Starting phenix.real_space_refine on Wed Aug 5 04:39:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vts_65343/08_2026/9vts_65343.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vts_65343/08_2026/9vts_65343.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vts_65343/08_2026/9vts_65343.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vts_65343/08_2026/9vts_65343.map" model { file = "/net/cci-nas-00/data/ceres_data/9vts_65343/08_2026/9vts_65343.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vts_65343/08_2026/9vts_65343.cif" } resolution = 2.56 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= 0.047 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 54 5.16 5 C 5319 2.51 5 N 1434 2.21 5 O 1581 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8388 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1139 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 142} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 743 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 875 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "C" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1139 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 142} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 743 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 875 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "E" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1139 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 142} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "F" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 743 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 875 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.01, per 1000 atoms: 0.24 Number of scatterers: 8388 At special positions: 0 Unit cell: (126.35, 138.7, 82.65, 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 54 16.00 O 1581 8.00 N 1434 7.00 C 5319 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 135 " distance=2.03 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 556 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 95 " distance=2.03 Simple disulfide: pdb=" SG CYS G 33 " - pdb=" SG CYS G 104 " distance=2.03 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 135 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.03 Simple disulfide: pdb=" SG CYS D 511 " - pdb=" SG CYS D 556 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 33 " - pdb=" SG CYS H 104 " distance=2.03 Simple disulfide: pdb=" SG CYS E 108 " - pdb=" SG CYS E 135 " distance=2.03 Simple disulfide: pdb=" SG CYS E 121 " - pdb=" SG CYS E 147 " distance=2.03 Simple disulfide: pdb=" SG CYS F 511 " - pdb=" SG CYS F 556 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 95 " distance=2.03 Simple disulfide: pdb=" SG CYS I 33 " - pdb=" SG CYS I 104 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " NAG-ASN " NAG J 1 " - " ASN B 563 " " NAG K 1 " - " ASN D 563 " " NAG L 1 " - " ASN F 563 " Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 462.8 milliseconds 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1992 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 24 sheets defined 19.1% alpha, 35.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 78 through 85 Processing helix chain 'B' and resid 538 through 542 removed outlier: 4.240A pdb=" N ILE B 542 " --> pdb=" O ALA B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 576 removed outlier: 3.524A pdb=" N THR B 566 " --> pdb=" O ALA B 562 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLN B 567 " --> pdb=" O ASN B 563 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ALA B 568 " --> pdb=" O GLU B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 598 removed outlier: 3.884A pdb=" N ARG B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 90 removed outlier: 3.720A pdb=" N THR G 90 " --> pdb=" O PRO G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 115 Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 71 through 74 Processing helix chain 'C' and resid 78 through 85 Processing helix chain 'D' and resid 538 through 542 removed outlier: 4.239A pdb=" N ILE D 542 " --> pdb=" O ALA D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 576 removed outlier: 3.524A pdb=" N THR D 566 " --> pdb=" O ALA D 562 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLN D 567 " --> pdb=" O ASN D 563 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ALA D 568 " --> pdb=" O GLU D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 598 removed outlier: 3.884A pdb=" N ARG D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.720A pdb=" N THR H 90 " --> pdb=" O PRO H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 115 Processing helix chain 'E' and resid 59 through 61 No H-bonds generated for 'chain 'E' and resid 59 through 61' Processing helix chain 'E' and resid 71 through 74 Processing helix chain 'E' and resid 78 through 85 Processing helix chain 'F' and resid 538 through 542 removed outlier: 4.239A pdb=" N ILE F 542 " --> pdb=" O ALA F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 553 through 576 removed outlier: 3.524A pdb=" N THR F 566 " --> pdb=" O ALA F 562 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLN F 567 " --> pdb=" O ASN F 563 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ALA F 568 " --> pdb=" O GLU F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 598 removed outlier: 3.884A pdb=" N ARG F 596 " --> pdb=" O PHE F 592 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 90 removed outlier: 3.721A pdb=" N THR I 90 " --> pdb=" O PRO I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 115 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 46 Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 7.020A pdb=" N VAL A 96 " --> pdb=" O THR B 581 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 89 Processing sheet with id=AA4, first strand: chain 'A' and resid 105 through 111 removed outlier: 6.013A pdb=" N GLU A 106 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N HIS A 139 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL A 141 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ASN A 110 " --> pdb=" O VAL A 141 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 514 through 519 Processing sheet with id=AA6, first strand: chain 'G' and resid 4 through 5 removed outlier: 3.609A pdb=" N LEU G 18 " --> pdb=" O MET G 82 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 57 through 59 removed outlier: 6.499A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ALA G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N MET G 34 " --> pdb=" O ALA G 50 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N CYS G 33 " --> pdb=" O ASP G 98 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL G 92 " --> pdb=" O GLN G 39 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N CYS G 95 " --> pdb=" O TRP G 118 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N TRP G 118 " --> pdb=" O CYS G 95 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN G 116 " --> pdb=" O ALA G 97 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 57 through 59 removed outlier: 6.499A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ALA G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N MET G 34 " --> pdb=" O ALA G 50 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N CYS G 33 " --> pdb=" O ASP G 98 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL G 92 " --> pdb=" O GLN G 39 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 42 through 46 Processing sheet with id=AB1, first strand: chain 'C' and resid 42 through 46 removed outlier: 6.985A pdb=" N VAL C 96 " --> pdb=" O THR D 581 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 86 through 89 Processing sheet with id=AB3, first strand: chain 'C' and resid 105 through 111 removed outlier: 6.013A pdb=" N GLU C 106 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N HIS C 139 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N CYS C 108 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL C 141 " --> pdb=" O CYS C 108 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ASN C 110 " --> pdb=" O VAL C 141 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 514 through 519 Processing sheet with id=AB5, first strand: chain 'H' and resid 4 through 5 removed outlier: 3.610A pdb=" N LEU H 18 " --> pdb=" O MET H 82 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.498A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ALA H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N MET H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N CYS H 33 " --> pdb=" O ASP H 98 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL H 92 " --> pdb=" O GLN H 39 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N CYS H 95 " --> pdb=" O TRP H 118 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N TRP H 118 " --> pdb=" O CYS H 95 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN H 116 " --> pdb=" O ALA H 97 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.498A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ALA H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N MET H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N CYS H 33 " --> pdb=" O ASP H 98 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL H 92 " --> pdb=" O GLN H 39 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 42 through 46 Processing sheet with id=AB9, first strand: chain 'E' and resid 42 through 46 removed outlier: 6.988A pdb=" N VAL E 96 " --> pdb=" O THR F 581 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 86 through 89 Processing sheet with id=AC2, first strand: chain 'E' and resid 105 through 111 removed outlier: 6.014A pdb=" N GLU E 106 " --> pdb=" O TYR E 137 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N HIS E 139 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N CYS E 108 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL E 141 " --> pdb=" O CYS E 108 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ASN E 110 " --> pdb=" O VAL E 141 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'F' and resid 514 through 519 Processing sheet with id=AC4, first strand: chain 'I' and resid 4 through 5 removed outlier: 3.609A pdb=" N LEU I 18 " --> pdb=" O MET I 82 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 57 through 59 removed outlier: 6.499A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ALA I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N MET I 34 " --> pdb=" O ALA I 50 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N CYS I 33 " --> pdb=" O ASP I 98 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL I 92 " --> pdb=" O GLN I 39 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N CYS I 95 " --> pdb=" O TRP I 118 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N TRP I 118 " --> pdb=" O CYS I 95 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN I 116 " --> pdb=" O ALA I 97 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 57 through 59 removed outlier: 6.499A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ALA I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N MET I 34 " --> pdb=" O ALA I 50 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N CYS I 33 " --> pdb=" O ASP I 98 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL I 92 " --> pdb=" O GLN I 39 " (cutoff:3.500A) 345 hydrogen bonds defined for protein. 891 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: 1.37 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2383 1.33 - 1.45: 1563 1.45 - 1.57: 4559 1.57 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 8577 Sorted by residual: bond pdb=" C2 BMA J 3 " pdb=" O2 BMA J 3 " ideal model delta sigma weight residual 1.402 1.429 -0.027 2.00e-02 2.50e+03 1.81e+00 bond pdb=" C3 NAG K 2 " pdb=" O3 NAG K 2 " ideal model delta sigma weight residual 1.403 1.430 -0.027 2.00e-02 2.50e+03 1.79e+00 bond pdb=" C2 BMA L 3 " pdb=" O2 BMA L 3 " ideal model delta sigma weight residual 1.402 1.429 -0.027 2.00e-02 2.50e+03 1.79e+00 bond pdb=" C3 NAG L 2 " pdb=" O3 NAG L 2 " ideal model delta sigma weight residual 1.403 1.430 -0.027 2.00e-02 2.50e+03 1.78e+00 bond pdb=" C3 BMA K 3 " pdb=" O3 BMA K 3 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.75e+00 ... (remaining 8572 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 11325 1.52 - 3.05: 259 3.05 - 4.57: 56 4.57 - 6.09: 16 6.09 - 7.61: 5 Bond angle restraints: 11661 Sorted by residual: angle pdb=" C ASN A 40 " pdb=" CA ASN A 40 " pdb=" CB ASN A 40 " ideal model delta sigma weight residual 110.42 116.03 -5.61 1.99e+00 2.53e-01 7.95e+00 angle pdb=" C ASN C 40 " pdb=" CA ASN C 40 " pdb=" CB ASN C 40 " ideal model delta sigma weight residual 110.42 116.02 -5.60 1.99e+00 2.53e-01 7.92e+00 angle pdb=" C ASN E 40 " pdb=" CA ASN E 40 " pdb=" CB ASN E 40 " ideal model delta sigma weight residual 110.42 116.01 -5.59 1.99e+00 2.53e-01 7.88e+00 angle pdb=" N GLY H 121 " pdb=" CA GLY H 121 " pdb=" C GLY H 121 " ideal model delta sigma weight residual 111.95 114.54 -2.59 9.50e-01 1.11e+00 7.46e+00 angle pdb=" N GLY G 121 " pdb=" CA GLY G 121 " pdb=" C GLY G 121 " ideal model delta sigma weight residual 111.95 114.53 -2.58 9.50e-01 1.11e+00 7.35e+00 ... (remaining 11656 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.56: 4696 21.56 - 43.13: 347 43.13 - 64.69: 75 64.69 - 86.25: 24 86.25 - 107.82: 12 Dihedral angle restraints: 5154 sinusoidal: 2028 harmonic: 3126 Sorted by residual: dihedral pdb=" CB CYS A 108 " pdb=" SG CYS A 108 " pdb=" SG CYS A 135 " pdb=" CB CYS A 135 " ideal model delta sinusoidal sigma weight residual -86.00 -164.92 78.92 1 1.00e+01 1.00e-02 7.75e+01 dihedral pdb=" CB CYS E 108 " pdb=" SG CYS E 108 " pdb=" SG CYS E 135 " pdb=" CB CYS E 135 " ideal model delta sinusoidal sigma weight residual -86.00 -164.91 78.91 1 1.00e+01 1.00e-02 7.75e+01 dihedral pdb=" CB CYS C 108 " pdb=" SG CYS C 108 " pdb=" SG CYS C 135 " pdb=" CB CYS C 135 " ideal model delta sinusoidal sigma weight residual -86.00 -164.90 78.90 1 1.00e+01 1.00e-02 7.75e+01 ... (remaining 5151 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1026 0.045 - 0.091: 213 0.091 - 0.136: 75 0.136 - 0.181: 3 0.181 - 0.227: 3 Chirality restraints: 1320 Sorted by residual: chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 1.96e+00 chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.50 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" C5 BMA K 3 " pdb=" C4 BMA K 3 " pdb=" C6 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.50 0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 1317 not shown) Planarity restraints: 1491 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 1 " -0.210 2.00e-02 2.50e+03 1.82e-01 4.12e+02 pdb=" C7 NAG K 1 " 0.039 2.00e-02 2.50e+03 pdb=" C8 NAG K 1 " 0.027 2.00e-02 2.50e+03 pdb=" N2 NAG K 1 " 0.304 2.00e-02 2.50e+03 pdb=" O7 NAG K 1 " -0.160 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 1 " 0.197 2.00e-02 2.50e+03 1.70e-01 3.60e+02 pdb=" C7 NAG L 1 " -0.037 2.00e-02 2.50e+03 pdb=" C8 NAG L 1 " -0.030 2.00e-02 2.50e+03 pdb=" N2 NAG L 1 " -0.282 2.00e-02 2.50e+03 pdb=" O7 NAG L 1 " 0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 1 " 0.180 2.00e-02 2.50e+03 1.55e-01 3.01e+02 pdb=" C7 NAG J 1 " -0.034 2.00e-02 2.50e+03 pdb=" C8 NAG J 1 " -0.030 2.00e-02 2.50e+03 pdb=" N2 NAG J 1 " -0.257 2.00e-02 2.50e+03 pdb=" O7 NAG J 1 " 0.141 2.00e-02 2.50e+03 ... (remaining 1488 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2001 2.79 - 3.32: 7353 3.32 - 3.84: 14786 3.84 - 4.37: 17898 4.37 - 4.90: 29753 Nonbonded interactions: 71791 Sorted by model distance: nonbonded pdb=" OG SER A 59 " pdb=" OD1 ASN A 61 " model vdw 2.259 3.040 nonbonded pdb=" OG SER C 59 " pdb=" OD1 ASN C 61 " model vdw 2.260 3.040 nonbonded pdb=" OG SER E 59 " pdb=" OD1 ASN E 61 " model vdw 2.260 3.040 nonbonded pdb=" O ASN C 61 " pdb=" NH2 ARG C 64 " model vdw 2.279 3.120 nonbonded pdb=" O ASN E 61 " pdb=" NH2 ARG E 64 " model vdw 2.280 3.120 ... (remaining 71786 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.670 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: 0.020 Set scattering table: 0.020 Process input model: 9.570 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 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 0.043 8601 Z= 0.138 Angle : 0.613 7.614 11718 Z= 0.299 Chirality : 0.043 0.227 1320 Planarity : 0.010 0.182 1488 Dihedral : 16.901 107.818 3117 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 23.57 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.98 (0.25), residues: 1062 helix: -0.20 (0.45), residues: 138 sheet: -0.47 (0.30), residues: 297 loop : -0.80 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 30 TYR 0.012 0.001 TYR G 32 PHE 0.010 0.001 PHE A 88 TRP 0.005 0.001 TRP D 518 HIS 0.005 0.001 HIS F 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 ( 8577) covalent geometry : angle 0.60520 / 0.30 (11661) SS BOND : bond 0.00207 / 0.13 ( 15) SS BOND : angle 0.82839 / 0.58 ( 30) hydrogen bonds : bond 0.24182 / 16.77 ( 285) hydrogen bonds : angle 10.16321 / 7.20 ( 891) link_BETA1-4 : bond 0.00363 / 0.18 ( 6) link_BETA1-4 : angle 1.96155 / 1.70 ( 18) link_NAG-ASN : bond 0.00121 / 0.06 ( 3) link_NAG-ASN : angle 2.30357 / 1.38 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.219 Fit side-chains REVERT: D 548 MET cc_start: 0.7777 (ttm) cc_final: 0.7503 (ttp) REVERT: D 558 LEU cc_start: 0.8506 (mp) cc_final: 0.8279 (mt) REVERT: H 82 MET cc_start: 0.6149 (mtt) cc_final: 0.5615 (mtt) REVERT: E 84 LYS cc_start: 0.7918 (mmtp) cc_final: 0.7617 (mmtm) REVERT: E 111 LEU cc_start: 0.8385 (mp) cc_final: 0.8142 (mt) REVERT: E 140 LYS cc_start: 0.8278 (mmtm) cc_final: 0.8030 (mmtm) REVERT: I 58 MET cc_start: 0.7922 (ttm) cc_final: 0.7711 (ttt) REVERT: I 78 MET cc_start: 0.6904 (ttp) cc_final: 0.6568 (ttp) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.4359 time to fit residues: 69.2955 Evaluate side-chains 140 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 0.1980 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 107 ASN B 514 ASN C 107 ASN D 514 ASN D 595 GLN H 71 GLN E 107 ASN F 514 ASN F 586 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.163608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.130698 restraints weight = 8312.309| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.73 r_work: 0.3420 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8601 Z= 0.148 Angle : 0.626 5.940 11718 Z= 0.315 Chirality : 0.045 0.157 1320 Planarity : 0.005 0.048 1488 Dihedral : 8.391 57.938 1368 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 5.00 % Allowed : 17.38 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.75 (0.25), residues: 1062 helix: 0.71 (0.47), residues: 138 sheet: -0.59 (0.29), residues: 294 loop : -0.68 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 85 TYR 0.017 0.002 TYR E 109 PHE 0.011 0.002 PHE F 572 TRP 0.006 0.001 TRP B 597 HIS 0.004 0.001 HIS F 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 8577) covalent geometry : angle 0.61205 / 0.31 (11661) SS BOND : bond 0.00216 / 0.13 ( 15) SS BOND : angle 1.03554 / 0.68 ( 30) hydrogen bonds : bond 0.04143 / 2.85 ( 285) hydrogen bonds : angle 6.41876 / 4.47 ( 891) link_BETA1-4 : bond 0.00496 / 0.28 ( 6) link_BETA1-4 : angle 2.92562 / 2.22 ( 18) link_NAG-ASN : bond 0.00413 / 0.21 ( 3) link_NAG-ASN : angle 1.85134 / 1.08 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 150 time to evaluate : 0.184 Fit side-chains REVERT: B 510 LYS cc_start: 0.7642 (OUTLIER) cc_final: 0.7000 (pttt) REVERT: D 595 GLN cc_start: 0.7715 (mt0) cc_final: 0.7476 (mt0) REVERT: E 84 LYS cc_start: 0.8177 (mmtp) cc_final: 0.7882 (mmtm) REVERT: E 112 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7009 (mp0) REVERT: F 545 GLU cc_start: 0.7146 (mp0) cc_final: 0.6822 (tt0) REVERT: I 34 MET cc_start: 0.7952 (mmm) cc_final: 0.7749 (mtp) REVERT: I 39 GLN cc_start: 0.6554 (tp-100) cc_final: 0.6316 (tp40) REVERT: I 58 MET cc_start: 0.7768 (ttm) cc_final: 0.7534 (ttt) REVERT: I 112 GLN cc_start: 0.6825 (OUTLIER) cc_final: 0.5875 (pp30) outliers start: 42 outliers final: 17 residues processed: 166 average time/residue: 0.4587 time to fit residues: 80.9511 Evaluate side-chains 153 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 510 LYS Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain D residue 510 LYS Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain D residue 602 HIS Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain F residue 558 LEU Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain F residue 602 HIS Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 112 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 42 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 76 ASN F 586 ASN I 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.160959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.126245 restraints weight = 8297.090| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.93 r_work: 0.3383 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8601 Z= 0.169 Angle : 0.617 6.289 11718 Z= 0.309 Chirality : 0.044 0.150 1320 Planarity : 0.005 0.041 1488 Dihedral : 6.105 31.931 1368 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 5.24 % Allowed : 15.12 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.65 (0.26), residues: 1062 helix: 1.08 (0.48), residues: 138 sheet: -0.60 (0.29), residues: 294 loop : -0.65 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 31 TYR 0.017 0.002 TYR I 32 PHE 0.011 0.002 PHE F 572 TRP 0.005 0.001 TRP E 104 HIS 0.003 0.001 HIS F 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 ( 8577) covalent geometry : angle 0.60005 / 0.30 (11661) SS BOND : bond 0.00247 / 0.15 ( 15) SS BOND : angle 1.22896 / 0.81 ( 30) hydrogen bonds : bond 0.03982 / 2.72 ( 285) hydrogen bonds : angle 5.92591 / 4.13 ( 891) link_BETA1-4 : bond 0.00434 / 0.24 ( 6) link_BETA1-4 : angle 3.13808 / 2.46 ( 18) link_NAG-ASN : bond 0.00381 / 0.19 ( 3) link_NAG-ASN : angle 2.00382 / 1.21 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 145 time to evaluate : 0.302 Fit side-chains REVERT: B 510 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.7077 (pttt) REVERT: B 545 GLU cc_start: 0.6989 (mp0) cc_final: 0.6654 (tt0) REVERT: C 64 ARG cc_start: 0.8071 (tpp-160) cc_final: 0.7778 (tpp80) REVERT: D 545 GLU cc_start: 0.6993 (mp0) cc_final: 0.6761 (tt0) REVERT: D 595 GLN cc_start: 0.7738 (mt0) cc_final: 0.7477 (mt0) REVERT: E 84 LYS cc_start: 0.8234 (mmtp) cc_final: 0.7910 (mmtm) REVERT: E 112 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.6984 (mp0) REVERT: F 545 GLU cc_start: 0.7320 (mp0) cc_final: 0.6928 (tt0) REVERT: I 39 GLN cc_start: 0.6539 (tp-100) cc_final: 0.6159 (tp40) REVERT: I 58 MET cc_start: 0.7770 (ttm) cc_final: 0.7539 (ttt) REVERT: I 112 GLN cc_start: 0.6942 (OUTLIER) cc_final: 0.5900 (pp30) outliers start: 44 outliers final: 20 residues processed: 165 average time/residue: 0.4607 time to fit residues: 80.9718 Evaluate side-chains 160 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain B residue 510 LYS Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain D residue 510 LYS Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain D residue 602 HIS Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain F residue 602 HIS Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 112 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 38 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 586 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.158017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.124004 restraints weight = 8440.040| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.85 r_work: 0.3323 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8601 Z= 0.221 Angle : 0.652 6.714 11718 Z= 0.330 Chirality : 0.046 0.196 1320 Planarity : 0.005 0.038 1488 Dihedral : 5.459 21.461 1368 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 5.36 % Allowed : 15.00 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.67 (0.25), residues: 1062 helix: 1.14 (0.48), residues: 138 sheet: -0.65 (0.28), residues: 294 loop : -0.67 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 134 TYR 0.016 0.002 TYR E 109 PHE 0.012 0.002 PHE F 572 TRP 0.007 0.001 TRP A 104 HIS 0.004 0.001 HIS F 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.22 ( 8577) covalent geometry : angle 0.63465 / 0.33 (11661) SS BOND : bond 0.00307 / 0.19 ( 15) SS BOND : angle 1.46770 / 0.95 ( 30) hydrogen bonds : bond 0.03955 / 2.71 ( 285) hydrogen bonds : angle 5.83289 / 4.07 ( 891) link_BETA1-4 : bond 0.00376 / 0.21 ( 6) link_BETA1-4 : angle 3.14523 / 2.54 ( 18) link_NAG-ASN : bond 0.00555 / 0.28 ( 3) link_NAG-ASN : angle 2.23205 / 1.36 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 136 time to evaluate : 0.293 Fit side-chains REVERT: B 510 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.7228 (pttt) REVERT: B 545 GLU cc_start: 0.7315 (mp0) cc_final: 0.6844 (pt0) REVERT: D 545 GLU cc_start: 0.7333 (mp0) cc_final: 0.6899 (pt0) REVERT: D 595 GLN cc_start: 0.7798 (mt0) cc_final: 0.7446 (mt0) REVERT: E 84 LYS cc_start: 0.8200 (mmtp) cc_final: 0.7844 (mmtm) REVERT: E 112 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7081 (mp0) REVERT: F 545 GLU cc_start: 0.7473 (mp0) cc_final: 0.7085 (tt0) REVERT: I 39 GLN cc_start: 0.6669 (tp-100) cc_final: 0.6243 (tp40) REVERT: I 58 MET cc_start: 0.7845 (ttm) cc_final: 0.7604 (ttt) REVERT: I 112 GLN cc_start: 0.7120 (OUTLIER) cc_final: 0.5982 (pp30) outliers start: 45 outliers final: 27 residues processed: 161 average time/residue: 0.4218 time to fit residues: 72.5972 Evaluate side-chains 155 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain B residue 510 LYS Chi-restraints excluded: chain B residue 566 THR Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain D residue 510 LYS Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain D residue 602 HIS Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain F residue 558 LEU Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain F residue 602 HIS Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 32 TYR Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 112 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 90 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 97 optimal weight: 0.0060 chunk 17 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 76 ASN F 586 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.160553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.126924 restraints weight = 8406.734| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.79 r_work: 0.3360 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8601 Z= 0.142 Angle : 0.583 6.951 11718 Z= 0.295 Chirality : 0.043 0.210 1320 Planarity : 0.004 0.036 1488 Dihedral : 4.847 18.299 1368 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 5.71 % Allowed : 14.52 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.53 (0.26), residues: 1062 helix: 1.36 (0.48), residues: 138 sheet: -0.57 (0.28), residues: 294 loop : -0.58 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 31 TYR 0.015 0.002 TYR E 109 PHE 0.013 0.001 PHE I 67 TRP 0.006 0.001 TRP A 104 HIS 0.003 0.001 HIS F 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 8577) covalent geometry : angle 0.56994 / 0.29 (11661) SS BOND : bond 0.00187 / 0.12 ( 15) SS BOND : angle 1.15696 / 0.77 ( 30) hydrogen bonds : bond 0.03447 / 2.33 ( 285) hydrogen bonds : angle 5.45558 / 3.80 ( 891) link_BETA1-4 : bond 0.00402 / 0.23 ( 6) link_BETA1-4 : angle 2.68213 / 2.13 ( 18) link_NAG-ASN : bond 0.00244 / 0.12 ( 3) link_NAG-ASN : angle 1.84828 / 1.09 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 141 time to evaluate : 0.221 Fit side-chains REVERT: A 64 ARG cc_start: 0.8145 (tpp-160) cc_final: 0.7890 (tpp80) REVERT: B 510 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7177 (pttt) REVERT: B 545 GLU cc_start: 0.7278 (mp0) cc_final: 0.6790 (pt0) REVERT: C 64 ARG cc_start: 0.8065 (tpp-160) cc_final: 0.7848 (tpp80) REVERT: D 540 GLU cc_start: 0.7702 (mp0) cc_final: 0.7490 (mp0) REVERT: D 545 GLU cc_start: 0.7233 (mp0) cc_final: 0.6933 (tt0) REVERT: D 595 GLN cc_start: 0.7764 (mt0) cc_final: 0.7370 (mt0) REVERT: E 71 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7589 (pt0) REVERT: E 84 LYS cc_start: 0.8259 (mmtp) cc_final: 0.7920 (mmtm) REVERT: E 112 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7112 (mp0) REVERT: F 545 GLU cc_start: 0.7406 (mp0) cc_final: 0.7081 (tt0) REVERT: I 39 GLN cc_start: 0.6690 (tp-100) cc_final: 0.6247 (tp40) REVERT: I 112 GLN cc_start: 0.7075 (OUTLIER) cc_final: 0.5936 (pp30) outliers start: 48 outliers final: 22 residues processed: 166 average time/residue: 0.4637 time to fit residues: 81.8337 Evaluate side-chains 160 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain B residue 510 LYS Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain D residue 510 LYS Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain D residue 602 HIS Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain F residue 602 HIS Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 112 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 16 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 586 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.155357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.121282 restraints weight = 8337.949| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.76 r_work: 0.3278 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 8601 Z= 0.302 Angle : 0.724 7.557 11718 Z= 0.368 Chirality : 0.049 0.288 1320 Planarity : 0.006 0.047 1488 Dihedral : 5.610 24.493 1368 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 5.71 % Allowed : 14.88 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.77 (0.25), residues: 1062 helix: 1.12 (0.47), residues: 138 sheet: -0.77 (0.28), residues: 294 loop : -0.70 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 31 TYR 0.019 0.002 TYR E 109 PHE 0.015 0.002 PHE I 67 TRP 0.012 0.002 TRP E 104 HIS 0.006 0.001 HIS F 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00699 / 0.30 ( 8577) covalent geometry : angle 0.70507 / 0.36 (11661) SS BOND : bond 0.00396 / 0.26 ( 15) SS BOND : angle 1.82913 / 1.19 ( 30) hydrogen bonds : bond 0.04298 / 2.95 ( 285) hydrogen bonds : angle 5.79110 / 4.04 ( 891) link_BETA1-4 : bond 0.00321 / 0.19 ( 6) link_BETA1-4 : angle 3.22387 / 2.73 ( 18) link_NAG-ASN : bond 0.00870 / 0.44 ( 3) link_NAG-ASN : angle 2.67661 / 1.66 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 132 time to evaluate : 0.273 Fit side-chains REVERT: A 71 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7791 (pt0) REVERT: B 510 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7299 (pttt) REVERT: B 545 GLU cc_start: 0.7588 (mp0) cc_final: 0.7057 (pt0) REVERT: D 545 GLU cc_start: 0.7593 (mp0) cc_final: 0.7088 (pt0) REVERT: D 595 GLN cc_start: 0.7780 (mt0) cc_final: 0.7402 (mt0) REVERT: E 84 LYS cc_start: 0.8285 (mmtp) cc_final: 0.7951 (mmtm) REVERT: E 112 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7106 (mp0) REVERT: F 545 GLU cc_start: 0.7455 (mp0) cc_final: 0.7119 (pt0) REVERT: I 39 GLN cc_start: 0.6759 (tp-100) cc_final: 0.6299 (tp40) REVERT: I 112 GLN cc_start: 0.7239 (OUTLIER) cc_final: 0.6234 (pp30) outliers start: 48 outliers final: 23 residues processed: 159 average time/residue: 0.4580 time to fit residues: 77.1070 Evaluate side-chains 155 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain B residue 510 LYS Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain D residue 510 LYS Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain D residue 602 HIS Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain F residue 510 LYS Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain F residue 602 HIS Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 112 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 71 optimal weight: 4.9990 chunk 87 optimal weight: 0.0670 chunk 22 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 71 GLN F 586 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.159023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.125341 restraints weight = 8369.755| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.78 r_work: 0.3335 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8601 Z= 0.154 Angle : 0.603 7.516 11718 Z= 0.306 Chirality : 0.044 0.254 1320 Planarity : 0.005 0.036 1488 Dihedral : 5.023 19.334 1368 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 4.76 % Allowed : 16.19 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.26), residues: 1062 helix: 1.38 (0.48), residues: 138 sheet: -0.67 (0.28), residues: 294 loop : -0.62 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 31 TYR 0.015 0.002 TYR G 32 PHE 0.015 0.001 PHE I 67 TRP 0.009 0.001 TRP A 104 HIS 0.004 0.001 HIS F 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 8577) covalent geometry : angle 0.58951 / 0.30 (11661) SS BOND : bond 0.00258 / 0.16 ( 15) SS BOND : angle 1.30998 / 0.87 ( 30) hydrogen bonds : bond 0.03519 / 2.37 ( 285) hydrogen bonds : angle 5.42746 / 3.77 ( 891) link_BETA1-4 : bond 0.00406 / 0.25 ( 6) link_BETA1-4 : angle 2.64054 / 2.14 ( 18) link_NAG-ASN : bond 0.00252 / 0.13 ( 3) link_NAG-ASN : angle 1.97176 / 1.16 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 138 time to evaluate : 0.182 Fit side-chains REVERT: B 510 LYS cc_start: 0.7798 (OUTLIER) cc_final: 0.7180 (pttt) REVERT: B 545 GLU cc_start: 0.7399 (mp0) cc_final: 0.6941 (pt0) REVERT: D 545 GLU cc_start: 0.7400 (mp0) cc_final: 0.7032 (pt0) REVERT: D 595 GLN cc_start: 0.7778 (mt0) cc_final: 0.7342 (mt0) REVERT: E 84 LYS cc_start: 0.8223 (mmtp) cc_final: 0.7876 (mmtm) REVERT: E 112 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7111 (mp0) REVERT: F 545 GLU cc_start: 0.7398 (mp0) cc_final: 0.7059 (pt0) REVERT: F 587 ARG cc_start: 0.7800 (ttm-80) cc_final: 0.7510 (ttm110) REVERT: I 39 GLN cc_start: 0.6753 (tp-100) cc_final: 0.6295 (tp40) REVERT: I 112 GLN cc_start: 0.7144 (OUTLIER) cc_final: 0.6018 (pp30) outliers start: 40 outliers final: 20 residues processed: 160 average time/residue: 0.4873 time to fit residues: 82.6277 Evaluate side-chains 153 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain B residue 510 LYS Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain D residue 602 HIS Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain F residue 602 HIS Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 112 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 71 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 39 optimal weight: 0.0020 chunk 38 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 71 GLN F 586 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.157496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.123789 restraints weight = 8300.222| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.75 r_work: 0.3316 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 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 : 0.005 0.046 8601 Z= 0.209 Angle : 0.645 7.988 11718 Z= 0.326 Chirality : 0.045 0.241 1320 Planarity : 0.005 0.041 1488 Dihedral : 5.190 20.781 1368 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.88 % Allowed : 17.02 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.65 (0.26), residues: 1062 helix: 1.33 (0.47), residues: 138 sheet: -0.71 (0.28), residues: 294 loop : -0.65 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 31 TYR 0.016 0.002 TYR E 109 PHE 0.016 0.002 PHE G 67 TRP 0.008 0.001 TRP A 104 HIS 0.003 0.001 HIS F 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.21 ( 8577) covalent geometry : angle 0.62876 / 0.32 (11661) SS BOND : bond 0.00311 / 0.20 ( 15) SS BOND : angle 1.51720 / 0.99 ( 30) hydrogen bonds : bond 0.03718 / 2.52 ( 285) hydrogen bonds : angle 5.46457 / 3.80 ( 891) link_BETA1-4 : bond 0.00373 / 0.21 ( 6) link_BETA1-4 : angle 2.83386 / 2.35 ( 18) link_NAG-ASN : bond 0.00521 / 0.26 ( 3) link_NAG-ASN : angle 2.20954 / 1.34 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 138 time to evaluate : 0.204 Fit side-chains REVERT: B 510 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7226 (pttt) REVERT: B 545 GLU cc_start: 0.7509 (mp0) cc_final: 0.7077 (pt0) REVERT: G 71 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.8354 (pt0) REVERT: D 545 GLU cc_start: 0.7439 (mp0) cc_final: 0.7057 (pt0) REVERT: D 595 GLN cc_start: 0.7732 (mt0) cc_final: 0.7261 (mt0) REVERT: E 84 LYS cc_start: 0.8250 (mmtp) cc_final: 0.7892 (mmtm) REVERT: E 112 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7069 (mp0) REVERT: F 545 GLU cc_start: 0.7507 (mp0) cc_final: 0.7133 (pt0) REVERT: I 39 GLN cc_start: 0.6791 (tp-100) cc_final: 0.6310 (tp40) REVERT: I 112 GLN cc_start: 0.7177 (OUTLIER) cc_final: 0.6164 (pp30) outliers start: 41 outliers final: 23 residues processed: 161 average time/residue: 0.4799 time to fit residues: 81.7155 Evaluate side-chains 161 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain B residue 510 LYS Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain G residue 71 GLN Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain D residue 510 LYS Chi-restraints excluded: chain D residue 548 MET Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain D residue 602 HIS Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain F residue 558 LEU Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain F residue 602 HIS Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 112 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 104 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 67 optimal weight: 0.4980 chunk 45 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 586 ASN I 71 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.159077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.125630 restraints weight = 8328.225| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.75 r_work: 0.3344 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8601 Z= 0.158 Angle : 0.610 8.141 11718 Z= 0.308 Chirality : 0.044 0.222 1320 Planarity : 0.005 0.040 1488 Dihedral : 5.009 18.948 1368 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 4.17 % Allowed : 17.62 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.57 (0.26), residues: 1062 helix: 1.44 (0.48), residues: 138 sheet: -0.63 (0.29), residues: 294 loop : -0.62 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 31 TYR 0.015 0.002 TYR E 109 PHE 0.015 0.001 PHE I 67 TRP 0.008 0.001 TRP A 104 HIS 0.003 0.001 HIS F 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 ( 8577) covalent geometry : angle 0.59663 / 0.31 (11661) SS BOND : bond 0.00272 / 0.17 ( 15) SS BOND : angle 1.31343 / 0.87 ( 30) hydrogen bonds : bond 0.03479 / 2.34 ( 285) hydrogen bonds : angle 5.34115 / 3.72 ( 891) link_BETA1-4 : bond 0.00387 / 0.21 ( 6) link_BETA1-4 : angle 2.63477 / 2.15 ( 18) link_NAG-ASN : bond 0.00339 / 0.17 ( 3) link_NAG-ASN : angle 2.00150 / 1.19 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 141 time to evaluate : 0.212 Fit side-chains REVERT: A 134 ARG cc_start: 0.7265 (OUTLIER) cc_final: 0.7036 (ptp-170) REVERT: B 510 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7167 (pttt) REVERT: B 545 GLU cc_start: 0.7390 (mp0) cc_final: 0.7015 (pt0) REVERT: D 545 GLU cc_start: 0.7387 (mp0) cc_final: 0.7030 (pt0) REVERT: D 595 GLN cc_start: 0.7719 (mt0) cc_final: 0.7261 (mt0) REVERT: E 84 LYS cc_start: 0.8232 (mmtp) cc_final: 0.7859 (mmtm) REVERT: E 112 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7061 (mp0) REVERT: F 545 GLU cc_start: 0.7519 (mp0) cc_final: 0.7133 (pt0) REVERT: F 587 ARG cc_start: 0.7782 (ttm-80) cc_final: 0.7547 (ttm110) REVERT: I 39 GLN cc_start: 0.6835 (tp-100) cc_final: 0.6362 (tp40) REVERT: I 112 GLN cc_start: 0.7141 (OUTLIER) cc_final: 0.6062 (pp30) outliers start: 35 outliers final: 23 residues processed: 159 average time/residue: 0.4617 time to fit residues: 77.8828 Evaluate side-chains 161 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain B residue 510 LYS Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain D residue 510 LYS Chi-restraints excluded: chain D residue 548 MET Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain D residue 602 HIS Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain F residue 558 LEU Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain F residue 602 HIS Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 112 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 73 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 79 optimal weight: 0.2980 chunk 98 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 586 ASN I 71 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.159856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.126382 restraints weight = 8297.401| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.76 r_work: 0.3349 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8601 Z= 0.154 Angle : 0.604 8.237 11718 Z= 0.305 Chirality : 0.044 0.202 1320 Planarity : 0.005 0.039 1488 Dihedral : 4.913 18.460 1368 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.17 % Allowed : 17.62 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.55 (0.26), residues: 1062 helix: 1.50 (0.48), residues: 138 sheet: -0.64 (0.29), residues: 294 loop : -0.61 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 31 TYR 0.015 0.002 TYR E 109 PHE 0.015 0.001 PHE I 67 TRP 0.007 0.001 TRP E 104 HIS 0.003 0.001 HIS F 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 ( 8577) covalent geometry : angle 0.59157 / 0.30 (11661) SS BOND : bond 0.00257 / 0.16 ( 15) SS BOND : angle 1.24814 / 0.83 ( 30) hydrogen bonds : bond 0.03400 / 2.29 ( 285) hydrogen bonds : angle 5.24372 / 3.66 ( 891) link_BETA1-4 : bond 0.00406 / 0.23 ( 6) link_BETA1-4 : angle 2.56845 / 2.09 ( 18) link_NAG-ASN : bond 0.00302 / 0.15 ( 3) link_NAG-ASN : angle 1.92431 / 1.14 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 0.182 Fit side-chains REVERT: B 510 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7135 (pttt) REVERT: B 545 GLU cc_start: 0.7378 (mp0) cc_final: 0.7053 (pt0) REVERT: D 545 GLU cc_start: 0.7374 (mp0) cc_final: 0.7027 (pt0) REVERT: D 595 GLN cc_start: 0.7715 (mt0) cc_final: 0.7265 (mt0) REVERT: E 84 LYS cc_start: 0.8286 (mmtp) cc_final: 0.7903 (mmtm) REVERT: E 112 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.6989 (mp0) REVERT: F 545 GLU cc_start: 0.7505 (mp0) cc_final: 0.7149 (pt0) REVERT: I 39 GLN cc_start: 0.6893 (tp-100) cc_final: 0.6440 (tp40) REVERT: I 112 GLN cc_start: 0.7122 (OUTLIER) cc_final: 0.5997 (pp30) outliers start: 35 outliers final: 24 residues processed: 154 average time/residue: 0.4231 time to fit residues: 69.0499 Evaluate side-chains 161 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain B residue 510 LYS Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain D residue 510 LYS Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 548 MET Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain D residue 602 HIS Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain F residue 558 LEU Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain F residue 602 HIS Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 112 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 10 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 586 ASN I 71 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.158643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.125009 restraints weight = 8304.974| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.77 r_work: 0.3335 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8601 Z= 0.186 Angle : 0.631 7.861 11718 Z= 0.319 Chirality : 0.045 0.215 1320 Planarity : 0.005 0.043 1488 Dihedral : 5.049 19.831 1368 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.93 % Allowed : 18.10 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.59 (0.26), residues: 1062 helix: 1.45 (0.47), residues: 138 sheet: -0.65 (0.29), residues: 294 loop : -0.64 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 31 TYR 0.015 0.002 TYR E 109 PHE 0.015 0.002 PHE G 67 TRP 0.009 0.001 TRP A 104 HIS 0.003 0.001 HIS F 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 ( 8577) covalent geometry : angle 0.61701 / 0.32 (11661) SS BOND : bond 0.00285 / 0.18 ( 15) SS BOND : angle 1.36557 / 0.91 ( 30) hydrogen bonds : bond 0.03550 / 2.40 ( 285) hydrogen bonds : angle 5.27608 / 3.68 ( 891) link_BETA1-4 : bond 0.00394 / 0.22 ( 6) link_BETA1-4 : angle 2.68640 / 2.21 ( 18) link_NAG-ASN : bond 0.00447 / 0.22 ( 3) link_NAG-ASN : angle 2.07715 / 1.25 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2913.40 seconds wall clock time: 50 minutes 9.11 seconds (3009.11 seconds total)