Starting phenix.real_space_refine on Wed May 14 21:00:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9go3_51489/05_2025/9go3_51489.cif Found real_map, /net/cci-nas-00/data/ceres_data/9go3_51489/05_2025/9go3_51489.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9go3_51489/05_2025/9go3_51489.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9go3_51489/05_2025/9go3_51489.map" model { file = "/net/cci-nas-00/data/ceres_data/9go3_51489/05_2025/9go3_51489.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9go3_51489/05_2025/9go3_51489.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.033 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: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 7686 2.51 5 N 2149 2.21 5 O 2331 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 12187 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1741 Classifications: {'peptide': 253} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 8, 'TRANS': 244} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 191 Unresolved non-hydrogen angles: 249 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 82 Chain: "B" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1741 Classifications: {'peptide': 253} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 8, 'TRANS': 244} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 191 Unresolved non-hydrogen angles: 249 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 82 Chain: "C" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1741 Classifications: {'peptide': 253} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 8, 'TRANS': 244} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 191 Unresolved non-hydrogen angles: 249 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 82 Chain: "D" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1741 Classifications: {'peptide': 253} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 8, 'TRANS': 244} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 191 Unresolved non-hydrogen angles: 249 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 82 Chain: "E" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1741 Classifications: {'peptide': 253} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 8, 'TRANS': 244} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 191 Unresolved non-hydrogen angles: 249 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 82 Chain: "F" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1741 Classifications: {'peptide': 253} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 8, 'TRANS': 244} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 191 Unresolved non-hydrogen angles: 249 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 82 Chain: "G" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1741 Classifications: {'peptide': 253} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 8, 'TRANS': 244} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 191 Unresolved non-hydrogen angles: 249 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 82 Time building chain proxies: 4.61, per 1000 atoms: 0.38 Number of scatterers: 12187 At special positions: 0 Unit cell: (101.38, 99.9, 113.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 21 16.00 O 2331 8.00 N 2149 7.00 C 7686 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: 2.97 Conformation dependent library (CDL) restraints added in 1.8 seconds 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3248 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 9 sheets defined 54.6% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 471 through 498 Processing helix chain 'A' and resid 506 through 532 Processing helix chain 'A' and resid 537 through 555 Processing helix chain 'A' and resid 555 through 571 Processing helix chain 'A' and resid 638 through 656 removed outlier: 3.632A pdb=" N ALA A 642 " --> pdb=" O ASP A 638 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN A 656 " --> pdb=" O GLU A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 663 Processing helix chain 'A' and resid 692 through 712 removed outlier: 3.506A pdb=" N VAL A 696 " --> pdb=" O LYS A 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 498 Processing helix chain 'B' and resid 506 through 532 Processing helix chain 'B' and resid 537 through 555 Processing helix chain 'B' and resid 555 through 571 Processing helix chain 'B' and resid 638 through 656 removed outlier: 3.598A pdb=" N ALA B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN B 656 " --> pdb=" O GLU B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 663 Processing helix chain 'B' and resid 692 through 712 removed outlier: 3.512A pdb=" N VAL B 696 " --> pdb=" O LYS B 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 498 Processing helix chain 'C' and resid 506 through 532 Processing helix chain 'C' and resid 537 through 555 Processing helix chain 'C' and resid 555 through 571 Processing helix chain 'C' and resid 638 through 656 removed outlier: 3.598A pdb=" N ALA C 642 " --> pdb=" O ASP C 638 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN C 656 " --> pdb=" O GLU C 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 663 Processing helix chain 'C' and resid 692 through 712 Processing helix chain 'D' and resid 472 through 498 Processing helix chain 'D' and resid 506 through 532 Processing helix chain 'D' and resid 537 through 555 Processing helix chain 'D' and resid 555 through 571 Processing helix chain 'D' and resid 638 through 656 removed outlier: 3.640A pdb=" N ALA D 642 " --> pdb=" O ASP D 638 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN D 656 " --> pdb=" O GLU D 652 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 663 Processing helix chain 'D' and resid 692 through 712 removed outlier: 3.511A pdb=" N VAL D 696 " --> pdb=" O LYS D 692 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 498 Processing helix chain 'E' and resid 506 through 532 Processing helix chain 'E' and resid 537 through 555 Processing helix chain 'E' and resid 555 through 571 Processing helix chain 'E' and resid 638 through 656 removed outlier: 3.648A pdb=" N ALA E 642 " --> pdb=" O ASP E 638 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN E 656 " --> pdb=" O GLU E 652 " (cutoff:3.500A) Processing helix chain 'E' and resid 656 through 663 Processing helix chain 'E' and resid 692 through 712 Processing helix chain 'F' and resid 472 through 498 Processing helix chain 'F' and resid 506 through 532 Processing helix chain 'F' and resid 537 through 555 Processing helix chain 'F' and resid 555 through 571 Processing helix chain 'F' and resid 638 through 656 removed outlier: 3.583A pdb=" N ALA F 642 " --> pdb=" O ASP F 638 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN F 656 " --> pdb=" O GLU F 652 " (cutoff:3.500A) Processing helix chain 'F' and resid 656 through 663 Processing helix chain 'F' and resid 692 through 712 Processing helix chain 'G' and resid 472 through 498 Processing helix chain 'G' and resid 506 through 532 Processing helix chain 'G' and resid 537 through 555 Processing helix chain 'G' and resid 555 through 571 Processing helix chain 'G' and resid 638 through 656 removed outlier: 3.638A pdb=" N ALA G 642 " --> pdb=" O ASP G 638 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN G 656 " --> pdb=" O GLU G 652 " (cutoff:3.500A) Processing helix chain 'G' and resid 656 through 663 Processing helix chain 'G' and resid 692 through 712 removed outlier: 3.512A pdb=" N VAL G 696 " --> pdb=" O LYS G 692 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 579 through 582 removed outlier: 5.856A pdb=" N VAL A 589 " --> pdb=" O ARG A 600 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ARG A 600 " --> pdb=" O VAL A 589 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG A 591 " --> pdb=" O GLY A 598 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N PHE G 617 " --> pdb=" O ILE A 608 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N VAL G 589 " --> pdb=" O ARG G 600 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ARG G 600 " --> pdb=" O VAL G 589 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG G 591 " --> pdb=" O GLY G 598 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE F 617 " --> pdb=" O ILE G 608 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N VAL F 589 " --> pdb=" O ARG F 600 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ARG F 600 " --> pdb=" O VAL F 589 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG F 591 " --> pdb=" O GLY F 598 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE E 617 " --> pdb=" O ILE F 608 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N VAL E 589 " --> pdb=" O ARG E 600 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ARG E 600 " --> pdb=" O VAL E 589 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG E 591 " --> pdb=" O GLY E 598 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE D 617 " --> pdb=" O ILE E 608 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N VAL D 589 " --> pdb=" O ARG D 600 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ARG D 600 " --> pdb=" O VAL D 589 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG D 591 " --> pdb=" O GLY D 598 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N PHE C 617 " --> pdb=" O ILE D 608 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL C 589 " --> pdb=" O ARG C 600 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ARG C 600 " --> pdb=" O VAL C 589 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG C 591 " --> pdb=" O GLY C 598 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE B 617 " --> pdb=" O ILE C 608 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N VAL B 589 " --> pdb=" O ARG B 600 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ARG B 600 " --> pdb=" O VAL B 589 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG B 591 " --> pdb=" O GLY B 598 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE A 617 " --> pdb=" O ILE B 608 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 625 through 634 removed outlier: 3.598A pdb=" N VAL A 627 " --> pdb=" O PHE A 686 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ALA A 679 " --> pdb=" O GLY A 674 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N GLY A 674 " --> pdb=" O ALA A 679 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N THR A 681 " --> pdb=" O ILE A 672 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ILE A 672 " --> pdb=" O THR A 681 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ARG A 683 " --> pdb=" O ALA A 670 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 718 through 722 Processing sheet with id=AA4, first strand: chain 'B' and resid 625 through 634 removed outlier: 3.623A pdb=" N VAL B 627 " --> pdb=" O PHE B 686 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ALA B 679 " --> pdb=" O GLY B 674 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N GLY B 674 " --> pdb=" O ALA B 679 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N THR B 681 " --> pdb=" O ILE B 672 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE B 672 " --> pdb=" O THR B 681 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ARG B 683 " --> pdb=" O ALA B 670 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 625 through 634 removed outlier: 3.557A pdb=" N VAL C 627 " --> pdb=" O PHE C 686 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ALA C 679 " --> pdb=" O GLY C 674 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N GLY C 674 " --> pdb=" O ALA C 679 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR C 681 " --> pdb=" O ILE C 672 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE C 672 " --> pdb=" O THR C 681 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ARG C 683 " --> pdb=" O ALA C 670 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 625 through 634 removed outlier: 3.585A pdb=" N VAL D 627 " --> pdb=" O PHE D 686 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ALA D 679 " --> pdb=" O GLY D 674 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N GLY D 674 " --> pdb=" O ALA D 679 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N THR D 681 " --> pdb=" O ILE D 672 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE D 672 " --> pdb=" O THR D 681 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ARG D 683 " --> pdb=" O ALA D 670 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 625 through 634 removed outlier: 3.610A pdb=" N VAL E 627 " --> pdb=" O PHE E 686 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ALA E 679 " --> pdb=" O GLY E 674 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N GLY E 674 " --> pdb=" O ALA E 679 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N THR E 681 " --> pdb=" O ILE E 672 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE E 672 " --> pdb=" O THR E 681 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ARG E 683 " --> pdb=" O ALA E 670 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 625 through 634 removed outlier: 3.599A pdb=" N VAL F 627 " --> pdb=" O PHE F 686 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ALA F 679 " --> pdb=" O GLY F 674 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N GLY F 674 " --> pdb=" O ALA F 679 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N THR F 681 " --> pdb=" O ILE F 672 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE F 672 " --> pdb=" O THR F 681 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ARG F 683 " --> pdb=" O ALA F 670 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 625 through 634 removed outlier: 3.635A pdb=" N VAL G 627 " --> pdb=" O PHE G 686 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ALA G 679 " --> pdb=" O GLY G 674 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N GLY G 674 " --> pdb=" O ALA G 679 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N THR G 681 " --> pdb=" O ILE G 672 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ILE G 672 " --> pdb=" O THR G 681 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ARG G 683 " --> pdb=" O ALA G 670 " (cutoff:3.500A) 956 hydrogen bonds defined for protein. 2763 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.82 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4214 1.34 - 1.46: 1510 1.46 - 1.57: 6596 1.57 - 1.69: 0 1.69 - 1.80: 42 Bond restraints: 12362 Sorted by residual: bond pdb=" CB GLU F 652 " pdb=" CG GLU F 652 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.91e+00 bond pdb=" C ALA A 538 " pdb=" N PRO A 539 " ideal model delta sigma weight residual 1.335 1.348 -0.013 1.30e-02 5.92e+03 9.48e-01 bond pdb=" N PRO A 502 " pdb=" CA PRO A 502 " ideal model delta sigma weight residual 1.468 1.475 -0.008 7.90e-03 1.60e+04 9.40e-01 bond pdb=" C ALA F 538 " pdb=" N PRO F 539 " ideal model delta sigma weight residual 1.335 1.348 -0.012 1.30e-02 5.92e+03 9.19e-01 bond pdb=" N PRO C 502 " pdb=" CA PRO C 502 " ideal model delta sigma weight residual 1.468 1.475 -0.008 7.90e-03 1.60e+04 9.05e-01 ... (remaining 12357 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 16274 1.27 - 2.54: 501 2.54 - 3.81: 87 3.81 - 5.08: 27 5.08 - 6.35: 2 Bond angle restraints: 16891 Sorted by residual: angle pdb=" N VAL G 673 " pdb=" CA VAL G 673 " pdb=" C VAL G 673 " ideal model delta sigma weight residual 113.10 109.80 3.30 9.70e-01 1.06e+00 1.16e+01 angle pdb=" N VAL D 673 " pdb=" CA VAL D 673 " pdb=" C VAL D 673 " ideal model delta sigma weight residual 113.10 109.83 3.27 9.70e-01 1.06e+00 1.14e+01 angle pdb=" N VAL C 673 " pdb=" CA VAL C 673 " pdb=" C VAL C 673 " ideal model delta sigma weight residual 113.10 109.88 3.22 9.70e-01 1.06e+00 1.10e+01 angle pdb=" N VAL A 673 " pdb=" CA VAL A 673 " pdb=" C VAL A 673 " ideal model delta sigma weight residual 113.20 110.05 3.15 9.60e-01 1.09e+00 1.07e+01 angle pdb=" N VAL B 673 " pdb=" CA VAL B 673 " pdb=" C VAL B 673 " ideal model delta sigma weight residual 113.10 109.96 3.14 9.70e-01 1.06e+00 1.05e+01 ... (remaining 16886 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 6561 17.81 - 35.62: 531 35.62 - 53.43: 134 53.43 - 71.24: 19 71.24 - 89.05: 14 Dihedral angle restraints: 7259 sinusoidal: 2226 harmonic: 5033 Sorted by residual: dihedral pdb=" CA ASN G 656 " pdb=" C ASN G 656 " pdb=" N GLU G 657 " pdb=" CA GLU G 657 " ideal model delta harmonic sigma weight residual -180.00 -163.05 -16.95 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CB GLU F 571 " pdb=" CG GLU F 571 " pdb=" CD GLU F 571 " pdb=" OE1 GLU F 571 " ideal model delta sinusoidal sigma weight residual 0.00 -89.05 89.05 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU G 571 " pdb=" CG GLU G 571 " pdb=" CD GLU G 571 " pdb=" OE1 GLU G 571 " ideal model delta sinusoidal sigma weight residual 0.00 89.02 -89.02 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 7256 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1320 0.030 - 0.061: 450 0.061 - 0.091: 177 0.091 - 0.122: 118 0.122 - 0.152: 14 Chirality restraints: 2079 Sorted by residual: chirality pdb=" CA GLU B 657 " pdb=" N GLU B 657 " pdb=" C GLU B 657 " pdb=" CB GLU B 657 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.77e-01 chirality pdb=" CA ILE F 624 " pdb=" N ILE F 624 " pdb=" C ILE F 624 " pdb=" CB ILE F 624 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.67e-01 chirality pdb=" CA ILE B 624 " pdb=" N ILE B 624 " pdb=" C ILE B 624 " pdb=" CB ILE B 624 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.59e-01 ... (remaining 2076 not shown) Planarity restraints: 2226 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU F 652 " 0.011 2.00e-02 2.50e+03 2.18e-02 4.74e+00 pdb=" CD GLU F 652 " -0.038 2.00e-02 2.50e+03 pdb=" OE1 GLU F 652 " 0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU F 652 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 652 " -0.009 2.00e-02 2.50e+03 1.87e-02 3.49e+00 pdb=" CD GLU B 652 " 0.032 2.00e-02 2.50e+03 pdb=" OE1 GLU B 652 " -0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU B 652 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU G 652 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.42e+00 pdb=" CD GLU G 652 " -0.032 2.00e-02 2.50e+03 pdb=" OE1 GLU G 652 " 0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU G 652 " 0.011 2.00e-02 2.50e+03 ... (remaining 2223 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1662 2.75 - 3.29: 12316 3.29 - 3.83: 20961 3.83 - 4.36: 22390 4.36 - 4.90: 40124 Nonbonded interactions: 97453 Sorted by model distance: nonbonded pdb=" OD1 ASP C 561 " pdb=" OG SER C 612 " model vdw 2.215 3.040 nonbonded pdb=" OD1 ASP F 561 " pdb=" OG SER F 612 " model vdw 2.216 3.040 nonbonded pdb=" OD1 ASP G 561 " pdb=" OG SER G 612 " model vdw 2.220 3.040 nonbonded pdb=" OD1 ASP E 561 " pdb=" OG SER E 612 " model vdw 2.223 3.040 nonbonded pdb=" OD1 ASP D 561 " pdb=" OG SER D 612 " model vdw 2.226 3.040 ... (remaining 97448 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 45.890 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 20.210 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 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 : 0.003 0.041 12362 Z= 0.134 Angle : 0.537 6.351 16891 Z= 0.340 Chirality : 0.042 0.152 2079 Planarity : 0.003 0.031 2226 Dihedral : 15.181 89.048 4011 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.34 % Allowed : 1.48 % Favored : 98.18 % Rotamer: Outliers : 0.38 % Allowed : 22.67 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.20), residues: 1757 helix: 3.66 (0.16), residues: 924 sheet: 0.76 (0.31), residues: 259 loop : -1.18 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 694 HIS 0.004 0.001 HIS A 636 PHE 0.007 0.001 PHE D 680 TYR 0.014 0.002 TYR G 720 ARG 0.002 0.000 ARG F 600 Details of bonding type rmsd hydrogen bonds : bond 0.16405 ( 956) hydrogen bonds : angle 5.54331 ( 2763) covalent geometry : bond 0.00251 (12362) covalent geometry : angle 0.53657 (16891) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 155 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 677 ASN cc_start: 0.7765 (m-40) cc_final: 0.7211 (t0) REVERT: B 720 TYR cc_start: 0.5056 (p90) cc_final: 0.4573 (p90) REVERT: C 677 ASN cc_start: 0.7674 (m-40) cc_final: 0.7126 (m-40) REVERT: D 677 ASN cc_start: 0.7839 (m-40) cc_final: 0.7409 (t0) REVERT: E 677 ASN cc_start: 0.7807 (m-40) cc_final: 0.7541 (t0) REVERT: G 592 MET cc_start: 0.6966 (mtt) cc_final: 0.6551 (mtt) outliers start: 4 outliers final: 2 residues processed: 158 average time/residue: 0.2406 time to fit residues: 55.7393 Evaluate side-chains 97 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 95 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 561 ASP Chi-restraints excluded: chain E residue 561 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 137 optimal weight: 0.3980 chunk 53 optimal weight: 0.3980 chunk 83 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 chunk 158 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3213 r_free = 0.3213 target = 0.038605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.028878 restraints weight = 99838.526| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 4.89 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12362 Z= 0.139 Angle : 0.566 5.020 16891 Z= 0.324 Chirality : 0.043 0.154 2079 Planarity : 0.004 0.043 2226 Dihedral : 3.904 16.984 1845 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.40 % Allowed : 1.25 % Favored : 98.35 % Rotamer: Outliers : 1.52 % Allowed : 22.48 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.20), residues: 1757 helix: 3.42 (0.15), residues: 952 sheet: 0.76 (0.30), residues: 245 loop : -0.88 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 694 HIS 0.001 0.000 HIS G 636 PHE 0.008 0.001 PHE F 567 TYR 0.031 0.003 TYR G 720 ARG 0.005 0.000 ARG D 635 Details of bonding type rmsd hydrogen bonds : bond 0.04580 ( 956) hydrogen bonds : angle 4.47518 ( 2763) covalent geometry : bond 0.00273 (12362) covalent geometry : angle 0.56597 (16891) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 1.394 Fit side-chains revert: symmetry clash REVERT: B 701 ASP cc_start: 0.9058 (m-30) cc_final: 0.8824 (m-30) REVERT: D 561 ASP cc_start: 0.9052 (m-30) cc_final: 0.8834 (m-30) REVERT: E 561 ASP cc_start: 0.9043 (m-30) cc_final: 0.8808 (m-30) REVERT: G 632 ASP cc_start: 0.8448 (p0) cc_final: 0.7908 (p0) outliers start: 16 outliers final: 12 residues processed: 114 average time/residue: 0.1723 time to fit residues: 32.4522 Evaluate side-chains 104 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 720 TYR Chi-restraints excluded: chain D residue 687 THR Chi-restraints excluded: chain D residue 720 TYR Chi-restraints excluded: chain E residue 592 MET Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain E residue 720 TYR Chi-restraints excluded: chain F residue 687 THR Chi-restraints excluded: chain F residue 720 TYR Chi-restraints excluded: chain G residue 720 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 18 optimal weight: 0.1980 chunk 25 optimal weight: 80.0000 chunk 170 optimal weight: 0.3980 chunk 150 optimal weight: 70.0000 chunk 174 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 chunk 96 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 138 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3202 r_free = 0.3202 target = 0.038209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.028521 restraints weight = 102964.302| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 4.77 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12362 Z= 0.112 Angle : 0.493 5.410 16891 Z= 0.280 Chirality : 0.042 0.143 2079 Planarity : 0.003 0.040 2226 Dihedral : 3.698 14.798 1841 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.40 % Allowed : 1.82 % Favored : 97.78 % Rotamer: Outliers : 1.52 % Allowed : 23.52 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.20), residues: 1757 helix: 3.43 (0.15), residues: 952 sheet: 0.61 (0.30), residues: 245 loop : -0.78 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 694 HIS 0.001 0.000 HIS A 636 PHE 0.006 0.001 PHE F 567 TYR 0.031 0.003 TYR G 720 ARG 0.004 0.000 ARG E 635 Details of bonding type rmsd hydrogen bonds : bond 0.03820 ( 956) hydrogen bonds : angle 4.12400 ( 2763) covalent geometry : bond 0.00211 (12362) covalent geometry : angle 0.49306 (16891) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 1.441 Fit side-chains revert: symmetry clash REVERT: C 632 ASP cc_start: 0.8582 (p0) cc_final: 0.8346 (p0) REVERT: D 561 ASP cc_start: 0.9069 (m-30) cc_final: 0.8866 (m-30) REVERT: D 632 ASP cc_start: 0.8533 (p0) cc_final: 0.8269 (p0) REVERT: F 632 ASP cc_start: 0.8548 (p0) cc_final: 0.8290 (p0) REVERT: G 632 ASP cc_start: 0.8495 (p0) cc_final: 0.8080 (p0) outliers start: 16 outliers final: 13 residues processed: 108 average time/residue: 0.1723 time to fit residues: 30.8740 Evaluate side-chains 102 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain C residue 720 TYR Chi-restraints excluded: chain D residue 687 THR Chi-restraints excluded: chain D residue 688 THR Chi-restraints excluded: chain D residue 720 TYR Chi-restraints excluded: chain E residue 720 TYR Chi-restraints excluded: chain F residue 687 THR Chi-restraints excluded: chain F residue 688 THR Chi-restraints excluded: chain F residue 720 TYR Chi-restraints excluded: chain G residue 688 THR Chi-restraints excluded: chain G residue 720 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 38 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 150 optimal weight: 80.0000 chunk 98 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 155 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 chunk 80 optimal weight: 8.9990 chunk 42 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 644 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.036541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.027187 restraints weight = 106004.761| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 4.66 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12362 Z= 0.167 Angle : 0.498 5.671 16891 Z= 0.284 Chirality : 0.042 0.142 2079 Planarity : 0.003 0.038 2226 Dihedral : 3.632 13.769 1841 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.34 % Allowed : 1.88 % Favored : 97.78 % Rotamer: Outliers : 3.43 % Allowed : 23.52 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.20), residues: 1757 helix: 3.71 (0.15), residues: 952 sheet: 0.40 (0.29), residues: 245 loop : -0.83 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 694 HIS 0.002 0.001 HIS D 636 PHE 0.012 0.001 PHE F 567 TYR 0.028 0.003 TYR G 720 ARG 0.003 0.000 ARG D 635 Details of bonding type rmsd hydrogen bonds : bond 0.03584 ( 956) hydrogen bonds : angle 4.20094 ( 2763) covalent geometry : bond 0.00332 (12362) covalent geometry : angle 0.49832 (16891) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 95 time to evaluate : 1.545 Fit side-chains revert: symmetry clash REVERT: D 561 ASP cc_start: 0.9160 (m-30) cc_final: 0.8949 (m-30) REVERT: D 632 ASP cc_start: 0.8569 (p0) cc_final: 0.8312 (p0) REVERT: F 632 ASP cc_start: 0.8665 (p0) cc_final: 0.8331 (p0) REVERT: G 632 ASP cc_start: 0.8569 (p0) cc_final: 0.8107 (p0) outliers start: 36 outliers final: 25 residues processed: 125 average time/residue: 0.1676 time to fit residues: 34.9746 Evaluate side-chains 104 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 720 TYR Chi-restraints excluded: chain D residue 687 THR Chi-restraints excluded: chain D residue 688 THR Chi-restraints excluded: chain D residue 720 TYR Chi-restraints excluded: chain E residue 597 VAL Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain E residue 695 THR Chi-restraints excluded: chain E residue 720 TYR Chi-restraints excluded: chain F residue 597 VAL Chi-restraints excluded: chain F residue 687 THR Chi-restraints excluded: chain F residue 688 THR Chi-restraints excluded: chain F residue 695 THR Chi-restraints excluded: chain F residue 720 TYR Chi-restraints excluded: chain G residue 597 VAL Chi-restraints excluded: chain G residue 688 THR Chi-restraints excluded: chain G residue 695 THR Chi-restraints excluded: chain G residue 720 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 3 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 15 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 40 optimal weight: 8.9990 chunk 152 optimal weight: 50.0000 chunk 78 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 126 optimal weight: 9.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.3157 r_free = 0.3157 target = 0.036396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.027058 restraints weight = 101265.955| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 4.67 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12362 Z= 0.115 Angle : 0.502 7.025 16891 Z= 0.280 Chirality : 0.043 0.136 2079 Planarity : 0.003 0.036 2226 Dihedral : 3.567 14.729 1841 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.34 % Allowed : 1.71 % Favored : 97.95 % Rotamer: Outliers : 2.10 % Allowed : 24.00 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.89 (0.20), residues: 1757 helix: 3.69 (0.15), residues: 952 sheet: 0.41 (0.30), residues: 245 loop : -0.68 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 694 HIS 0.001 0.001 HIS A 636 PHE 0.008 0.001 PHE E 567 TYR 0.029 0.002 TYR G 720 ARG 0.002 0.000 ARG D 635 Details of bonding type rmsd hydrogen bonds : bond 0.03369 ( 956) hydrogen bonds : angle 3.94484 ( 2763) covalent geometry : bond 0.00226 (12362) covalent geometry : angle 0.50211 (16891) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 1.362 Fit side-chains revert: symmetry clash REVERT: D 561 ASP cc_start: 0.9093 (m-30) cc_final: 0.8878 (m-30) REVERT: D 632 ASP cc_start: 0.8610 (p0) cc_final: 0.8300 (p0) REVERT: F 632 ASP cc_start: 0.8598 (p0) cc_final: 0.8269 (p0) REVERT: G 632 ASP cc_start: 0.8513 (p0) cc_final: 0.8035 (p0) outliers start: 22 outliers final: 14 residues processed: 108 average time/residue: 0.1694 time to fit residues: 31.0565 Evaluate side-chains 90 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain C residue 720 TYR Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 687 THR Chi-restraints excluded: chain D residue 720 TYR Chi-restraints excluded: chain E residue 720 TYR Chi-restraints excluded: chain F residue 687 THR Chi-restraints excluded: chain F residue 688 THR Chi-restraints excluded: chain F residue 720 TYR Chi-restraints excluded: chain G residue 688 THR Chi-restraints excluded: chain G residue 720 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 86 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 111 optimal weight: 0.0010 chunk 97 optimal weight: 5.9990 chunk 125 optimal weight: 80.0000 chunk 9 optimal weight: 4.9990 chunk 2 optimal weight: 50.0000 chunk 166 optimal weight: 0.8980 chunk 147 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- 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 = 0.3154 r_free = 0.3154 target = 0.036337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.027064 restraints weight = 103438.260| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 4.70 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12362 Z= 0.102 Angle : 0.480 8.945 16891 Z= 0.267 Chirality : 0.043 0.138 2079 Planarity : 0.003 0.036 2226 Dihedral : 3.528 13.431 1841 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.90 % Allowed : 24.29 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.92 (0.20), residues: 1757 helix: 3.71 (0.15), residues: 952 sheet: 0.39 (0.30), residues: 245 loop : -0.63 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 694 HIS 0.001 0.000 HIS D 636 PHE 0.008 0.001 PHE E 567 TYR 0.027 0.002 TYR G 720 ARG 0.002 0.000 ARG E 635 Details of bonding type rmsd hydrogen bonds : bond 0.03232 ( 956) hydrogen bonds : angle 4.01403 ( 2763) covalent geometry : bond 0.00198 (12362) covalent geometry : angle 0.48025 (16891) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 1.494 Fit side-chains revert: symmetry clash REVERT: D 561 ASP cc_start: 0.9122 (m-30) cc_final: 0.8887 (m-30) REVERT: D 632 ASP cc_start: 0.8645 (p0) cc_final: 0.8277 (p0) REVERT: F 632 ASP cc_start: 0.8596 (p0) cc_final: 0.8256 (p0) REVERT: G 632 ASP cc_start: 0.8538 (p0) cc_final: 0.8117 (p0) outliers start: 20 outliers final: 15 residues processed: 93 average time/residue: 0.1851 time to fit residues: 28.3553 Evaluate side-chains 87 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain C residue 720 TYR Chi-restraints excluded: chain D residue 687 THR Chi-restraints excluded: chain D residue 688 THR Chi-restraints excluded: chain D residue 720 TYR Chi-restraints excluded: chain E residue 592 MET Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain E residue 720 TYR Chi-restraints excluded: chain F residue 687 THR Chi-restraints excluded: chain F residue 688 THR Chi-restraints excluded: chain F residue 720 TYR Chi-restraints excluded: chain G residue 720 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 91 optimal weight: 9.9990 chunk 156 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 153 optimal weight: 0.9990 chunk 137 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 77 optimal weight: 50.0000 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 = 0.3135 r_free = 0.3135 target = 0.035689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.026419 restraints weight = 108006.452| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 4.61 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12362 Z= 0.158 Angle : 0.528 8.304 16891 Z= 0.294 Chirality : 0.043 0.139 2079 Planarity : 0.003 0.037 2226 Dihedral : 3.515 12.159 1841 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.10 % Allowed : 23.71 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.01 (0.21), residues: 1757 helix: 3.87 (0.16), residues: 952 sheet: 0.26 (0.29), residues: 245 loop : -0.67 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 694 HIS 0.002 0.001 HIS D 636 PHE 0.009 0.001 PHE E 567 TYR 0.026 0.002 TYR G 720 ARG 0.004 0.000 ARG E 714 Details of bonding type rmsd hydrogen bonds : bond 0.03359 ( 956) hydrogen bonds : angle 4.00282 ( 2763) covalent geometry : bond 0.00318 (12362) covalent geometry : angle 0.52849 (16891) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 1.341 Fit side-chains revert: symmetry clash REVERT: D 561 ASP cc_start: 0.9106 (m-30) cc_final: 0.8870 (m-30) REVERT: D 632 ASP cc_start: 0.8657 (p0) cc_final: 0.8285 (p0) REVERT: F 632 ASP cc_start: 0.8546 (p0) cc_final: 0.8230 (p0) REVERT: G 632 ASP cc_start: 0.8517 (p0) cc_final: 0.8054 (p0) outliers start: 22 outliers final: 19 residues processed: 90 average time/residue: 0.1669 time to fit residues: 25.3718 Evaluate side-chains 86 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain C residue 720 TYR Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 687 THR Chi-restraints excluded: chain D residue 688 THR Chi-restraints excluded: chain D residue 695 THR Chi-restraints excluded: chain D residue 720 TYR Chi-restraints excluded: chain E residue 592 MET Chi-restraints excluded: chain E residue 687 THR Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain E residue 720 TYR Chi-restraints excluded: chain F residue 687 THR Chi-restraints excluded: chain F residue 688 THR Chi-restraints excluded: chain G residue 688 THR Chi-restraints excluded: chain G residue 720 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 23 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 149 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 1 optimal weight: 20.0000 chunk 44 optimal weight: 6.9990 chunk 173 optimal weight: 0.7980 chunk 151 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 102 optimal weight: 50.0000 chunk 49 optimal weight: 5.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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 = 0.3123 r_free = 0.3123 target = 0.035272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.026120 restraints weight = 106745.314| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 4.59 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12362 Z= 0.162 Angle : 0.507 7.220 16891 Z= 0.285 Chirality : 0.043 0.135 2079 Planarity : 0.003 0.037 2226 Dihedral : 3.566 11.735 1841 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.81 % Allowed : 24.86 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.01 (0.21), residues: 1757 helix: 3.86 (0.16), residues: 952 sheet: 0.20 (0.29), residues: 245 loop : -0.63 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 694 HIS 0.002 0.001 HIS G 636 PHE 0.009 0.001 PHE E 567 TYR 0.025 0.002 TYR G 720 ARG 0.003 0.000 ARG E 714 Details of bonding type rmsd hydrogen bonds : bond 0.03388 ( 956) hydrogen bonds : angle 4.13318 ( 2763) covalent geometry : bond 0.00325 (12362) covalent geometry : angle 0.50650 (16891) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 1.501 Fit side-chains revert: symmetry clash REVERT: D 561 ASP cc_start: 0.9127 (m-30) cc_final: 0.8883 (m-30) REVERT: D 632 ASP cc_start: 0.8609 (p0) cc_final: 0.8248 (p0) REVERT: F 632 ASP cc_start: 0.8569 (p0) cc_final: 0.8218 (p0) REVERT: G 632 ASP cc_start: 0.8527 (p0) cc_final: 0.8056 (p0) outliers start: 19 outliers final: 18 residues processed: 87 average time/residue: 0.1741 time to fit residues: 25.7549 Evaluate side-chains 84 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain C residue 720 TYR Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 687 THR Chi-restraints excluded: chain D residue 688 THR Chi-restraints excluded: chain D residue 695 THR Chi-restraints excluded: chain D residue 720 TYR Chi-restraints excluded: chain E residue 687 THR Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain E residue 720 TYR Chi-restraints excluded: chain F residue 687 THR Chi-restraints excluded: chain F residue 688 THR Chi-restraints excluded: chain G residue 688 THR Chi-restraints excluded: chain G residue 720 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 2 optimal weight: 50.0000 chunk 120 optimal weight: 0.8980 chunk 74 optimal weight: 6.9990 chunk 102 optimal weight: 50.0000 chunk 66 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 36 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 chunk 128 optimal weight: 0.0980 chunk 84 optimal weight: 0.7980 chunk 144 optimal weight: 6.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3141 r_free = 0.3141 target = 0.035919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.026728 restraints weight = 102515.491| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 4.56 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12362 Z= 0.101 Angle : 0.497 7.972 16891 Z= 0.276 Chirality : 0.043 0.146 2079 Planarity : 0.003 0.036 2226 Dihedral : 3.479 13.657 1841 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.33 % Allowed : 25.33 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.02 (0.21), residues: 1757 helix: 3.79 (0.16), residues: 952 sheet: 0.30 (0.30), residues: 245 loop : -0.50 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 694 HIS 0.001 0.000 HIS G 636 PHE 0.008 0.001 PHE E 567 TYR 0.025 0.002 TYR G 720 ARG 0.004 0.000 ARG E 714 Details of bonding type rmsd hydrogen bonds : bond 0.03182 ( 956) hydrogen bonds : angle 3.96117 ( 2763) covalent geometry : bond 0.00197 (12362) covalent geometry : angle 0.49735 (16891) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 1.437 Fit side-chains REVERT: B 720 TYR cc_start: 0.7131 (p90) cc_final: 0.6367 (p90) REVERT: D 561 ASP cc_start: 0.9120 (m-30) cc_final: 0.8851 (m-30) REVERT: D 632 ASP cc_start: 0.8615 (p0) cc_final: 0.8253 (p0) REVERT: F 632 ASP cc_start: 0.8561 (p0) cc_final: 0.8237 (p0) REVERT: G 632 ASP cc_start: 0.8536 (p0) cc_final: 0.8086 (p0) outliers start: 14 outliers final: 11 residues processed: 81 average time/residue: 0.1650 time to fit residues: 23.2783 Evaluate side-chains 81 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain C residue 720 TYR Chi-restraints excluded: chain D residue 592 MET Chi-restraints excluded: chain D residue 687 THR Chi-restraints excluded: chain E residue 687 THR Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain E residue 720 TYR Chi-restraints excluded: chain F residue 687 THR Chi-restraints excluded: chain G residue 720 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 106 optimal weight: 0.0000 chunk 77 optimal weight: 50.0000 chunk 149 optimal weight: 5.9990 chunk 128 optimal weight: 0.0770 chunk 140 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 136 optimal weight: 0.2980 chunk 38 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 52 optimal weight: 50.0000 overall best weight: 1.0746 ------------------------------------------------------------------------------- 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 = 0.3148 r_free = 0.3148 target = 0.036195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.026964 restraints weight = 106290.487| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 4.60 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12362 Z= 0.108 Angle : 0.550 12.388 16891 Z= 0.299 Chirality : 0.043 0.200 2079 Planarity : 0.003 0.036 2226 Dihedral : 3.442 13.291 1841 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.86 % Allowed : 25.90 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.97 (0.21), residues: 1757 helix: 3.72 (0.16), residues: 952 sheet: 0.34 (0.30), residues: 245 loop : -0.51 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 694 HIS 0.001 0.000 HIS D 636 PHE 0.007 0.001 PHE E 567 TYR 0.026 0.002 TYR G 720 ARG 0.004 0.000 ARG E 714 Details of bonding type rmsd hydrogen bonds : bond 0.03238 ( 956) hydrogen bonds : angle 4.02058 ( 2763) covalent geometry : bond 0.00214 (12362) covalent geometry : angle 0.55028 (16891) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 1.352 Fit side-chains REVERT: B 720 TYR cc_start: 0.7231 (p90) cc_final: 0.6460 (p90) REVERT: D 561 ASP cc_start: 0.9147 (m-30) cc_final: 0.8858 (m-30) REVERT: D 632 ASP cc_start: 0.8631 (p0) cc_final: 0.8245 (p0) REVERT: F 632 ASP cc_start: 0.8587 (p0) cc_final: 0.8259 (p0) REVERT: G 632 ASP cc_start: 0.8572 (p0) cc_final: 0.8110 (p0) outliers start: 9 outliers final: 8 residues processed: 79 average time/residue: 0.1639 time to fit residues: 22.3046 Evaluate side-chains 82 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 720 TYR Chi-restraints excluded: chain D residue 687 THR Chi-restraints excluded: chain E residue 687 THR Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain E residue 720 TYR Chi-restraints excluded: chain F residue 687 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 89 optimal weight: 0.0470 chunk 26 optimal weight: 20.0000 chunk 114 optimal weight: 5.9990 chunk 39 optimal weight: 20.0000 chunk 41 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 80 optimal weight: 20.0000 chunk 36 optimal weight: 0.2980 chunk 132 optimal weight: 5.9990 chunk 157 optimal weight: 0.9990 overall best weight: 0.8684 ------------------------------------------------------------------------------- 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 = 0.3142 r_free = 0.3142 target = 0.035931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.026787 restraints weight = 101830.712| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 4.58 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12362 Z= 0.105 Angle : 0.528 7.997 16891 Z= 0.295 Chirality : 0.043 0.176 2079 Planarity : 0.003 0.036 2226 Dihedral : 3.392 13.490 1841 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.86 % Allowed : 26.10 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.99 (0.21), residues: 1757 helix: 3.71 (0.16), residues: 952 sheet: 0.41 (0.30), residues: 245 loop : -0.48 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 694 HIS 0.001 0.000 HIS D 636 PHE 0.008 0.001 PHE C 570 TYR 0.025 0.002 TYR G 720 ARG 0.004 0.000 ARG E 714 Details of bonding type rmsd hydrogen bonds : bond 0.03191 ( 956) hydrogen bonds : angle 4.01367 ( 2763) covalent geometry : bond 0.00207 (12362) covalent geometry : angle 0.52816 (16891) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4448.83 seconds wall clock time: 79 minutes 46.99 seconds (4786.99 seconds total)