), residues: 930 sheet: 0.25 (0.33), residues: 192 loop : -0.03 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 476 HIS 0.002 0.001 HIS F 499 PHE 0.018 0.001 PHE A 771 TYR 0.029 0.001 TYR F 517 ARG 0.002 0.000 ARG D 653 Details of bonding type rmsd hydrogen bonds : bond 0.03404 ( 674) hydrogen bonds : angle 3.05627 ( 1938) covalent geometry : bond 0.00266 (14262) covalent geometry : angle 0.54147 (19224) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 1.686 Fit side-chains REVERT: A 669 ASP cc_start: 0.7255 (t70) cc_final: 0.6694 (t70) REVERT: B 580 ASP cc_start: 0.8872 (p0) cc_final: 0.8647 (p0) REVERT: E 512 LYS cc_start: 0.8489 (tppt) cc_final: 0.7959 (ttpt) REVERT: E 522 CYS cc_start: 0.8156 (m) cc_final: 0.7665 (m) REVERT: E 742 PHE cc_start: 0.8889 (m-80) cc_final: 0.8018 (m-10) REVERT: F 512 LYS cc_start: 0.8310 (tppt) cc_final: 0.7978 (ttpt) outliers start: 22 outliers final: 21 residues processed: 170 average time/residue: 0.2682 time to fit residues: 67.1416 Evaluate side-chains 176 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain E residue 564 ASP Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain F residue 762 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 106 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 76 optimal weight: 0.0370 chunk 59 optimal weight: 0.6980 chunk 139 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 143 optimal weight: 0.9980 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.141839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.113832 restraints weight = 20347.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.117347 restraints weight = 12581.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.119730 restraints weight = 9167.087| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14262 Z= 0.117 Angle : 0.545 9.298 19224 Z= 0.249 Chirality : 0.041 0.152 2070 Planarity : 0.004 0.053 2502 Dihedral : 10.288 132.861 2012 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.71 % Allowed : 18.72 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.83 (0.21), residues: 1698 helix: 2.24 (0.18), residues: 924 sheet: 0.19 (0.33), residues: 204 loop : -0.06 (0.28), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 476 HIS 0.002 0.001 HIS D 499 PHE 0.019 0.001 PHE A 771 TYR 0.029 0.001 TYR F 517 ARG 0.002 0.000 ARG B 753 Details of bonding type rmsd hydrogen bonds : bond 0.03427 ( 674) hydrogen bonds : angle 3.05619 ( 1938) covalent geometry : bond 0.00281 (14262) covalent geometry : angle 0.54505 (19224) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 4372.69 seconds wall clock time: 82 minutes 24.07 seconds (4944.07 seconds total)