Starting phenix.real_space_refine on Sat Sep 12 07:41:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6qd7_4520/09_2026/6qd7_4520.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qd7_4520/09_2026/6qd7_4520.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6qd7_4520/09_2026/6qd7_4520.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qd7_4520/09_2026/6qd7_4520.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6qd7_4520/09_2026/6qd7_4520.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6qd7_4520/09_2026/6qd7_4520.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6qd7_4520/09_2026/6qd7_4520.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qd7_4520/09_2026/6qd7_4520.map" } resolution = 3.1 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= 0.003 sd= 0.103 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 51 5.16 5 C 9123 2.51 5 N 2466 2.21 5 O 2805 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 126 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14445 Number of models: 1 Model: "" Number of chains: 24 Chain: "L" Number of atoms: 827 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Conformer: "B" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} bond proxies already assigned to first conformer: 839 Chain: "H" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 909 Classifications: {'peptide': 120} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 114} Chain: "A" Number of atoms: 1928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1928 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 233} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 44 Classifications: {'peptide': 9} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1032 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "C" Number of atoms: 1928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1928 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 233} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 44 Classifications: {'peptide': 9} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 1928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1928 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 233} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 44 Classifications: {'peptide': 9} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1032 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "F" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1032 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "X" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 909 Classifications: {'peptide': 120} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 114} Chain: "U" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 909 Classifications: {'peptide': 120} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 114} Chain: "Z" Number of atoms: 827 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Conformer: "B" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} bond proxies already assigned to first conformer: 839 Chain: "P" Number of atoms: 827 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Conformer: "B" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} bond proxies already assigned to first conformer: 839 Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "J" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.84, per 1000 atoms: 0.27 Number of scatterers: 14445 At special positions: 0 Unit cell: (133.45, 123.25, 126.65, 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 51 16.00 O 2805 8.00 N 2466 7.00 C 9123 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 93 " distance=2.05 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS B 609 " distance=2.01 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 135 " distance=2.04 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.04 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 556 " distance=2.04 Simple disulfide: pdb=" SG CYS B 601 " - pdb=" SG CYS B 608 " distance=2.03 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS D 609 " distance=2.20 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 135 " distance=2.04 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.04 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS F 609 " distance=1.90 Simple disulfide: pdb=" SG CYS E 108 " - pdb=" SG CYS E 135 " distance=2.04 Simple disulfide: pdb=" SG CYS E 121 " - pdb=" SG CYS E 147 " distance=2.04 Simple disulfide: pdb=" SG CYS D 511 " - pdb=" SG CYS D 556 " distance=2.04 Simple disulfide: pdb=" SG CYS D 601 " - pdb=" SG CYS D 608 " distance=2.03 Simple disulfide: pdb=" SG CYS F 511 " - pdb=" SG CYS F 556 " distance=2.04 Simple disulfide: pdb=" SG CYS F 601 " - pdb=" SG CYS F 608 " distance=2.03 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS X 93 " distance=2.05 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 93 " distance=2.05 Simple disulfide: pdb=" SG CYS Z 23 " - pdb=" SG CYS Z 88 " distance=2.04 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.04 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 ALPHA1-6 " BMA G 3 " - " MAN G 4 " " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 4 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG B 701 " - " ASN B 618 " " NAG D 701 " - " ASN D 618 " " NAG F 701 " - " ASN F 618 " " NAG G 1 " - " ASN B 563 " " NAG I 1 " - " ASN D 563 " " NAG J 1 " - " ASN F 563 " Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 868.6 milliseconds 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3372 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 33 sheets defined 19.2% alpha, 36.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.591A pdb=" N VAL L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 84 through 88 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 84 removed outlier: 3.676A pdb=" N LYS A 84 " --> pdb=" O PRO A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 264 Processing helix chain 'B' and resid 538 through 541 Processing helix chain 'B' and resid 550 through 552 No H-bonds generated for 'chain 'B' and resid 550 through 552' Processing helix chain 'B' and resid 553 through 576 removed outlier: 3.565A pdb=" N GLN B 560 " --> pdb=" O CYS B 556 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLN B 567 " --> pdb=" O ASN B 563 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ALA B 568 " --> pdb=" O GLU B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 598 Processing helix chain 'B' and resid 612 through 622 Processing helix chain 'B' and resid 623 through 628 removed outlier: 3.520A pdb=" N ILE B 627 " --> pdb=" O ILE B 623 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N HIS B 628 " --> pdb=" O ASP B 624 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 623 through 628' 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 84 removed outlier: 3.676A pdb=" N LYS C 84 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 264 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 84 removed outlier: 3.676A pdb=" N LYS E 84 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 264 Processing helix chain 'D' and resid 538 through 541 Processing helix chain 'D' and resid 550 through 552 No H-bonds generated for 'chain 'D' and resid 550 through 552' Processing helix chain 'D' and resid 553 through 576 removed outlier: 3.565A pdb=" N GLN D 560 " --> pdb=" O CYS D 556 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLN D 567 " --> pdb=" O ASN D 563 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ALA D 568 " --> pdb=" O GLU D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 598 Processing helix chain 'D' and resid 612 through 622 Processing helix chain 'D' and resid 623 through 628 removed outlier: 3.520A pdb=" N ILE D 627 " --> pdb=" O ILE D 623 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS D 628 " --> pdb=" O ASP D 624 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 623 through 628' Processing helix chain 'F' and resid 538 through 541 Processing helix chain 'F' and resid 550 through 552 No H-bonds generated for 'chain 'F' and resid 550 through 552' Processing helix chain 'F' and resid 553 through 576 removed outlier: 3.565A pdb=" N GLN F 560 " --> pdb=" O CYS F 556 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLN F 567 " --> pdb=" O ASN F 563 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ALA F 568 " --> pdb=" O GLU F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 598 Processing helix chain 'F' and resid 612 through 622 Processing helix chain 'F' and resid 623 through 628 removed outlier: 3.520A pdb=" N ILE F 627 " --> pdb=" O ILE F 623 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS F 628 " --> pdb=" O ASP F 624 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 623 through 628' Processing helix chain 'X' and resid 28 through 32 Processing helix chain 'X' and resid 62 through 65 Processing helix chain 'X' and resid 74 through 76 No H-bonds generated for 'chain 'X' and resid 74 through 76' Processing helix chain 'X' and resid 84 through 88 Processing helix chain 'U' and resid 28 through 32 Processing helix chain 'U' and resid 62 through 65 Processing helix chain 'U' and resid 74 through 76 No H-bonds generated for 'chain 'U' and resid 74 through 76' Processing helix chain 'U' and resid 84 through 88 Processing helix chain 'Z' and resid 79 through 83 removed outlier: 3.549A pdb=" N VAL Z 83 " --> pdb=" O PRO Z 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 83 removed outlier: 3.555A pdb=" N VAL P 83 " --> pdb=" O PRO P 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 13 removed outlier: 5.882A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 10 through 13 removed outlier: 5.882A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.996A pdb=" N GLY H 10 " --> pdb=" O THR H 115 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N MET H 34 " --> pdb=" O THR H 50 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N THR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.996A pdb=" N GLY H 10 " --> pdb=" O THR H 115 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU H 107 " --> pdb=" O LYS H 95 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 42 through 45 Processing sheet with id=AA8, first strand: chain 'A' and resid 42 through 45 removed outlier: 7.026A pdb=" N VAL A 96 " --> pdb=" O THR B 581 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 86 through 89 Processing sheet with id=AB1, first strand: chain 'A' and resid 102 through 103 Processing sheet with id=AB2, first strand: chain 'A' and resid 105 through 114 removed outlier: 6.091A pdb=" N GLU A 106 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N HIS A 139 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N VAL A 141 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ASN A 110 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N GLY A 143 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLU A 112 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ARG A 219 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TYR A 232 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR A 241 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TRP A 275 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLN A 243 " --> pdb=" O TRP A 275 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LYS A 272 " --> pdb=" O UNK A 472 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N UNK A 474 " --> pdb=" O LYS A 272 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE A 274 " --> pdb=" O UNK A 474 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N UNK A 476 " --> pdb=" O ILE A 274 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 42 through 45 Processing sheet with id=AB4, first strand: chain 'C' and resid 42 through 45 removed outlier: 6.831A pdb=" N VAL C 96 " --> pdb=" O THR D 581 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 86 through 89 Processing sheet with id=AB6, first strand: chain 'C' and resid 101 through 103 Processing sheet with id=AB7, first strand: chain 'C' and resid 105 through 114 removed outlier: 6.091A pdb=" N GLU C 106 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N HIS C 139 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N CYS C 108 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N VAL C 141 " --> pdb=" O CYS C 108 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ASN C 110 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N GLY C 143 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLU C 112 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ARG C 219 " --> pdb=" O GLU C 235 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N TYR C 232 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR C 241 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TRP C 275 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN C 243 " --> pdb=" O TRP C 275 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LYS C 272 " --> pdb=" O UNK C 472 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N UNK C 474 " --> pdb=" O LYS C 272 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE C 274 " --> pdb=" O UNK C 474 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N UNK C 476 " --> pdb=" O ILE C 274 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 42 through 45 Processing sheet with id=AB9, first strand: chain 'E' and resid 42 through 45 removed outlier: 7.032A 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 102 through 103 Processing sheet with id=AC3, first strand: chain 'E' and resid 105 through 114 removed outlier: 6.091A pdb=" N GLU E 106 " --> pdb=" O TYR E 137 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N HIS E 139 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N CYS E 108 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N VAL E 141 " --> pdb=" O CYS E 108 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ASN E 110 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N GLY E 143 " --> pdb=" O ASN E 110 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLU E 112 " --> pdb=" O GLY E 143 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ARG E 219 " --> pdb=" O GLU E 235 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N TYR E 232 " --> pdb=" O LEU E 244 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR E 241 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TRP E 275 " --> pdb=" O TYR E 241 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLN E 243 " --> pdb=" O TRP E 275 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LYS E 272 " --> pdb=" O UNK E 472 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N UNK E 474 " --> pdb=" O LYS E 272 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE E 274 " --> pdb=" O UNK E 474 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N UNK E 476 " --> pdb=" O ILE E 274 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'X' and resid 3 through 7 Processing sheet with id=AC5, first strand: chain 'X' and resid 10 through 12 removed outlier: 5.996A pdb=" N GLY X 10 " --> pdb=" O THR X 115 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N MET X 34 " --> pdb=" O THR X 50 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N THR X 50 " --> pdb=" O MET X 34 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N TRP X 36 " --> pdb=" O VAL X 48 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'X' and resid 10 through 12 removed outlier: 5.996A pdb=" N GLY X 10 " --> pdb=" O THR X 115 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU X 107 " --> pdb=" O LYS X 95 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'U' and resid 3 through 7 Processing sheet with id=AC8, first strand: chain 'U' and resid 10 through 12 removed outlier: 5.995A pdb=" N GLY U 10 " --> pdb=" O THR U 115 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N MET U 34 " --> pdb=" O THR U 50 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N THR U 50 " --> pdb=" O MET U 34 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N TRP U 36 " --> pdb=" O VAL U 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'U' and resid 10 through 12 removed outlier: 5.995A pdb=" N GLY U 10 " --> pdb=" O THR U 115 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU U 107 " --> pdb=" O LYS U 95 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Z' and resid 4 through 7 Processing sheet with id=AD2, first strand: chain 'Z' and resid 10 through 13 removed outlier: 5.910A pdb=" N LEU Z 11 " --> pdb=" O GLU Z 105 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA Z 84 " --> pdb=" O VAL Z 104 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU Z 33 " --> pdb=" O TYR Z 49 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N TYR Z 49 " --> pdb=" O LEU Z 33 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TRP Z 35 " --> pdb=" O LEU Z 47 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Z' and resid 10 through 13 removed outlier: 5.910A pdb=" N LEU Z 11 " --> pdb=" O GLU Z 105 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA Z 84 " --> pdb=" O VAL Z 104 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR Z 97 " --> pdb=" O GLN Z 90 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 4 through 7 Processing sheet with id=AD5, first strand: chain 'P' and resid 10 through 13 removed outlier: 5.961A pdb=" N LEU P 11 " --> pdb=" O GLU P 105 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA P 84 " --> pdb=" O VAL P 104 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU P 33 " --> pdb=" O TYR P 49 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N TYR P 49 " --> pdb=" O LEU P 33 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'P' and resid 10 through 13 removed outlier: 5.961A pdb=" N LEU P 11 " --> pdb=" O GLU P 105 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA P 84 " --> pdb=" O VAL P 104 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N THR P 97 " --> pdb=" O GLN P 90 " (cutoff:3.500A) 570 hydrogen bonds defined for protein. 1413 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.55 Time building geometry restraints manager: 1.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4220 1.34 - 1.46: 3679 1.46 - 1.59: 6807 1.59 - 1.71: 3 1.71 - 1.83: 60 Bond restraints: 14769 Sorted by residual: bond pdb=" C1 NAG D 701 " pdb=" O5 NAG D 701 " ideal model delta sigma weight residual 1.406 1.522 -0.116 2.00e-02 2.50e+03 3.37e+01 bond pdb=" C1 NAG F 701 " pdb=" O5 NAG F 701 " ideal model delta sigma weight residual 1.406 1.522 -0.116 2.00e-02 2.50e+03 3.37e+01 bond pdb=" C1 NAG B 701 " pdb=" O5 NAG B 701 " ideal model delta sigma weight residual 1.406 1.522 -0.116 2.00e-02 2.50e+03 3.34e+01 bond pdb=" C5 MAN J 4 " pdb=" O5 MAN J 4 " ideal model delta sigma weight residual 1.418 1.492 -0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C5 MAN G 4 " pdb=" O5 MAN G 4 " ideal model delta sigma weight residual 1.418 1.492 -0.074 2.00e-02 2.50e+03 1.37e+01 ... (remaining 14764 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.25: 19538 4.25 - 8.49: 475 8.49 - 12.74: 45 12.74 - 16.99: 12 16.99 - 21.23: 6 Bond angle restraints: 20076 Sorted by residual: angle pdb=" CA LEU A 256 " pdb=" CB LEU A 256 " pdb=" CG LEU A 256 " ideal model delta sigma weight residual 116.30 137.53 -21.23 3.50e+00 8.16e-02 3.68e+01 angle pdb=" CA LEU E 256 " pdb=" CB LEU E 256 " pdb=" CG LEU E 256 " ideal model delta sigma weight residual 116.30 137.53 -21.23 3.50e+00 8.16e-02 3.68e+01 angle pdb=" CA LEU C 256 " pdb=" CB LEU C 256 " pdb=" CG LEU C 256 " ideal model delta sigma weight residual 116.30 137.48 -21.18 3.50e+00 8.16e-02 3.66e+01 angle pdb=" CA GLU A 229 " pdb=" CB GLU A 229 " pdb=" CG GLU A 229 " ideal model delta sigma weight residual 114.10 125.69 -11.59 2.00e+00 2.50e-01 3.36e+01 angle pdb=" CA GLU C 229 " pdb=" CB GLU C 229 " pdb=" CG GLU C 229 " ideal model delta sigma weight residual 114.10 125.65 -11.55 2.00e+00 2.50e-01 3.34e+01 ... (remaining 20071 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.16: 7878 17.16 - 34.33: 549 34.33 - 51.49: 143 51.49 - 68.65: 41 68.65 - 85.81: 29 Dihedral angle restraints: 8640 sinusoidal: 3375 harmonic: 5265 Sorted by residual: dihedral pdb=" C ASN F 618 " pdb=" N ASN F 618 " pdb=" CA ASN F 618 " pdb=" CB ASN F 618 " ideal model delta harmonic sigma weight residual -122.60 -135.12 12.52 0 2.50e+00 1.60e-01 2.51e+01 dihedral pdb=" C ASN B 618 " pdb=" N ASN B 618 " pdb=" CA ASN B 618 " pdb=" CB ASN B 618 " ideal model delta harmonic sigma weight residual -122.60 -135.09 12.49 0 2.50e+00 1.60e-01 2.50e+01 dihedral pdb=" C ASN D 618 " pdb=" N ASN D 618 " pdb=" CA ASN D 618 " pdb=" CB ASN D 618 " ideal model delta harmonic sigma weight residual -122.60 -135.09 12.49 0 2.50e+00 1.60e-01 2.49e+01 ... (remaining 8637 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1784 0.097 - 0.193: 423 0.193 - 0.290: 56 0.290 - 0.387: 13 0.387 - 0.483: 10 Chirality restraints: 2286 Sorted by residual: chirality pdb=" CB ILE E 274 " pdb=" CA ILE E 274 " pdb=" CG1 ILE E 274 " pdb=" CG2 ILE E 274 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.48 2.00e-01 2.50e+01 5.84e+00 chirality pdb=" CB ILE A 274 " pdb=" CA ILE A 274 " pdb=" CG1 ILE A 274 " pdb=" CG2 ILE A 274 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.48 2.00e-01 2.50e+01 5.81e+00 chirality pdb=" CB ILE C 274 " pdb=" CA ILE C 274 " pdb=" CG1 ILE C 274 " pdb=" CG2 ILE C 274 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.48 2.00e-01 2.50e+01 5.80e+00 ... (remaining 2283 not shown) Planarity restraints: 2580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU E 235 " 0.044 2.00e-02 2.50e+03 8.66e-02 7.49e+01 pdb=" CD GLU E 235 " -0.150 2.00e-02 2.50e+03 pdb=" OE1 GLU E 235 " 0.058 2.00e-02 2.50e+03 pdb=" OE2 GLU E 235 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 235 " -0.044 2.00e-02 2.50e+03 8.64e-02 7.47e+01 pdb=" CD GLU A 235 " 0.149 2.00e-02 2.50e+03 pdb=" OE1 GLU A 235 " -0.057 2.00e-02 2.50e+03 pdb=" OE2 GLU A 235 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 235 " -0.044 2.00e-02 2.50e+03 8.63e-02 7.44e+01 pdb=" CD GLU C 235 " 0.149 2.00e-02 2.50e+03 pdb=" OE1 GLU C 235 " -0.057 2.00e-02 2.50e+03 pdb=" OE2 GLU C 235 " -0.048 2.00e-02 2.50e+03 ... (remaining 2577 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1938 2.77 - 3.30: 12944 3.30 - 3.83: 23167 3.83 - 4.37: 27292 4.37 - 4.90: 47553 Nonbonded interactions: 112894 Sorted by model distance: nonbonded pdb=" OD2 ASP C 78 " pdb=" OG SER C 246 " model vdw 2.233 3.040 nonbonded pdb=" OD2 ASP E 78 " pdb=" OG SER E 246 " model vdw 2.233 3.040 nonbonded pdb=" OD2 ASP A 78 " pdb=" OG SER A 246 " model vdw 2.234 3.040 nonbonded pdb=" NZ LYS F 622 " pdb=" O7 NAG F 701 " model vdw 2.310 3.120 nonbonded pdb=" NZ LYS B 622 " pdb=" O7 NAG B 701 " model vdw 2.310 3.120 ... (remaining 112889 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: 0.00 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 'I' selection = chain 'J' } ncs_group { reference = chain 'H' selection = chain 'U' selection = chain 'X' } ncs_group { reference = (chain 'L' and (resid 1 through 21 or resid 23 through 108)) selection = (chain 'P' and (resid 1 through 21 or resid 23 through 108)) selection = (chain 'Z' and (resid 1 through 21 or resid 23 through 108)) } 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=0.49 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: 5.180 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: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.180 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 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 : 0.009 0.167 14805 Z= 0.415 Angle : 1.665 21.233 20163 Z= 0.879 Chirality : 0.088 0.483 2286 Planarity : 0.010 0.087 2574 Dihedral : 14.571 85.814 5205 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.72 % Favored : 95.11 % Rotamer: Outliers : 4.53 % Allowed : 6.43 % Favored : 89.04 % Cbeta Deviations : 0.71 % Peptide Plane: Cis-proline : 9.68 % 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: -0.85 (0.18), residues: 1782 helix: 0.20 (0.30), residues: 210 sheet: -0.42 (0.20), residues: 549 loop : -0.76 (0.18), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.003 ARG X 19 TYR 0.052 0.005 TYR C 241 PHE 0.078 0.005 PHE E 307 TRP 0.036 0.004 TRP Z 35 HIS 0.014 0.003 HIS B 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00862 / 0.41 (14769) covalent geometry : angle 1.61506 / 0.87 (20076) SS BOND : bond 0.04739 / 3.08 ( 21) SS BOND : angle 3.49351 / 2.22 ( 42) hydrogen bonds : bond 0.15840 / 10.51 ( 528) hydrogen bonds : angle 7.85565 / 5.21 ( 1413) link_ALPHA1-6 : bond 0.00502 / 0.25 ( 3) link_ALPHA1-6 : angle 5.53135 / 2.82 ( 9) link_BETA1-4 : bond 0.00865 / 0.52 ( 6) link_BETA1-4 : angle 5.56072 / 3.51 ( 18) link_NAG-ASN : bond 0.01419 / 0.63 ( 6) link_NAG-ASN : angle 10.98824 / 7.13 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 192 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 618 ASN cc_start: -0.2380 (OUTLIER) cc_final: -0.3042 (p0) REVERT: D 618 ASN cc_start: -0.2241 (OUTLIER) cc_final: -0.2828 (p0) REVERT: F 618 ASN cc_start: -0.1413 (OUTLIER) cc_final: -0.2105 (p0) outliers start: 66 outliers final: 31 residues processed: 252 average time/residue: 0.1478 time to fit residues: 52.4781 Evaluate side-chains 164 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 130 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 251 GLN Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 251 GLN Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 251 GLN Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain D residue 604 LEU Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 626 ILE Chi-restraints excluded: chain F residue 604 LEU Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 626 ILE Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain U residue 5 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 ASN A 257 ASN B 516 HIS ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 ASN C 257 ASN E 61 ASN E 257 ASN ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.231440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.191047 restraints weight = 29348.716| |-----------------------------------------------------------------------------| r_work (start): 0.4165 rms_B_bonded: 4.59 r_work (final): 0.4165 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4163 r_free = 0.4163 target_work(ls_wunit_k1) = 0.188 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4163 r_free = 0.4163 target_work(ls_wunit_k1) = 0.188 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (6 function evaluations) r_final: 0.4163 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14805 Z= 0.176 Angle : 0.799 13.574 20163 Z= 0.406 Chirality : 0.049 0.229 2286 Planarity : 0.006 0.092 2574 Dihedral : 7.272 57.829 2050 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.56 % Allowed : 11.35 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: -0.20 (0.19), residues: 1782 helix: 1.01 (0.35), residues: 219 sheet: -0.34 (0.20), residues: 534 loop : -0.17 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG Z 61 TYR 0.018 0.002 TYR X 80 PHE 0.016 0.002 PHE A 194 TRP 0.013 0.002 TRP L 35 HIS 0.006 0.001 HIS F 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (14769) covalent geometry : angle 0.76637 / 0.40 (20076) SS BOND : bond 0.00792 / 0.52 ( 21) SS BOND : angle 1.49292 / 0.90 ( 42) hydrogen bonds : bond 0.05570 / 3.79 ( 528) hydrogen bonds : angle 6.22648 / 4.13 ( 1413) link_ALPHA1-6 : bond 0.00638 / 0.32 ( 3) link_ALPHA1-6 : angle 1.83081 / 0.91 ( 9) link_BETA1-4 : bond 0.00557 / 0.29 ( 6) link_BETA1-4 : angle 3.01426 / 1.92 ( 18) link_NAG-ASN : bond 0.01062 / 0.47 ( 6) link_NAG-ASN : angle 6.63097 / 4.42 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 156 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 80 TYR cc_start: 0.7308 (m-80) cc_final: 0.6697 (m-80) REVERT: B 618 ASN cc_start: -0.1559 (OUTLIER) cc_final: -0.2224 (p0) REVERT: D 618 ASN cc_start: -0.2205 (OUTLIER) cc_final: -0.3159 (p0) REVERT: F 618 ASN cc_start: -0.1317 (OUTLIER) cc_final: -0.1893 (p0) outliers start: 36 outliers final: 16 residues processed: 186 average time/residue: 0.1436 time to fit residues: 38.0930 Evaluate side-chains 149 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain B residue 609 CYS Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 308 THR Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 626 ILE Chi-restraints excluded: chain F residue 609 CYS Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 626 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 115 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 151 optimal weight: 0.0570 chunk 56 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 38 HIS A 154 HIS ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 GLN C 154 HIS E 61 ASN E 154 HIS ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 ASN F 567 GLN Z 6 GLN Z 38 HIS P 38 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.228384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.190061 restraints weight = 30101.970| |-----------------------------------------------------------------------------| r_work (start): 0.4183 rms_B_bonded: 3.89 r_work (final): 0.4183 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4182 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4182 r_free = 0.4182 target_work(ls_wunit_k1) = 0.187 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4182 r_free = 0.4182 target_work(ls_wunit_k1) = 0.187 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.4182 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 14805 Z= 0.221 Angle : 0.797 12.656 20163 Z= 0.398 Chirality : 0.049 0.225 2286 Planarity : 0.006 0.072 2574 Dihedral : 6.289 46.940 2010 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.02 % Allowed : 11.55 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.45 (0.19), residues: 1782 helix: 1.04 (0.35), residues: 219 sheet: -0.45 (0.22), residues: 510 loop : -0.44 (0.19), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 596 TYR 0.017 0.002 TYR E 232 PHE 0.017 0.002 PHE C 194 TRP 0.015 0.002 TRP B 531 HIS 0.005 0.001 HIS C 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.22 (14769) covalent geometry : angle 0.76574 / 0.39 (20076) SS BOND : bond 0.00589 / 0.38 ( 21) SS BOND : angle 1.47720 / 0.91 ( 42) hydrogen bonds : bond 0.05474 / 3.74 ( 528) hydrogen bonds : angle 6.22447 / 4.16 ( 1413) link_ALPHA1-6 : bond 0.00510 / 0.25 ( 3) link_ALPHA1-6 : angle 1.82500 / 0.90 ( 9) link_BETA1-4 : bond 0.00338 / 0.16 ( 6) link_BETA1-4 : angle 3.35249 / 2.19 ( 18) link_NAG-ASN : bond 0.00939 / 0.42 ( 6) link_NAG-ASN : angle 6.34250 / 4.17 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 150 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 618 ASN cc_start: -0.1471 (OUTLIER) cc_final: -0.2560 (p0) REVERT: C 103 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.7068 (pt0) REVERT: D 618 ASN cc_start: -0.2048 (OUTLIER) cc_final: -0.2965 (p0) REVERT: F 591 ASP cc_start: 0.7605 (m-30) cc_final: 0.7373 (m-30) REVERT: F 618 ASN cc_start: -0.1147 (OUTLIER) cc_final: -0.1802 (p0) outliers start: 43 outliers final: 25 residues processed: 184 average time/residue: 0.1413 time to fit residues: 36.9992 Evaluate side-chains 161 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 93 CYS Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 609 CYS Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 626 ILE Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain F residue 595 GLN Chi-restraints excluded: chain F residue 609 CYS Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain X residue 93 CYS Chi-restraints excluded: chain U residue 93 CYS Chi-restraints excluded: chain P residue 74 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 91 optimal weight: 0.5980 chunk 77 optimal weight: 20.0000 chunk 5 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 102 optimal weight: 8.9990 chunk 111 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 0.0070 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.227141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.167889 restraints weight = 30885.861| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 4.98 r_work: 0.3494 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3493 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3493 r_free = 0.3493 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3493 r_free = 0.3493 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (15 function evaluations) r_final: 0.3493 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14805 Z= 0.134 Angle : 0.669 11.736 20163 Z= 0.335 Chirality : 0.045 0.208 2286 Planarity : 0.005 0.050 2574 Dihedral : 5.698 44.763 2008 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.95 % Allowed : 12.80 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: -0.50 (0.19), residues: 1782 helix: 1.08 (0.35), residues: 219 sheet: -0.49 (0.21), residues: 555 loop : -0.48 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 45 TYR 0.013 0.001 TYR X 80 PHE 0.013 0.001 PHE A 234 TRP 0.010 0.001 TRP B 531 HIS 0.005 0.001 HIS F 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (14769) covalent geometry : angle 0.63891 / 0.33 (20076) SS BOND : bond 0.00346 / 0.24 ( 21) SS BOND : angle 1.32993 / 0.79 ( 42) hydrogen bonds : bond 0.04275 / 2.88 ( 528) hydrogen bonds : angle 5.77837 / 3.85 ( 1413) link_ALPHA1-6 : bond 0.00471 / 0.23 ( 3) link_ALPHA1-6 : angle 1.68587 / 0.81 ( 9) link_BETA1-4 : bond 0.00528 / 0.28 ( 6) link_BETA1-4 : angle 2.69541 / 1.74 ( 18) link_NAG-ASN : bond 0.00832 / 0.37 ( 6) link_NAG-ASN : angle 5.71090 / 3.81 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 140 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 73 ASP cc_start: 0.6425 (OUTLIER) cc_final: 0.6016 (p0) REVERT: H 76 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7551 (ttpt) REVERT: B 618 ASN cc_start: -0.3173 (OUTLIER) cc_final: -0.3564 (p0) REVERT: E 115 LYS cc_start: 0.5868 (mptt) cc_final: 0.5534 (mmtp) REVERT: D 618 ASN cc_start: -0.3670 (OUTLIER) cc_final: -0.4087 (p0) REVERT: F 618 ASN cc_start: -0.2313 (OUTLIER) cc_final: -0.2638 (p0) REVERT: U 80 TYR cc_start: 0.7520 (m-80) cc_final: 0.7141 (m-80) REVERT: P 6 GLN cc_start: 0.5856 (mt0) cc_final: 0.5596 (mt0) outliers start: 42 outliers final: 25 residues processed: 170 average time/residue: 0.1315 time to fit residues: 32.4848 Evaluate side-chains 162 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 609 CYS Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain D residue 504 ILE Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 626 ILE Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain F residue 595 GLN Chi-restraints excluded: chain F residue 609 CYS Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 626 ILE Chi-restraints excluded: chain U residue 73 ASP Chi-restraints excluded: chain P residue 74 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 137 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 104 optimal weight: 40.0000 chunk 162 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 152 optimal weight: 0.7980 chunk 14 optimal weight: 0.4980 chunk 163 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 GLN E 61 ASN ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.225204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.164537 restraints weight = 31548.567| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 5.55 r_work: 0.3468 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3413 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3413 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14805 Z= 0.161 Angle : 0.695 10.829 20163 Z= 0.345 Chirality : 0.046 0.194 2286 Planarity : 0.005 0.045 2574 Dihedral : 5.696 47.376 2008 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.81 % Allowed : 12.60 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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 (0.19), residues: 1782 helix: 1.15 (0.35), residues: 219 sheet: -0.52 (0.21), residues: 585 loop : -0.61 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 45 TYR 0.013 0.002 TYR E 232 PHE 0.012 0.002 PHE L 62 TRP 0.021 0.002 TRP B 531 HIS 0.005 0.001 HIS F 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (14769) covalent geometry : angle 0.66772 / 0.34 (20076) SS BOND : bond 0.00374 / 0.27 ( 21) SS BOND : angle 1.14401 / 0.70 ( 42) hydrogen bonds : bond 0.04541 / 3.08 ( 528) hydrogen bonds : angle 5.78410 / 3.86 ( 1413) link_ALPHA1-6 : bond 0.00553 / 0.28 ( 3) link_ALPHA1-6 : angle 1.73840 / 0.85 ( 9) link_BETA1-4 : bond 0.00453 / 0.22 ( 6) link_BETA1-4 : angle 2.93167 / 1.92 ( 18) link_NAG-ASN : bond 0.00688 / 0.31 ( 6) link_NAG-ASN : angle 5.46837 / 3.60 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 142 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 52 SER cc_start: 0.7535 (m) cc_final: 0.7288 (p) REVERT: H 73 ASP cc_start: 0.6340 (p0) cc_final: 0.5838 (p0) REVERT: B 618 ASN cc_start: -0.3434 (OUTLIER) cc_final: -0.3752 (p0) REVERT: E 115 LYS cc_start: 0.5884 (mptt) cc_final: 0.5565 (mmtp) REVERT: D 618 ASN cc_start: -0.3718 (OUTLIER) cc_final: -0.4211 (p0) REVERT: F 618 ASN cc_start: -0.2520 (OUTLIER) cc_final: -0.3014 (p0) REVERT: X 51 ILE cc_start: 0.8106 (OUTLIER) cc_final: 0.7489 (tt) REVERT: U 80 TYR cc_start: 0.7578 (m-80) cc_final: 0.7098 (m-80) REVERT: U 87 ASP cc_start: 0.5521 (m-30) cc_final: 0.4943 (t0) outliers start: 55 outliers final: 34 residues processed: 186 average time/residue: 0.1347 time to fit residues: 36.1979 Evaluate side-chains 170 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 132 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 609 CYS Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain D residue 504 ILE Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 626 ILE Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain F residue 595 GLN Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 626 ILE Chi-restraints excluded: chain X residue 51 ILE Chi-restraints excluded: chain X residue 98 ARG Chi-restraints excluded: chain U residue 73 ASP Chi-restraints excluded: chain U residue 93 CYS Chi-restraints excluded: chain P residue 74 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 69 optimal weight: 1.9990 chunk 164 optimal weight: 0.8980 chunk 141 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 103 optimal weight: 30.0000 chunk 46 optimal weight: 0.6980 chunk 157 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 130 optimal weight: 0.0470 chunk 112 optimal weight: 2.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 ASN ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 586 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.226544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.183384 restraints weight = 27776.306| |-----------------------------------------------------------------------------| r_work (start): 0.4108 rms_B_bonded: 5.09 r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4106 r_free = 0.4106 target_work(ls_wunit_k1) = 0.182 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4106 r_free = 0.4106 target_work(ls_wunit_k1) = 0.182 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.4106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14805 Z= 0.133 Angle : 0.645 10.047 20163 Z= 0.323 Chirality : 0.045 0.201 2286 Planarity : 0.005 0.039 2574 Dihedral : 5.582 49.289 2008 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.74 % Allowed : 12.86 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.51 (0.19), residues: 1782 helix: 1.30 (0.35), residues: 219 sheet: -0.38 (0.22), residues: 543 loop : -0.63 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 19 TYR 0.022 0.001 TYR U 32 PHE 0.011 0.001 PHE U 92 TRP 0.023 0.001 TRP B 531 HIS 0.004 0.001 HIS F 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (14769) covalent geometry : angle 0.61843 / 0.32 (20076) SS BOND : bond 0.00346 / 0.26 ( 21) SS BOND : angle 1.57049 / 1.21 ( 42) hydrogen bonds : bond 0.04029 / 2.71 ( 528) hydrogen bonds : angle 5.61689 / 3.74 ( 1413) link_ALPHA1-6 : bond 0.00577 / 0.29 ( 3) link_ALPHA1-6 : angle 1.72306 / 0.84 ( 9) link_BETA1-4 : bond 0.00522 / 0.27 ( 6) link_BETA1-4 : angle 2.66056 / 1.72 ( 18) link_NAG-ASN : bond 0.00625 / 0.28 ( 6) link_NAG-ASN : angle 5.02217 / 3.33 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 140 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 618 ASN cc_start: -0.2227 (OUTLIER) cc_final: -0.2713 (p0) REVERT: E 49 ASP cc_start: 0.5473 (p0) cc_final: 0.5169 (p0) REVERT: D 618 ASN cc_start: -0.2574 (OUTLIER) cc_final: -0.3477 (p0) REVERT: F 618 ASN cc_start: -0.1615 (OUTLIER) cc_final: -0.2413 (p0) REVERT: X 51 ILE cc_start: 0.8002 (OUTLIER) cc_final: 0.7583 (tt) REVERT: U 80 TYR cc_start: 0.7300 (m-80) cc_final: 0.7085 (m-80) REVERT: U 87 ASP cc_start: 0.5428 (m-30) cc_final: 0.5128 (t0) outliers start: 54 outliers final: 33 residues processed: 180 average time/residue: 0.1308 time to fit residues: 34.5216 Evaluate side-chains 170 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 133 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 609 CYS Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain D residue 504 ILE Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 626 ILE Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain F residue 595 GLN Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 626 ILE Chi-restraints excluded: chain X residue 51 ILE Chi-restraints excluded: chain X residue 98 ARG Chi-restraints excluded: chain U residue 73 ASP Chi-restraints excluded: chain U residue 93 CYS Chi-restraints excluded: chain P residue 74 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 98 optimal weight: 1.9990 chunk 67 optimal weight: 0.4980 chunk 69 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 41 optimal weight: 50.0000 chunk 115 optimal weight: 0.0970 chunk 24 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 3 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 71.8375 > 50:) chunk 139 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 GLN E 61 ASN ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 586 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.223199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.172786 restraints weight = 26835.127| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 5.77 r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3994 r_free = 0.3994 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3994 r_free = 0.3994 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 14805 Z= 0.200 Angle : 0.724 9.269 20163 Z= 0.357 Chirality : 0.046 0.172 2286 Planarity : 0.005 0.042 2574 Dihedral : 5.832 52.085 2008 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 3.28 % Allowed : 13.25 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: -0.68 (0.19), residues: 1782 helix: 1.35 (0.35), residues: 219 sheet: -0.59 (0.22), residues: 549 loop : -0.73 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 85 TYR 0.014 0.002 TYR E 232 PHE 0.013 0.002 PHE A 153 TRP 0.026 0.002 TRP D 531 HIS 0.006 0.001 HIS C 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.20 (14769) covalent geometry : angle 0.70011 / 0.35 (20076) SS BOND : bond 0.00356 / 0.26 ( 21) SS BOND : angle 1.44698 / 1.07 ( 42) hydrogen bonds : bond 0.04921 / 3.35 ( 528) hydrogen bonds : angle 5.88130 / 3.93 ( 1413) link_ALPHA1-6 : bond 0.00534 / 0.27 ( 3) link_ALPHA1-6 : angle 1.76931 / 0.86 ( 9) link_BETA1-4 : bond 0.00365 / 0.17 ( 6) link_BETA1-4 : angle 3.19820 / 2.12 ( 18) link_NAG-ASN : bond 0.00543 / 0.25 ( 6) link_NAG-ASN : angle 4.93217 / 3.19 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 144 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 80 TYR cc_start: 0.7560 (m-80) cc_final: 0.7103 (m-80) REVERT: A 49 ASP cc_start: 0.5549 (p0) cc_final: 0.5305 (p0) REVERT: B 618 ASN cc_start: -0.2475 (OUTLIER) cc_final: -0.2951 (p0) REVERT: D 618 ASN cc_start: -0.2929 (OUTLIER) cc_final: -0.4065 (p0) REVERT: F 595 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7569 (mp10) REVERT: F 618 ASN cc_start: -0.2390 (OUTLIER) cc_final: -0.3037 (p0) REVERT: X 51 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7728 (tt) REVERT: U 87 ASP cc_start: 0.5733 (m-30) cc_final: 0.5425 (t0) outliers start: 47 outliers final: 34 residues processed: 179 average time/residue: 0.1294 time to fit residues: 34.0211 Evaluate side-chains 178 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 139 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 93 CYS Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 609 CYS Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain D residue 504 ILE Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 626 ILE Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain F residue 595 GLN Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 626 ILE Chi-restraints excluded: chain X residue 51 ILE Chi-restraints excluded: chain X residue 93 CYS Chi-restraints excluded: chain X residue 98 ARG Chi-restraints excluded: chain U residue 73 ASP Chi-restraints excluded: chain U residue 93 CYS Chi-restraints excluded: chain P residue 74 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 36 optimal weight: 0.6980 chunk 172 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 153 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 102 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 GLN ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 586 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.223004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.163097 restraints weight = 30064.018| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 5.45 r_work: 0.3446 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3382 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3382 r_free = 0.3382 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3382 r_free = 0.3382 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3382 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14805 Z= 0.176 Angle : 0.693 8.740 20163 Z= 0.344 Chirality : 0.045 0.163 2286 Planarity : 0.005 0.042 2574 Dihedral : 5.823 53.696 2008 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.02 % Allowed : 13.91 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: -0.68 (0.19), residues: 1782 helix: 1.41 (0.35), residues: 219 sheet: -0.59 (0.22), residues: 549 loop : -0.75 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 587 TYR 0.015 0.002 TYR U 32 PHE 0.012 0.002 PHE U 92 TRP 0.027 0.002 TRP B 531 HIS 0.005 0.001 HIS C 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (14769) covalent geometry : angle 0.66967 / 0.34 (20076) SS BOND : bond 0.00377 / 0.26 ( 21) SS BOND : angle 1.54187 / 0.93 ( 42) hydrogen bonds : bond 0.04599 / 3.12 ( 528) hydrogen bonds : angle 5.76655 / 3.85 ( 1413) link_ALPHA1-6 : bond 0.00599 / 0.30 ( 3) link_ALPHA1-6 : angle 1.79019 / 0.87 ( 9) link_BETA1-4 : bond 0.00456 / 0.22 ( 6) link_BETA1-4 : angle 3.09509 / 2.05 ( 18) link_NAG-ASN : bond 0.00512 / 0.25 ( 6) link_NAG-ASN : angle 4.60768 / 3.00 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 145 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 73 ASP cc_start: 0.6476 (p0) cc_final: 0.6259 (p0) REVERT: H 80 TYR cc_start: 0.7860 (m-80) cc_final: 0.7408 (m-80) REVERT: B 618 ASN cc_start: -0.3447 (OUTLIER) cc_final: -0.3833 (p0) REVERT: D 618 ASN cc_start: -0.4222 (OUTLIER) cc_final: -0.4951 (p0) REVERT: F 595 GLN cc_start: 0.7481 (OUTLIER) cc_final: 0.7119 (mp10) REVERT: F 618 ASN cc_start: -0.3408 (OUTLIER) cc_final: -0.3905 (p0) REVERT: X 51 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.7729 (tt) REVERT: U 54 ASN cc_start: 0.5890 (p0) cc_final: 0.5430 (t0) REVERT: U 87 ASP cc_start: 0.5735 (m-30) cc_final: 0.5154 (t0) outliers start: 43 outliers final: 32 residues processed: 179 average time/residue: 0.1296 time to fit residues: 34.0274 Evaluate side-chains 178 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 141 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 93 CYS Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 609 CYS Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain D residue 504 ILE Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 626 ILE Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain F residue 595 GLN Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 626 ILE Chi-restraints excluded: chain X residue 51 ILE Chi-restraints excluded: chain X residue 98 ARG Chi-restraints excluded: chain U residue 93 CYS Chi-restraints excluded: chain P residue 74 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 0 optimal weight: 6.9990 chunk 81 optimal weight: 50.0000 chunk 1 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 157 optimal weight: 5.9990 chunk 167 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 144 optimal weight: 10.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 6 GLN ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 586 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.220762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.160644 restraints weight = 30594.030| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 6.38 r_work: 0.3395 rms_B_bonded: 5.01 restraints_weight: 2.0000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3391 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3391 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 14805 Z= 0.286 Angle : 0.824 8.541 20163 Z= 0.406 Chirality : 0.050 0.168 2286 Planarity : 0.006 0.056 2574 Dihedral : 6.206 55.490 2008 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 3.35 % Allowed : 13.91 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: -0.72 (0.19), residues: 1782 helix: 1.77 (0.35), residues: 201 sheet: -0.42 (0.22), residues: 567 loop : -0.96 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG Z 61 TYR 0.017 0.002 TYR E 232 PHE 0.018 0.003 PHE C 153 TRP 0.032 0.002 TRP D 531 HIS 0.008 0.001 HIS C 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00696 / 0.29 (14769) covalent geometry : angle 0.80102 / 0.40 (20076) SS BOND : bond 0.00413 / 0.30 ( 21) SS BOND : angle 1.62411 / 1.00 ( 42) hydrogen bonds : bond 0.05806 / 3.98 ( 528) hydrogen bonds : angle 6.28540 / 4.21 ( 1413) link_ALPHA1-6 : bond 0.00466 / 0.23 ( 3) link_ALPHA1-6 : angle 1.84961 / 0.90 ( 9) link_BETA1-4 : bond 0.00300 / 0.13 ( 6) link_BETA1-4 : angle 3.70386 / 2.50 ( 18) link_NAG-ASN : bond 0.00418 / 0.19 ( 6) link_NAG-ASN : angle 4.76181 / 2.98 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 146 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 70 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6686 (mm-30) REVERT: H 73 ASP cc_start: 0.6509 (p0) cc_final: 0.5956 (p0) REVERT: H 76 LYS cc_start: 0.8211 (pttm) cc_final: 0.7935 (pttm) REVERT: H 80 TYR cc_start: 0.7952 (m-80) cc_final: 0.7426 (m-80) REVERT: B 618 ASN cc_start: -0.4053 (OUTLIER) cc_final: -0.4365 (p0) REVERT: C 103 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7441 (pt0) REVERT: D 596 ARG cc_start: 0.7197 (mtp180) cc_final: 0.6840 (mtp180) REVERT: D 618 ASN cc_start: -0.4462 (OUTLIER) cc_final: -0.5146 (p0) REVERT: F 595 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7318 (mp10) REVERT: F 618 ASN cc_start: -0.3636 (OUTLIER) cc_final: -0.4170 (p0) REVERT: X 51 ILE cc_start: 0.8330 (OUTLIER) cc_final: 0.7872 (tt) REVERT: U 87 ASP cc_start: 0.5871 (m-30) cc_final: 0.5272 (t0) outliers start: 48 outliers final: 34 residues processed: 184 average time/residue: 0.1249 time to fit residues: 33.6424 Evaluate side-chains 179 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 139 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 93 CYS Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 609 CYS Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain D residue 504 ILE Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 626 ILE Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain F residue 595 GLN Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 626 ILE Chi-restraints excluded: chain X residue 51 ILE Chi-restraints excluded: chain X residue 93 CYS Chi-restraints excluded: chain X residue 98 ARG Chi-restraints excluded: chain U residue 93 CYS Chi-restraints excluded: chain P residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 49 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 131 optimal weight: 7.9990 chunk 129 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 110 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 GLN ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 586 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.224310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.171708 restraints weight = 23006.325| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 5.35 r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3982 r_free = 0.3982 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3982 r_free = 0.3982 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14805 Z= 0.162 Angle : 0.678 8.106 20163 Z= 0.339 Chirality : 0.045 0.154 2286 Planarity : 0.005 0.046 2574 Dihedral : 5.882 57.473 2008 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.89 % Allowed : 14.24 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: -0.76 (0.20), residues: 1782 helix: 1.43 (0.35), residues: 219 sheet: -0.55 (0.22), residues: 564 loop : -0.88 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 587 TYR 0.015 0.002 TYR E 232 PHE 0.012 0.002 PHE U 92 TRP 0.032 0.002 TRP D 531 HIS 0.005 0.001 HIS E 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (14769) covalent geometry : angle 0.65797 / 0.33 (20076) SS BOND : bond 0.00299 / 0.22 ( 21) SS BOND : angle 1.28002 / 0.81 ( 42) hydrogen bonds : bond 0.04468 / 3.03 ( 528) hydrogen bonds : angle 5.80750 / 3.87 ( 1413) link_ALPHA1-6 : bond 0.00612 / 0.31 ( 3) link_ALPHA1-6 : angle 1.79080 / 0.87 ( 9) link_BETA1-4 : bond 0.00507 / 0.25 ( 6) link_BETA1-4 : angle 3.08345 / 2.05 ( 18) link_NAG-ASN : bond 0.00455 / 0.23 ( 6) link_NAG-ASN : angle 4.12160 / 2.66 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 145 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 80 TYR cc_start: 0.7399 (m-80) cc_final: 0.7072 (m-80) REVERT: B 618 ASN cc_start: -0.2816 (OUTLIER) cc_final: -0.3549 (p0) REVERT: D 595 GLN cc_start: 0.8059 (mm-40) cc_final: 0.7696 (mp10) REVERT: D 618 ASN cc_start: -0.3319 (OUTLIER) cc_final: -0.4436 (p0) REVERT: F 595 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7564 (mp10) REVERT: F 618 ASN cc_start: -0.3007 (OUTLIER) cc_final: -0.3864 (p0) REVERT: X 51 ILE cc_start: 0.8079 (OUTLIER) cc_final: 0.7742 (tt) REVERT: Z 61 ARG cc_start: 0.6195 (ptp90) cc_final: 0.5933 (ptt-90) outliers start: 41 outliers final: 32 residues processed: 177 average time/residue: 0.1295 time to fit residues: 33.6861 Evaluate side-chains 175 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 138 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 93 CYS Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain D residue 504 ILE Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 626 ILE Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain F residue 595 GLN Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 626 ILE Chi-restraints excluded: chain X residue 51 ILE Chi-restraints excluded: chain X residue 98 ARG Chi-restraints excluded: chain U residue 93 CYS Chi-restraints excluded: chain P residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 133 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 chunk 136 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 117 optimal weight: 20.0000 chunk 81 optimal weight: 9.9990 chunk 146 optimal weight: 2.9990 chunk 157 optimal weight: 6.9990 chunk 17 optimal weight: 0.0020 chunk 134 optimal weight: 0.6980 chunk 131 optimal weight: 7.9990 overall best weight: 1.0990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 586 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.224154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.170167 restraints weight = 23052.467| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 5.28 r_work: 0.3410 rms_B_bonded: 5.24 restraints_weight: 2.0000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3413 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (10 function evaluations) r_final: 0.3413 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14805 Z= 0.165 Angle : 0.686 8.164 20163 Z= 0.343 Chirality : 0.045 0.165 2286 Planarity : 0.005 0.042 2574 Dihedral : 5.945 58.552 2008 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 3.08 % Allowed : 14.04 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.20), residues: 1782 helix: 2.03 (0.36), residues: 201 sheet: -0.59 (0.22), residues: 543 loop : -0.81 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG P 61 TYR 0.018 0.002 TYR X 80 PHE 0.011 0.002 PHE U 92 TRP 0.032 0.002 TRP D 531 HIS 0.005 0.001 HIS E 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 (14769) covalent geometry : angle 0.66590 / 0.34 (20076) SS BOND : bond 0.00350 / 0.23 ( 21) SS BOND : angle 1.54024 / 0.87 ( 42) hydrogen bonds : bond 0.04481 / 3.04 ( 528) hydrogen bonds : angle 5.77826 / 3.85 ( 1413) link_ALPHA1-6 : bond 0.00586 / 0.29 ( 3) link_ALPHA1-6 : angle 1.77871 / 0.86 ( 9) link_BETA1-4 : bond 0.00440 / 0.22 ( 6) link_BETA1-4 : angle 3.01716 / 2.01 ( 18) link_NAG-ASN : bond 0.00372 / 0.17 ( 6) link_NAG-ASN : angle 3.98702 / 2.55 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3685.88 seconds wall clock time: 64 minutes 1.55 seconds (3841.55 seconds total)