Starting phenix.real_space_refine on Sun Jan 19 16:10:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vov_43392/01_2025/8vov_43392.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vov_43392/01_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_43392/01_2025/8vov_43392.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vov_43392/01_2025/8vov_43392.map" model { file = "/net/cci-nas-00/data/ceres_data/8vov_43392/01_2025/8vov_43392.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vov_43392/01_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 9.18, per 1000 atoms: 0.66 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: 3.59 Conformation dependent library (CDL) restraints added in 2.1 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: 1.55 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: 3.87 Time building geometry restraints manager: 4.07 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: 0.02 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: 2.680 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: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 32.800 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.770 ------------------------------------------------------------------------------- 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= 0.819 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 *********************** 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 : 1.697 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: 0.2779 time to fit residues: 66.8136 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 : 1.889 ------------------------------------------------------------------------------- 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 = 38)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.102693 restraints weight = 20201.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.105839 restraints weight = 12661.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.108010 restraints weight = 9297.813| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 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= 0.248 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 *********************** 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 : 1.769 Fit side-chains REVERT: E 522 CYS cc_start: 0.8444 (m) cc_final: 0.8065 (m) REVERT: E 742 PHE cc_start: 0.8913 (m-80) cc_final: 0.8196 (m-10) outliers start: 22 outliers final: 6 residues processed: 181 average time/residue: 0.2847 time to fit residues: 75.7765 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 : 1.950 ------------------------------------------------------------------------------- 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: 7.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 45 optimal weight: 0.0170 chunk 20 optimal weight: 0.6980 chunk 139 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 165 optimal weight: 10.0000 chunk 146 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 overall best weight: 0.9220 ------------------------------------------------------------------------------- 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 = 0.3511 r_free = 0.3511 target = 0.131332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.102844 restraints weight = 20296.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.106303 restraints weight = 12200.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.108655 restraints weight = 8777.191| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14262 Z= 0.198 Angle : 0.553 7.731 19224 Z= 0.260 Chirality : 0.041 0.141 2070 Planarity : 0.004 0.052 2502 Dihedral : 12.323 125.902 2012 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.16 % Allowed : 16.33 % Favored : 82.51 % 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: 1.86 (0.21), residues: 1698 helix: 2.23 (0.18), residues: 930 sheet: 0.18 (0.36), residues: 186 loop : 0.02 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 476 HIS 0.002 0.001 HIS F 499 PHE 0.013 0.001 PHE F 516 TYR 0.009 0.001 TYR D 495 ARG 0.002 0.000 ARG E 653 *********************** 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 177 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 1.646 Fit side-chains REVERT: A 669 ASP cc_start: 0.7705 (t70) cc_final: 0.7004 (t70) REVERT: B 580 ASP cc_start: 0.8839 (p0) cc_final: 0.8622 (p0) REVERT: D 550 MET cc_start: 0.8988 (mtp) cc_final: 0.8741 (mtp) REVERT: E 475 THR cc_start: 0.8697 (OUTLIER) cc_final: 0.8494 (p) REVERT: E 522 CYS cc_start: 0.8379 (m) cc_final: 0.7918 (m) REVERT: E 742 PHE cc_start: 0.8883 (m-80) cc_final: 0.8120 (m-10) REVERT: F 756 GLU cc_start: 0.8269 (mm-30) cc_final: 0.8012 (mm-30) outliers start: 17 outliers final: 8 residues processed: 171 average time/residue: 0.2695 time to fit residues: 68.1927 Evaluate side-chains 159 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 150 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 82 optimal weight: 7.9990 chunk 80 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 105 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 75 optimal weight: 0.6980 overall best weight: 3.1386 ------------------------------------------------------------------------------- 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 = 0.3447 r_free = 0.3447 target = 0.126083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.098458 restraints weight = 20450.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.101525 restraints weight = 12960.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.103641 restraints weight = 9597.039| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.050 14262 Z= 0.495 Angle : 0.679 8.958 19224 Z= 0.325 Chirality : 0.048 0.147 2070 Planarity : 0.005 0.055 2502 Dihedral : 12.257 129.560 2012 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.60 % Allowed : 17.35 % 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: 1.43 (0.21), residues: 1698 helix: 1.88 (0.18), residues: 930 sheet: -0.10 (0.35), residues: 192 loop : -0.13 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 476 HIS 0.007 0.002 HIS F 499 PHE 0.018 0.002 PHE F 516 TYR 0.014 0.002 TYR B 495 ARG 0.003 0.000 ARG D 733 *********************** 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 192 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 154 time to evaluate : 1.742 Fit side-chains REVERT: A 669 ASP cc_start: 0.7701 (t70) cc_final: 0.7056 (t70) REVERT: B 484 ASP cc_start: 0.7305 (m-30) cc_final: 0.7060 (t0) REVERT: B 550 MET cc_start: 0.9267 (OUTLIER) cc_final: 0.8871 (mtp) REVERT: B 580 ASP cc_start: 0.8964 (p0) cc_final: 0.8748 (p0) REVERT: E 522 CYS cc_start: 0.8464 (m) cc_final: 0.8220 (m) REVERT: E 701 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8156 (tm-30) REVERT: E 742 PHE cc_start: 0.8965 (m-80) cc_final: 0.8101 (m-10) REVERT: F 488 GLU cc_start: 0.7889 (tp30) cc_final: 0.7659 (tp30) REVERT: F 756 GLU cc_start: 0.8268 (mm-30) cc_final: 0.8009 (mm-30) outliers start: 38 outliers final: 22 residues processed: 177 average time/residue: 0.2718 time to fit residues: 71.6706 Evaluate side-chains 173 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 526 LEU 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 701 GLU 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 Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 762 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: 7.9990 chunk 51 optimal weight: 2.9990 chunk 159 optimal weight: 0.8980 chunk 151 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 31 optimal weight: 0.4980 chunk 76 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3494 r_free = 0.3494 target = 0.129959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.102248 restraints weight = 20448.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.105391 restraints weight = 12757.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.107634 restraints weight = 9383.858| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1553 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= 0.183 Angle : 0.549 8.422 19224 Z= 0.257 Chirality : 0.041 0.125 2070 Planarity : 0.004 0.054 2502 Dihedral : 11.468 129.676 2012 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.78 % Allowed : 18.31 % 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: 1.56 (0.21), residues: 1698 helix: 2.00 (0.18), residues: 930 sheet: 0.07 (0.36), residues: 174 loop : -0.16 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 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 0.002 0.000 ARG D 653 *********************** 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 183 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 1.994 Fit side-chains REVERT: A 669 ASP cc_start: 0.7615 (t70) cc_final: 0.6890 (t70) REVERT: B 580 ASP cc_start: 0.8942 (p0) cc_final: 0.8728 (p0) REVERT: E 522 CYS cc_start: 0.8417 (m) cc_final: 0.8009 (m) REVERT: E 742 PHE cc_start: 0.8917 (m-80) cc_final: 0.7977 (m-10) REVERT: F 488 GLU cc_start: 0.7832 (tp30) cc_final: 0.7563 (tp30) REVERT: F 512 LYS cc_start: 0.8311 (tppt) cc_final: 0.7943 (ttpt) REVERT: F 756 GLU cc_start: 0.8221 (mm-30) cc_final: 0.8013 (mm-30) outliers start: 26 outliers final: 16 residues processed: 173 average time/residue: 0.2748 time to fit residues: 69.7044 Evaluate side-chains 163 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 611 MET 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 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 527 LEU Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain E residue 564 ASP Chi-restraints excluded: chain E residue 611 MET Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 527 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 146 optimal weight: 0.9990 chunk 156 optimal weight: 0.5980 chunk 124 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 166 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 128 optimal weight: 0.0370 chunk 76 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 overall best weight: 0.6658 ------------------------------------------------------------------------------- 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 = 0.3629 r_free = 0.3629 target = 0.141664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.113662 restraints weight = 20296.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.117207 restraints weight = 12566.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.119547 restraints weight = 9116.856| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14262 Z= 0.165 Angle : 0.536 8.549 19224 Z= 0.246 Chirality : 0.041 0.125 2070 Planarity : 0.004 0.054 2502 Dihedral : 10.965 135.580 2012 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.12 % Allowed : 18.31 % 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: 1.67 (0.21), residues: 1698 helix: 2.12 (0.18), residues: 930 sheet: 0.14 (0.34), residues: 174 loop : -0.16 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 476 HIS 0.001 0.000 HIS F 499 PHE 0.014 0.001 PHE B 742 TYR 0.032 0.001 TYR F 517 ARG 0.004 0.000 ARG F 766 *********************** 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 193 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 1.698 Fit side-chains REVERT: A 669 ASP cc_start: 0.7480 (t70) cc_final: 0.6736 (t70) REVERT: B 580 ASP cc_start: 0.8885 (p0) cc_final: 0.8663 (p0) REVERT: B 742 PHE cc_start: 0.8917 (m-10) cc_final: 0.8716 (m-10) REVERT: E 475 THR cc_start: 0.8762 (OUTLIER) cc_final: 0.8538 (p) REVERT: E 512 LYS cc_start: 0.8553 (tppt) cc_final: 0.8001 (ttpt) REVERT: E 522 CYS cc_start: 0.8175 (m) cc_final: 0.7740 (m) REVERT: E 742 PHE cc_start: 0.8913 (m-80) cc_final: 0.8034 (m-10) REVERT: F 488 GLU cc_start: 0.7838 (tp30) cc_final: 0.7603 (tp30) REVERT: F 512 LYS cc_start: 0.8286 (tppt) cc_final: 0.7966 (ttpt) REVERT: F 668 LYS cc_start: 0.7933 (mmmt) cc_final: 0.6841 (tttt) REVERT: F 669 ASP cc_start: 0.7734 (t70) cc_final: 0.7068 (t70) outliers start: 31 outliers final: 19 residues processed: 184 average time/residue: 0.2738 time to fit residues: 74.2209 Evaluate side-chains 175 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 1.662 ------------------------------------------------------------------------------- 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 526 LEU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain D residue 549 THR 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 61 optimal weight: 0.0980 chunk 76 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.141541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.113504 restraints weight = 20227.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.117015 restraints weight = 12538.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.119368 restraints weight = 9119.736| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14262 Z= 0.184 Angle : 0.538 8.948 19224 Z= 0.247 Chirality : 0.041 0.124 2070 Planarity : 0.004 0.053 2502 Dihedral : 10.849 135.985 2012 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.05 % Allowed : 18.24 % Favored : 79.71 % 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: 2.16 (0.18), residues: 930 sheet: 0.03 (0.32), residues: 204 loop : -0.02 (0.28), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 476 HIS 0.003 0.001 HIS D 499 PHE 0.018 0.001 PHE A 771 TYR 0.029 0.001 TYR F 517 ARG 0.002 0.000 ARG F 766 *********************** 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 188 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 158 time to evaluate : 1.625 Fit side-chains REVERT: A 669 ASP cc_start: 0.7424 (t70) cc_final: 0.6671 (t70) REVERT: B 580 ASP cc_start: 0.8873 (p0) cc_final: 0.8646 (p0) REVERT: B 742 PHE cc_start: 0.8935 (m-10) cc_final: 0.8710 (m-10) REVERT: D 550 MET cc_start: 0.9100 (mtp) cc_final: 0.8838 (mtp) REVERT: E 512 LYS cc_start: 0.8542 (tppt) cc_final: 0.7979 (ttpt) REVERT: E 522 CYS cc_start: 0.8170 (m) cc_final: 0.7712 (m) REVERT: E 742 PHE cc_start: 0.8893 (m-80) cc_final: 0.8046 (m-10) REVERT: F 488 GLU cc_start: 0.7843 (tp30) cc_final: 0.7600 (tp30) REVERT: F 512 LYS cc_start: 0.8288 (tppt) cc_final: 0.7987 (ttpt) REVERT: F 668 LYS cc_start: 0.7883 (mmmt) cc_final: 0.6804 (tttt) REVERT: F 669 ASP cc_start: 0.7691 (t70) cc_final: 0.7351 (t70) outliers start: 30 outliers final: 20 residues processed: 179 average time/residue: 0.2685 time to fit residues: 70.6393 Evaluate side-chains 175 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 1.726 ------------------------------------------------------------------------------- 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 B residue 509 THR Chi-restraints excluded: chain B residue 683 SER 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 549 THR Chi-restraints excluded: chain D 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 110 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 14 optimal weight: 0.1980 chunk 83 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 120 optimal weight: 0.8980 chunk 105 optimal weight: 0.0980 chunk 0 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 = 0.142267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.114151 restraints weight = 20090.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.117659 restraints weight = 12486.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.120016 restraints weight = 9100.694| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1974 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= 0.159 Angle : 0.530 8.958 19224 Z= 0.243 Chirality : 0.040 0.124 2070 Planarity : 0.004 0.053 2502 Dihedral : 10.685 134.216 2012 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.19 % Allowed : 17.83 % Favored : 79.99 % 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 (0.17), residues: 930 sheet: 0.14 (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 0.002 0.001 HIS D 499 PHE 0.013 0.001 PHE A 742 TYR 0.030 0.001 TYR F 517 ARG 0.002 0.000 ARG A 772 *********************** 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 197 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 165 time to evaluate : 1.795 Fit side-chains REVERT: A 669 ASP cc_start: 0.7431 (t70) cc_final: 0.6685 (t70) REVERT: A 772 ARG cc_start: 0.7914 (ptt180) cc_final: 0.7614 (ptt90) REVERT: B 580 ASP cc_start: 0.8863 (p0) cc_final: 0.8633 (p0) REVERT: B 742 PHE cc_start: 0.8907 (m-10) cc_final: 0.8654 (m-10) REVERT: C 731 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8220 (mp) REVERT: D 550 MET cc_start: 0.9064 (mtp) cc_final: 0.8799 (mtp) REVERT: E 487 ARG cc_start: 0.7527 (tmm-80) cc_final: 0.7300 (tmm-80) REVERT: E 512 LYS cc_start: 0.8533 (tppt) cc_final: 0.7986 (ttpt) REVERT: E 522 CYS cc_start: 0.8140 (m) cc_final: 0.7652 (m) REVERT: E 742 PHE cc_start: 0.8890 (m-80) cc_final: 0.8034 (m-10) REVERT: F 488 GLU cc_start: 0.7834 (tp30) cc_final: 0.7597 (tp30) REVERT: F 512 LYS cc_start: 0.8261 (tppt) cc_final: 0.7993 (ttpt) REVERT: F 669 ASP cc_start: 0.7662 (t70) cc_final: 0.6677 (t70) outliers start: 32 outliers final: 22 residues processed: 184 average time/residue: 0.2667 time to fit residues: 72.1342 Evaluate side-chains 180 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 157 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 643 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 731 ILE Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain D residue 549 THR 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 611 MET 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 633 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 138 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 6 optimal weight: 0.0770 chunk 146 optimal weight: 0.8980 chunk 139 optimal weight: 0.9980 chunk 160 optimal weight: 0.0980 chunk 119 optimal weight: 3.9990 chunk 161 optimal weight: 0.9980 chunk 128 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 = 0.3451 r_free = 0.3451 target = 0.126977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.099156 restraints weight = 20023.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.102518 restraints weight = 12186.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.104808 restraints weight = 8781.558| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14262 Z= 0.154 Angle : 0.529 9.103 19224 Z= 0.241 Chirality : 0.040 0.125 2070 Planarity : 0.004 0.053 2502 Dihedral : 10.639 132.463 2012 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.64 % Allowed : 18.37 % Favored : 79.99 % 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: 1.89 (0.21), residues: 1698 helix: 2.23 (0.18), residues: 930 sheet: 0.24 (0.32), residues: 204 loop : 0.05 (0.28), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 476 HIS 0.001 0.001 HIS F 499 PHE 0.012 0.001 PHE F 742 TYR 0.029 0.001 TYR F 517 ARG 0.002 0.000 ARG D 653 *********************** 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 185 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 1.588 Fit side-chains REVERT: A 669 ASP cc_start: 0.7371 (t70) cc_final: 0.6575 (t70) REVERT: B 580 ASP cc_start: 0.8929 (p0) cc_final: 0.8696 (p0) REVERT: C 731 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8153 (mp) REVERT: D 550 MET cc_start: 0.9064 (mtp) cc_final: 0.8777 (mtp) REVERT: E 512 LYS cc_start: 0.8450 (tppt) cc_final: 0.7862 (ttpt) REVERT: E 522 CYS cc_start: 0.8189 (m) cc_final: 0.7663 (m) REVERT: E 742 PHE cc_start: 0.8834 (m-80) cc_final: 0.7929 (m-10) REVERT: F 488 GLU cc_start: 0.7826 (tp30) cc_final: 0.7497 (tp30) REVERT: F 512 LYS cc_start: 0.8272 (tppt) cc_final: 0.7921 (ttpt) outliers start: 24 outliers final: 20 residues processed: 174 average time/residue: 0.2740 time to fit residues: 70.0929 Evaluate side-chains 175 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 643 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 611 MET Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 731 ILE Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain D residue 549 THR 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 611 MET 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 640 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 33 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 73 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 161 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3630 r_free = 0.3630 target = 0.141608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.113631 restraints weight = 20119.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.117119 restraints weight = 12520.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.119474 restraints weight = 9134.490| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14262 Z= 0.182 Angle : 0.534 9.319 19224 Z= 0.245 Chirality : 0.041 0.124 2070 Planarity : 0.004 0.053 2502 Dihedral : 10.462 132.396 2012 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.64 % Allowed : 18.51 % Favored : 79.85 % 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: 1.87 (0.21), residues: 1698 helix: 2.26 (0.18), residues: 924 sheet: 0.27 (0.32), residues: 204 loop : -0.03 (0.28), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 476 HIS 0.002 0.001 HIS D 499 PHE 0.012 0.001 PHE B 742 TYR 0.029 0.001 TYR F 517 ARG 0.002 0.000 ARG E 487 ********************** 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 178 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 1.614 Fit side-chains REVERT: A 669 ASP cc_start: 0.7384 (t70) cc_final: 0.6633 (t70) REVERT: B 580 ASP cc_start: 0.8877 (p0) cc_final: 0.8647 (p0) REVERT: C 731 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8203 (mp) REVERT: D 550 MET cc_start: 0.9086 (mtp) cc_final: 0.8817 (mtp) REVERT: E 487 ARG cc_start: 0.7542 (tmm-80) cc_final: 0.7322 (tmm-80) REVERT: E 512 LYS cc_start: 0.8517 (tppt) cc_final: 0.7980 (ttpt) REVERT: E 522 CYS cc_start: 0.8135 (m) cc_final: 0.7648 (m) REVERT: E 742 PHE cc_start: 0.8891 (m-80) cc_final: 0.8078 (m-10) REVERT: F 488 GLU cc_start: 0.7843 (tp30) cc_final: 0.7605 (tp30) REVERT: F 512 LYS cc_start: 0.8330 (tppt) cc_final: 0.8017 (ttpt) REVERT: F 680 ASN cc_start: 0.8166 (t0) cc_final: 0.7449 (m-40) outliers start: 24 outliers final: 22 residues processed: 168 average time/residue: 0.2695 time to fit residues: 67.1453 Evaluate side-chains 178 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 1.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 643 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 611 MET Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 731 ILE Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain D residue 549 THR 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 611 MET 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 633 ILE Chi-restraints excluded: chain F residue 640 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 106 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 76 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 139 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3634 r_free = 0.3634 target = 0.142093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.113926 restraints weight = 20252.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.117411 restraints weight = 12579.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.119760 restraints weight = 9181.844| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2147 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= 0.170 Angle : 0.539 9.472 19224 Z= 0.245 Chirality : 0.041 0.134 2070 Planarity : 0.004 0.053 2502 Dihedral : 10.062 130.179 2012 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.84 % Allowed : 18.44 % Favored : 79.71 % 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: 1.88 (0.21), residues: 1698 helix: 2.25 (0.17), residues: 924 sheet: 0.33 (0.33), residues: 204 loop : -0.03 (0.28), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 476 HIS 0.002 0.001 HIS F 499 PHE 0.019 0.001 PHE B 742 TYR 0.029 0.001 TYR F 517 ARG 0.002 0.000 ARG B 753 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 3517.77 seconds wall clock time: 64 minutes 53.13 seconds (3893.13 seconds total)