Starting phenix.real_space_refine on Thu Sep 18 04:22:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vov_43392/09_2025/8vov_43392.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vov_43392/09_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_43392/09_2025/8vov_43392.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vov_43392/09_2025/8vov_43392.map" model { file = "/net/cci-nas-00/data/ceres_data/8vov_43392/09_2025/8vov_43392.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vov_43392/09_2025/8vov_43392.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.87, per 1000 atoms: 0.21 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: 1.21 Conformation dependent library (CDL) restraints added in 536.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.28 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: 1.69 Time building geometry restraints manager: 1.51 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: 0.01 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: 4.290 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.240 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.210 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG B 753 TYR 0.006 0.001 TYR E 517 PHE 0.010 0.001 PHE F 516 TRP 0.006 0.001 TRP D 476 HIS 0.003 0.001 HIS C 499 Details of bonding type rmsd covalent geometry : bond 0.01157 (14262) covalent geometry : angle 0.87670 (19224) hydrogen bonds : bond 0.15869 ( 674) hydrogen bonds : angle 4.78040 ( 1938) *********************** 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 : 0.402 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: 0.1080 time to fit residues: 26.3138 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 : 0.464 ------------------------------------------------------------------------------- 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 98 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.3498 r_free = 0.3498 target = 0.130327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.102658 restraints weight = 20335.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.105872 restraints weight = 12757.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.108034 restraints weight = 9349.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.109501 restraints weight = 7569.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.110531 restraints weight = 6545.246| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.0818 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 : 0.591 6.863 19224 Z= 0.281 Chirality : 0.042 0.129 2070 Planarity : 0.004 0.050 2502 Dihedral : 13.284 134.853 2012 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.43 % Allowed : 16.67 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.86 (0.21), residues: 1698 helix: 2.24 (0.18), residues: 930 sheet: -0.09 (0.35), residues: 186 loop : 0.10 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 744 TYR 0.012 0.001 TYR B 495 PHE 0.012 0.001 PHE D 771 TRP 0.010 0.001 TRP C 476 HIS 0.003 0.001 HIS F 499 Details of bonding type rmsd covalent geometry : bond 0.00379 (14262) covalent geometry : angle 0.59083 (19224) hydrogen bonds : bond 0.05006 ( 674) hydrogen bonds : angle 3.74699 ( 1938) *********************** 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 187 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 0.497 Fit side-chains REVERT: C 560 ARG cc_start: 0.7680 (ttm-80) cc_final: 0.7213 (mtp85) REVERT: E 522 CYS cc_start: 0.8467 (m) cc_final: 0.8073 (m) REVERT: E 742 PHE cc_start: 0.8916 (m-80) cc_final: 0.8211 (m-10) outliers start: 21 outliers final: 6 residues processed: 179 average time/residue: 0.1145 time to fit residues: 30.1477 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 : 0.398 ------------------------------------------------------------------------------- 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 62 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 14 optimal weight: 0.0470 chunk 87 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 overall best weight: 1.1682 ------------------------------------------------------------------------------- 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 = 0.3500 r_free = 0.3500 target = 0.130623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.102681 restraints weight = 20538.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.105913 restraints weight = 12817.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.108113 restraints weight = 9380.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.109643 restraints weight = 7602.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.110606 restraints weight = 6554.685| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1137 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= 0.142 Angle : 0.563 7.847 19224 Z= 0.265 Chirality : 0.042 0.145 2070 Planarity : 0.004 0.052 2502 Dihedral : 12.440 126.304 2012 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.30 % Allowed : 16.53 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.83 (0.21), residues: 1698 helix: 2.20 (0.18), residues: 930 sheet: 0.15 (0.36), residues: 186 loop : 0.02 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 653 TYR 0.009 0.001 TYR D 495 PHE 0.014 0.001 PHE F 516 TRP 0.008 0.001 TRP E 476 HIS 0.002 0.001 HIS F 499 Details of bonding type rmsd covalent geometry : bond 0.00344 (14262) covalent geometry : angle 0.56265 (19224) hydrogen bonds : bond 0.04336 ( 674) hydrogen bonds : angle 3.43524 ( 1938) *********************** 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 179 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.546 Fit side-chains REVERT: A 669 ASP cc_start: 0.7702 (t70) cc_final: 0.7017 (t70) REVERT: D 550 MET cc_start: 0.9006 (mtp) cc_final: 0.8766 (mtp) REVERT: E 522 CYS cc_start: 0.8429 (m) cc_final: 0.7966 (m) REVERT: E 742 PHE cc_start: 0.8886 (m-80) cc_final: 0.8127 (m-10) REVERT: F 756 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7986 (mm-30) outliers start: 19 outliers final: 7 residues processed: 172 average time/residue: 0.1079 time to fit residues: 27.5624 Evaluate side-chains 159 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 152 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 682 PHE 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 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 79 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 146 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3500 r_free = 0.3500 target = 0.130460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.102806 restraints weight = 20386.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.106027 restraints weight = 12765.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.108203 restraints weight = 9345.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.109697 restraints weight = 7577.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.110654 restraints weight = 6547.630| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14262 Z= 0.138 Angle : 0.550 8.259 19224 Z= 0.256 Chirality : 0.042 0.131 2070 Planarity : 0.004 0.053 2502 Dihedral : 11.660 127.839 2012 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.78 % Allowed : 16.94 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.80 (0.21), residues: 1698 helix: 2.16 (0.18), residues: 930 sheet: 0.35 (0.37), residues: 174 loop : -0.05 (0.27), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 586 TYR 0.010 0.001 TYR B 495 PHE 0.013 0.001 PHE B 771 TRP 0.008 0.001 TRP E 476 HIS 0.002 0.001 HIS F 499 Details of bonding type rmsd covalent geometry : bond 0.00339 (14262) covalent geometry : angle 0.55025 (19224) hydrogen bonds : bond 0.04012 ( 674) hydrogen bonds : angle 3.28582 ( 1938) *********************** 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 181 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.549 Fit side-chains REVERT: A 669 ASP cc_start: 0.7609 (t70) cc_final: 0.6864 (t70) REVERT: B 550 MET cc_start: 0.9218 (OUTLIER) cc_final: 0.8810 (mtp) REVERT: C 560 ARG cc_start: 0.7627 (ttm-80) cc_final: 0.7180 (mtp85) REVERT: D 550 MET cc_start: 0.9071 (mtp) cc_final: 0.8817 (mtp) REVERT: E 522 CYS cc_start: 0.8386 (m) cc_final: 0.7924 (m) REVERT: E 742 PHE cc_start: 0.8935 (m-80) cc_final: 0.8127 (m-10) REVERT: F 488 GLU cc_start: 0.7795 (tp30) cc_final: 0.7384 (tt0) REVERT: F 756 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7995 (mm-30) outliers start: 26 outliers final: 15 residues processed: 170 average time/residue: 0.1038 time to fit residues: 25.9002 Evaluate side-chains 164 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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 550 MET Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain D residue 549 THR 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 38 optimal weight: 0.0470 chunk 131 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 167 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 165 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 overall best weight: 0.8882 ------------------------------------------------------------------------------- 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 = 0.3432 r_free = 0.3432 target = 0.125622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.097844 restraints weight = 20371.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.101216 restraints weight = 12264.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.103513 restraints weight = 8784.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.105002 restraints weight = 6995.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.106172 restraints weight = 5999.863| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 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 0.024 14262 Z= 0.118 Angle : 0.532 8.290 19224 Z= 0.245 Chirality : 0.041 0.125 2070 Planarity : 0.004 0.053 2502 Dihedral : 11.171 131.646 2012 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.43 % Allowed : 17.62 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.21), residues: 1698 helix: 2.19 (0.18), residues: 930 sheet: 0.26 (0.35), residues: 192 loop : -0.04 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 653 TYR 0.007 0.001 TYR B 495 PHE 0.010 0.001 PHE C 539 TRP 0.006 0.001 TRP F 476 HIS 0.002 0.001 HIS F 499 Details of bonding type rmsd covalent geometry : bond 0.00282 (14262) covalent geometry : angle 0.53154 (19224) hydrogen bonds : bond 0.03721 ( 674) hydrogen bonds : angle 3.18859 ( 1938) *********************** 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 179 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 0.565 Fit side-chains REVERT: A 669 ASP cc_start: 0.7507 (t70) cc_final: 0.6673 (t70) REVERT: C 560 ARG cc_start: 0.7625 (ttm-80) cc_final: 0.7146 (mtp85) REVERT: D 550 MET cc_start: 0.9054 (mtp) cc_final: 0.8785 (mtp) REVERT: E 522 CYS cc_start: 0.8383 (m) cc_final: 0.7907 (m) REVERT: E 742 PHE cc_start: 0.8932 (m-80) cc_final: 0.8055 (m-10) REVERT: F 488 GLU cc_start: 0.7796 (tp30) cc_final: 0.7474 (tp30) REVERT: F 512 LYS cc_start: 0.8194 (tppt) cc_final: 0.7843 (ttpt) REVERT: F 756 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7982 (mm-30) outliers start: 21 outliers final: 15 residues processed: 172 average time/residue: 0.1133 time to fit residues: 28.8435 Evaluate side-chains 164 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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 C residue 526 LEU Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 549 THR 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 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 9 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 133 optimal weight: 0.9990 chunk 44 optimal weight: 0.0670 chunk 158 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 147 optimal weight: 0.0370 chunk 165 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 overall best weight: 0.8200 ------------------------------------------------------------------------------- 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 = 0.3439 r_free = 0.3439 target = 0.126344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.098264 restraints weight = 20175.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.101732 restraints weight = 11880.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.104127 restraints weight = 8428.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.105732 restraints weight = 6661.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.106668 restraints weight = 5665.799| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14262 Z= 0.113 Angle : 0.531 8.833 19224 Z= 0.244 Chirality : 0.041 0.127 2070 Planarity : 0.004 0.053 2502 Dihedral : 10.867 134.522 2012 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.21), residues: 1698 helix: 2.22 (0.18), residues: 930 sheet: 0.24 (0.34), residues: 192 loop : -0.03 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 487 TYR 0.034 0.001 TYR F 517 PHE 0.011 0.001 PHE B 742 TRP 0.007 0.001 TRP F 476 HIS 0.001 0.001 HIS F 499 Details of bonding type rmsd covalent geometry : bond 0.00269 (14262) covalent geometry : angle 0.53080 (19224) hydrogen bonds : bond 0.03556 ( 674) hydrogen bonds : angle 3.11397 ( 1938) *********************** 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 182 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 0.587 Fit side-chains REVERT: A 669 ASP cc_start: 0.7430 (t70) cc_final: 0.6644 (t70) REVERT: C 560 ARG cc_start: 0.7589 (ttm-80) cc_final: 0.7096 (mtp85) REVERT: D 550 MET cc_start: 0.9043 (mtp) cc_final: 0.8775 (mtp) REVERT: E 512 LYS cc_start: 0.8429 (tppt) cc_final: 0.7821 (ttpt) REVERT: E 522 CYS cc_start: 0.8312 (m) cc_final: 0.7779 (m) REVERT: E 742 PHE cc_start: 0.8927 (m-80) cc_final: 0.8044 (m-10) REVERT: F 488 GLU cc_start: 0.7801 (tp30) cc_final: 0.7484 (tp30) REVERT: F 512 LYS cc_start: 0.8146 (tppt) cc_final: 0.7814 (ttpt) REVERT: F 668 LYS cc_start: 0.7937 (mmmt) cc_final: 0.6828 (tttt) REVERT: F 756 GLU cc_start: 0.8258 (mm-30) cc_final: 0.8030 (mm-30) outliers start: 25 outliers final: 16 residues processed: 173 average time/residue: 0.1114 time to fit residues: 28.3694 Evaluate side-chains 170 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 C residue 526 LEU Chi-restraints excluded: chain D residue 508 MET 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 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 158 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 chunk 109 optimal weight: 6.9990 chunk 160 optimal weight: 0.0570 chunk 129 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.9900 ------------------------------------------------------------------------------- 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 = 0.3614 r_free = 0.3614 target = 0.139629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.112476 restraints weight = 20053.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.115954 restraints weight = 12272.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.118263 restraints weight = 8847.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.119817 restraints weight = 7085.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.120890 restraints weight = 6082.080| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1752 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= 0.123 Angle : 0.536 8.820 19224 Z= 0.245 Chirality : 0.041 0.125 2070 Planarity : 0.004 0.053 2502 Dihedral : 10.811 136.092 2012 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.78 % Allowed : 17.83 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.83 (0.21), residues: 1698 helix: 2.21 (0.18), residues: 930 sheet: 0.25 (0.33), residues: 192 loop : -0.05 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 653 TYR 0.030 0.001 TYR F 517 PHE 0.016 0.001 PHE A 771 TRP 0.006 0.001 TRP F 476 HIS 0.004 0.001 HIS D 499 Details of bonding type rmsd covalent geometry : bond 0.00297 (14262) covalent geometry : angle 0.53636 (19224) hydrogen bonds : bond 0.03588 ( 674) hydrogen bonds : angle 3.10957 ( 1938) *********************** 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 182 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 0.563 Fit side-chains REVERT: A 669 ASP cc_start: 0.7386 (t70) cc_final: 0.6649 (t70) REVERT: D 550 MET cc_start: 0.9078 (mtp) cc_final: 0.8811 (mtp) REVERT: E 512 LYS cc_start: 0.8461 (tppt) cc_final: 0.7948 (ttpt) REVERT: E 522 CYS cc_start: 0.8217 (m) cc_final: 0.7716 (m) REVERT: E 742 PHE cc_start: 0.8961 (m-80) cc_final: 0.8147 (m-10) REVERT: F 488 GLU cc_start: 0.7817 (tp30) cc_final: 0.7585 (tp30) REVERT: F 512 LYS cc_start: 0.8197 (tppt) cc_final: 0.7910 (ttpt) outliers start: 26 outliers final: 19 residues processed: 171 average time/residue: 0.1118 time to fit residues: 28.6668 Evaluate side-chains 175 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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 C residue 526 LEU Chi-restraints excluded: chain C residue 703 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 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 489 LEU Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain F residue 647 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 18 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 120 optimal weight: 0.3980 chunk 67 optimal weight: 1.9990 chunk 40 optimal weight: 0.2980 chunk 17 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3640 r_free = 0.3640 target = 0.142607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.114708 restraints weight = 20065.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.118240 restraints weight = 12425.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.120558 restraints weight = 9012.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.122190 restraints weight = 7260.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.123212 restraints weight = 6228.108| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1837 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= 0.108 Angle : 0.526 9.074 19224 Z= 0.242 Chirality : 0.041 0.123 2070 Planarity : 0.004 0.053 2502 Dihedral : 10.713 134.964 2012 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.78 % Allowed : 17.62 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.89 (0.21), residues: 1698 helix: 2.24 (0.17), residues: 930 sheet: 0.36 (0.33), residues: 192 loop : -0.03 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 653 TYR 0.031 0.001 TYR F 517 PHE 0.016 0.001 PHE B 742 TRP 0.006 0.001 TRP F 476 HIS 0.002 0.001 HIS D 499 Details of bonding type rmsd covalent geometry : bond 0.00254 (14262) covalent geometry : angle 0.52594 (19224) hydrogen bonds : bond 0.03368 ( 674) hydrogen bonds : angle 3.04033 ( 1938) *********************** 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 194 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 0.444 Fit side-chains REVERT: A 669 ASP cc_start: 0.7385 (t70) cc_final: 0.6635 (t70) REVERT: A 772 ARG cc_start: 0.7871 (ptt180) cc_final: 0.7575 (ptt90) REVERT: C 731 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8241 (mp) REVERT: D 550 MET cc_start: 0.9062 (mtp) cc_final: 0.8798 (mtp) REVERT: E 512 LYS cc_start: 0.8450 (tppt) cc_final: 0.7952 (ttpt) REVERT: E 522 CYS cc_start: 0.8145 (m) cc_final: 0.7656 (m) REVERT: E 742 PHE cc_start: 0.8906 (m-80) cc_final: 0.8086 (m-10) REVERT: F 488 GLU cc_start: 0.7818 (tp30) cc_final: 0.7601 (tp30) REVERT: F 512 LYS cc_start: 0.8195 (tppt) cc_final: 0.7912 (ttpt) REVERT: F 669 ASP cc_start: 0.7585 (t70) cc_final: 0.6685 (t70) outliers start: 26 outliers final: 20 residues processed: 184 average time/residue: 0.1068 time to fit residues: 29.0669 Evaluate side-chains 178 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 0.540 ------------------------------------------------------------------------------- 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 731 ILE Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain D residue 508 MET 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 163 optimal weight: 3.9990 chunk 147 optimal weight: 0.0770 chunk 77 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 116 optimal weight: 4.9990 chunk 124 optimal weight: 9.9990 chunk 154 optimal weight: 0.3980 chunk 24 optimal weight: 9.9990 overall best weight: 1.4342 ------------------------------------------------------------------------------- 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 = 0.3613 r_free = 0.3613 target = 0.140298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.112022 restraints weight = 20329.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.115497 restraints weight = 12720.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.117824 restraints weight = 9277.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.119336 restraints weight = 7492.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.120430 restraints weight = 6479.825| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 14262 Z= 0.156 Angle : 0.570 9.520 19224 Z= 0.260 Chirality : 0.042 0.127 2070 Planarity : 0.004 0.054 2502 Dihedral : 10.922 138.144 2012 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.91 % Allowed : 18.10 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.21), residues: 1698 helix: 2.19 (0.18), residues: 930 sheet: 0.29 (0.33), residues: 192 loop : -0.03 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 653 TYR 0.030 0.001 TYR F 517 PHE 0.011 0.001 PHE B 742 TRP 0.007 0.001 TRP F 476 HIS 0.003 0.001 HIS D 499 Details of bonding type rmsd covalent geometry : bond 0.00384 (14262) covalent geometry : angle 0.56987 (19224) hydrogen bonds : bond 0.03864 ( 674) hydrogen bonds : angle 3.18693 ( 1938) *********************** 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 183 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 0.456 Fit side-chains REVERT: A 669 ASP cc_start: 0.7398 (t70) cc_final: 0.6655 (t70) REVERT: D 550 MET cc_start: 0.9134 (mtp) cc_final: 0.8835 (mtp) REVERT: E 512 LYS cc_start: 0.8506 (tppt) cc_final: 0.7950 (ttpt) REVERT: E 522 CYS cc_start: 0.8281 (m) cc_final: 0.7802 (m) REVERT: E 742 PHE cc_start: 0.8955 (m-80) cc_final: 0.8108 (m-10) REVERT: F 488 GLU cc_start: 0.7848 (tp30) cc_final: 0.7623 (tp30) REVERT: F 512 LYS cc_start: 0.8280 (tppt) cc_final: 0.7980 (ttpt) REVERT: F 669 ASP cc_start: 0.7610 (t70) cc_final: 0.6827 (t70) outliers start: 28 outliers final: 22 residues processed: 173 average time/residue: 0.1031 time to fit residues: 26.9162 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 : 0.588 ------------------------------------------------------------------------------- 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 550 MET 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 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 489 LEU Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 527 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 143 optimal weight: 0.8980 chunk 147 optimal weight: 0.0770 chunk 93 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 73 optimal weight: 0.0270 chunk 68 optimal weight: 0.1980 chunk 123 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- 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 = 0.3458 r_free = 0.3458 target = 0.127622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.099659 restraints weight = 20104.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.103056 restraints weight = 12189.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.105379 restraints weight = 8765.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.106955 restraints weight = 7009.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.108037 restraints weight = 5988.571| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14262 Z= 0.099 Angle : 0.533 9.063 19224 Z= 0.244 Chirality : 0.041 0.128 2070 Planarity : 0.004 0.053 2502 Dihedral : 10.431 132.146 2012 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.64 % Allowed : 18.58 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.88 (0.21), residues: 1698 helix: 2.20 (0.18), residues: 936 sheet: 0.46 (0.33), residues: 192 loop : -0.02 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 586 TYR 0.030 0.001 TYR F 517 PHE 0.013 0.001 PHE B 742 TRP 0.005 0.001 TRP F 476 HIS 0.002 0.001 HIS F 499 Details of bonding type rmsd covalent geometry : bond 0.00227 (14262) covalent geometry : angle 0.53323 (19224) hydrogen bonds : bond 0.03230 ( 674) hydrogen bonds : angle 2.99414 ( 1938) ********************** 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 187 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 0.531 Fit side-chains REVERT: A 669 ASP cc_start: 0.7325 (t70) cc_final: 0.6540 (t70) REVERT: D 550 MET cc_start: 0.9001 (mtp) cc_final: 0.8734 (mtp) REVERT: E 512 LYS cc_start: 0.8365 (tppt) cc_final: 0.7788 (ttpt) REVERT: E 522 CYS cc_start: 0.8142 (m) cc_final: 0.7617 (m) REVERT: E 742 PHE cc_start: 0.8840 (m-80) cc_final: 0.7976 (m-10) REVERT: F 488 GLU cc_start: 0.7815 (tp30) cc_final: 0.7496 (tp30) REVERT: F 512 LYS cc_start: 0.8180 (tppt) cc_final: 0.7848 (ttpt) outliers start: 24 outliers final: 21 residues processed: 176 average time/residue: 0.1062 time to fit residues: 27.8969 Evaluate side-chains 178 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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 762 LEU Chi-restraints excluded: chain D residue 508 MET 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 642 LEU 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 28 optimal weight: 4.9990 chunk 133 optimal weight: 0.8980 chunk 115 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 104 optimal weight: 5.9990 chunk 126 optimal weight: 0.8980 chunk 41 optimal weight: 0.2980 chunk 16 optimal weight: 0.0020 chunk 55 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- 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 = 0.3651 r_free = 0.3651 target = 0.143463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.115572 restraints weight = 20201.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.119115 restraints weight = 12494.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.121494 restraints weight = 9080.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.123135 restraints weight = 7289.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.124039 restraints weight = 6241.523| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14262 Z= 0.100 Angle : 0.534 9.181 19224 Z= 0.242 Chirality : 0.040 0.153 2070 Planarity : 0.004 0.053 2502 Dihedral : 10.095 130.156 2012 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.95 (0.21), residues: 1698 helix: 2.33 (0.17), residues: 924 sheet: 0.49 (0.33), residues: 192 loop : -0.09 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 653 TYR 0.028 0.001 TYR F 517 PHE 0.014 0.001 PHE A 742 TRP 0.005 0.001 TRP F 476 HIS 0.002 0.001 HIS D 499 Details of bonding type rmsd covalent geometry : bond 0.00231 (14262) covalent geometry : angle 0.53374 (19224) hydrogen bonds : bond 0.03148 ( 674) hydrogen bonds : angle 2.97627 ( 1938) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 1801.35 seconds wall clock time: 31 minutes 38.08 seconds (1898.08 seconds total)