Starting phenix.real_space_refine on Tue Nov 18 12:51:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qd8_4521/11_2025/6qd8_4521.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qd8_4521/11_2025/6qd8_4521.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6qd8_4521/11_2025/6qd8_4521.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qd8_4521/11_2025/6qd8_4521.map" model { file = "/net/cci-nas-00/data/ceres_data/6qd8_4521/11_2025/6qd8_4521.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qd8_4521/11_2025/6qd8_4521.cif" } resolution = 3.3 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= 0.004 sd= 0.089 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 45 5.16 5 C 8976 2.51 5 N 2394 2.21 5 O 2739 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 126 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14154 Number of models: 1 Model: "" Number of chains: 7 Chain: "Z" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 795 Classifications: {'peptide': 104} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 97} 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: "H" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 866 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: Y, L, C, E, F, D, W, Q, I, J Time building chain proxies: 3.01, per 1000 atoms: 0.21 Number of scatterers: 14154 At special positions: 0 Unit cell: (127.5, 136.85, 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 45 16.00 O 2739 8.00 N 2394 7.00 C 8976 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS Z 23 " - pdb=" SG CYS Z 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 135 " distance=2.03 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 23 " - pdb=" SG CYS Y 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 135 " distance=2.03 Simple disulfide: pdb=" SG CYS E 108 " - pdb=" SG CYS E 135 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.03 Simple disulfide: pdb=" SG CYS E 121 " - pdb=" SG CYS E 147 " 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 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 F 563 " " NAG J 1 " - " ASN D 563 " Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 694.8 milliseconds 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3300 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 27 sheets defined 14.8% alpha, 33.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 78 through 84 removed outlier: 3.866A 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: 3.771A pdb=" N ASN B 563 " --> pdb=" O ARG B 559 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR B 566 " --> pdb=" O ALA B 562 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N GLN B 567 " --> pdb=" O ASN B 563 " (cutoff:3.500A) removed outlier: 4.924A 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 removed outlier: 4.022A pdb=" N LYS B 622 " --> pdb=" O ASN B 618 " (cutoff:3.500A) 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: 3.866A 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: 3.866A 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 '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: 3.770A pdb=" N ASN F 563 " --> pdb=" O ARG F 559 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR F 566 " --> pdb=" O ALA F 562 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLN F 567 " --> pdb=" O ASN F 563 " (cutoff:3.500A) removed outlier: 4.923A 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 removed outlier: 4.022A pdb=" N LYS F 622 " --> pdb=" O ASN F 618 " (cutoff:3.500A) 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: 3.771A pdb=" N ASN D 563 " --> pdb=" O ARG D 559 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR D 566 " --> pdb=" O ALA D 562 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N GLN D 567 " --> pdb=" O ASN D 563 " (cutoff:3.500A) removed outlier: 4.923A 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 removed outlier: 4.022A pdb=" N LYS D 622 " --> pdb=" O ASN D 618 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Z' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'Z' and resid 53 through 54 removed outlier: 5.354A pdb=" N PHE Z 46 " --> pdb=" O GLN Z 37 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLN Z 37 " --> pdb=" O PHE Z 46 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 45 removed outlier: 3.585A pdb=" N ILE A 38 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU A 103 " --> pdb=" O GLY A 67 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ASN A 69 " --> pdb=" O GLU A 103 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 42 through 45 removed outlier: 3.585A pdb=" N ILE A 38 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL A 96 " --> pdb=" O THR B 581 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 86 through 89 Processing sheet with id=AA6, first strand: chain 'A' and resid 105 through 114 removed outlier: 6.645A pdb=" N GLU A 106 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N HIS A 139 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N VAL A 141 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ASN A 110 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N GLY A 143 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLU A 112 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ARG A 136 " --> pdb=" O THR A 216 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ILE A 218 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N VAL A 138 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N TYR A 220 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LYS A 140 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ALA A 222 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N SER A 142 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ARG A 219 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TYR A 241 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TRP A 275 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN A 243 " --> pdb=" O TRP A 275 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LYS A 272 " --> pdb=" O UNK A 472 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N UNK A 474 " --> pdb=" O LYS A 272 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE A 274 " --> pdb=" O UNK A 474 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N UNK A 476 " --> pdb=" O ILE A 274 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Y' and resid 4 through 7 Processing sheet with id=AA8, first strand: chain 'Y' and resid 53 through 54 removed outlier: 5.353A pdb=" N PHE Y 46 " --> pdb=" O GLN Y 37 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLN Y 37 " --> pdb=" O PHE Y 46 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'L' and resid 53 through 54 removed outlier: 5.354A pdb=" N PHE L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLN L 37 " --> pdb=" O PHE L 46 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'H' and resid 59 through 60 removed outlier: 6.667A pdb=" N TRP H 37 " --> pdb=" O ILE H 49 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLU H 51 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TRP H 35 " --> pdb=" O GLU H 51 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 59 through 60 removed outlier: 6.667A pdb=" N TRP H 37 " --> pdb=" O ILE H 49 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLU H 51 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TRP H 35 " --> pdb=" O GLU H 51 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 42 through 45 removed outlier: 3.584A pdb=" N ILE C 38 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU C 103 " --> pdb=" O GLY C 67 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ASN C 69 " --> pdb=" O GLU C 103 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 42 through 45 removed outlier: 3.584A pdb=" N ILE C 38 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL C 96 " --> pdb=" O THR D 581 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 86 through 89 Processing sheet with id=AB8, first strand: chain 'C' and resid 105 through 114 removed outlier: 6.645A pdb=" N GLU C 106 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N HIS C 139 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N CYS C 108 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N VAL C 141 " --> pdb=" O CYS C 108 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ASN C 110 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N GLY C 143 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLU C 112 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ARG C 136 " --> pdb=" O THR C 216 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ILE C 218 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N VAL C 138 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N TYR C 220 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LYS C 140 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ALA C 222 " --> pdb=" O LYS C 140 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N SER C 142 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ARG C 219 " --> pdb=" O GLU C 235 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR C 241 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TRP C 275 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN C 243 " --> pdb=" O TRP C 275 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LYS C 272 " --> pdb=" O UNK C 472 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N UNK C 474 " --> pdb=" O LYS C 272 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE C 274 " --> pdb=" O UNK C 474 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N UNK C 476 " --> pdb=" O ILE C 274 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 42 through 45 removed outlier: 3.584A pdb=" N ILE E 38 " --> pdb=" O ILE E 185 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU E 103 " --> pdb=" O GLY E 67 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ASN E 69 " --> pdb=" O GLU E 103 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 42 through 45 removed outlier: 3.584A pdb=" N ILE E 38 " --> pdb=" O ILE E 185 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL E 96 " --> pdb=" O THR F 581 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 86 through 89 Processing sheet with id=AC3, first strand: chain 'E' and resid 105 through 114 removed outlier: 6.645A pdb=" N GLU E 106 " --> pdb=" O TYR E 137 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N HIS E 139 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N CYS E 108 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N VAL E 141 " --> pdb=" O CYS E 108 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ASN E 110 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N GLY E 143 " --> pdb=" O ASN E 110 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLU E 112 " --> pdb=" O GLY E 143 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ARG E 136 " --> pdb=" O THR E 216 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ILE E 218 " --> pdb=" O ARG E 136 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N VAL E 138 " --> pdb=" O ILE E 218 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N TYR E 220 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LYS E 140 " --> pdb=" O TYR E 220 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ALA E 222 " --> pdb=" O LYS E 140 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N SER E 142 " --> pdb=" O ALA E 222 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ARG E 219 " --> pdb=" O GLU E 235 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TYR E 241 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TRP E 275 " --> pdb=" O TYR E 241 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN E 243 " --> pdb=" O TRP E 275 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LYS E 272 " --> pdb=" O UNK E 472 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N UNK E 474 " --> pdb=" O LYS E 272 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE E 274 " --> pdb=" O UNK E 474 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N UNK E 476 " --> pdb=" O ILE E 274 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'W' and resid 3 through 7 Processing sheet with id=AC5, first strand: chain 'W' and resid 59 through 60 removed outlier: 6.666A pdb=" N TRP W 37 " --> pdb=" O ILE W 49 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLU W 51 " --> pdb=" O TRP W 35 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TRP W 35 " --> pdb=" O GLU W 51 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'W' and resid 59 through 60 removed outlier: 6.666A pdb=" N TRP W 37 " --> pdb=" O ILE W 49 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLU W 51 " --> pdb=" O TRP W 35 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TRP W 35 " --> pdb=" O GLU W 51 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'Q' and resid 3 through 7 Processing sheet with id=AC8, first strand: chain 'Q' and resid 59 through 60 removed outlier: 6.667A pdb=" N TRP Q 37 " --> pdb=" O ILE Q 49 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLU Q 51 " --> pdb=" O TRP Q 35 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TRP Q 35 " --> pdb=" O GLU Q 51 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Q' and resid 59 through 60 removed outlier: 6.667A pdb=" N TRP Q 37 " --> pdb=" O ILE Q 49 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLU Q 51 " --> pdb=" O TRP Q 35 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TRP Q 35 " --> pdb=" O GLU Q 51 " (cutoff:3.500A) 531 hydrogen bonds defined for protein. 1341 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: 2.73 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 4568 1.34 - 1.49: 4726 1.49 - 1.64: 5145 1.64 - 1.79: 24 1.79 - 1.94: 24 Bond restraints: 14487 Sorted by residual: bond pdb=" CD1 TYR L 32 " pdb=" CE1 TYR L 32 " ideal model delta sigma weight residual 1.382 1.248 0.134 3.00e-02 1.11e+03 2.00e+01 bond pdb=" CD1 TYR Z 32 " pdb=" CE1 TYR Z 32 " ideal model delta sigma weight residual 1.382 1.248 0.134 3.00e-02 1.11e+03 2.00e+01 bond pdb=" CD1 TYR Y 32 " pdb=" CE1 TYR Y 32 " ideal model delta sigma weight residual 1.382 1.249 0.133 3.00e-02 1.11e+03 1.98e+01 bond pdb=" C1 NAG D 701 " pdb=" O5 NAG D 701 " ideal model delta sigma weight residual 1.406 1.492 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" C1 NAG B 701 " pdb=" O5 NAG B 701 " ideal model delta sigma weight residual 1.406 1.492 -0.086 2.00e-02 2.50e+03 1.86e+01 ... (remaining 14482 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.83: 18997 3.83 - 7.66: 596 7.66 - 11.50: 87 11.50 - 15.33: 21 15.33 - 19.16: 9 Bond angle restraints: 19710 Sorted by residual: angle pdb=" N GLN B 521 " pdb=" CA GLN B 521 " pdb=" C GLN B 521 " ideal model delta sigma weight residual 107.99 119.89 -11.90 1.76e+00 3.23e-01 4.57e+01 angle pdb=" N GLN F 521 " pdb=" CA GLN F 521 " pdb=" C GLN F 521 " ideal model delta sigma weight residual 107.99 119.88 -11.89 1.76e+00 3.23e-01 4.56e+01 angle pdb=" N GLN D 521 " pdb=" CA GLN D 521 " pdb=" C GLN D 521 " ideal model delta sigma weight residual 107.99 119.87 -11.88 1.76e+00 3.23e-01 4.55e+01 angle pdb=" N VAL C 52 " pdb=" CA VAL C 52 " pdb=" C VAL C 52 " ideal model delta sigma weight residual 109.34 96.71 12.63 2.08e+00 2.31e-01 3.68e+01 angle pdb=" N VAL A 52 " pdb=" CA VAL A 52 " pdb=" C VAL A 52 " ideal model delta sigma weight residual 109.34 96.73 12.61 2.08e+00 2.31e-01 3.68e+01 ... (remaining 19705 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.21: 7853 20.21 - 40.41: 613 40.41 - 60.61: 132 60.61 - 80.82: 36 80.82 - 101.02: 18 Dihedral angle restraints: 8652 sinusoidal: 3489 harmonic: 5163 Sorted by residual: dihedral pdb=" CA PHE Y 46 " pdb=" C PHE Y 46 " pdb=" N LEU Y 47 " pdb=" CA LEU Y 47 " ideal model delta harmonic sigma weight residual 180.00 149.47 30.53 0 5.00e+00 4.00e-02 3.73e+01 dihedral pdb=" CA PHE L 46 " pdb=" C PHE L 46 " pdb=" N LEU L 47 " pdb=" CA LEU L 47 " ideal model delta harmonic sigma weight residual 180.00 149.50 30.50 0 5.00e+00 4.00e-02 3.72e+01 dihedral pdb=" CA PHE Z 46 " pdb=" C PHE Z 46 " pdb=" N LEU Z 47 " pdb=" CA LEU Z 47 " ideal model delta harmonic sigma weight residual 180.00 149.50 30.50 0 5.00e+00 4.00e-02 3.72e+01 ... (remaining 8649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1236 0.057 - 0.115: 622 0.115 - 0.172: 253 0.172 - 0.230: 89 0.230 - 0.287: 35 Chirality restraints: 2235 Sorted by residual: chirality pdb=" CB ILE F 610 " pdb=" CA ILE F 610 " pdb=" CG1 ILE F 610 " pdb=" CG2 ILE F 610 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CB ILE B 610 " pdb=" CA ILE B 610 " pdb=" CG1 ILE B 610 " pdb=" CG2 ILE B 610 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CB ILE D 610 " pdb=" CA ILE D 610 " pdb=" CG1 ILE D 610 " pdb=" CG2 ILE D 610 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 2232 not shown) Planarity restraints: 2523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE E 274 " 0.022 2.00e-02 2.50e+03 4.40e-02 1.93e+01 pdb=" C ILE E 274 " -0.076 2.00e-02 2.50e+03 pdb=" O ILE E 274 " 0.029 2.00e-02 2.50e+03 pdb=" N TRP E 275 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 274 " -0.022 2.00e-02 2.50e+03 4.37e-02 1.91e+01 pdb=" C ILE A 274 " 0.076 2.00e-02 2.50e+03 pdb=" O ILE A 274 " -0.029 2.00e-02 2.50e+03 pdb=" N TRP A 275 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 274 " 0.022 2.00e-02 2.50e+03 4.36e-02 1.90e+01 pdb=" C ILE C 274 " -0.075 2.00e-02 2.50e+03 pdb=" O ILE C 274 " 0.029 2.00e-02 2.50e+03 pdb=" N TRP C 275 " 0.025 2.00e-02 2.50e+03 ... (remaining 2520 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 124 2.55 - 3.14: 10175 3.14 - 3.73: 20540 3.73 - 4.31: 27690 4.31 - 4.90: 48759 Nonbonded interactions: 107288 Sorted by model distance: nonbonded pdb=" SG CYS A 53 " pdb=" SG CYS B 609 " model vdw 1.965 3.760 nonbonded pdb=" SG CYS D 511 " pdb=" SG CYS D 556 " model vdw 2.025 3.760 nonbonded pdb=" SG CYS F 511 " pdb=" SG CYS F 556 " model vdw 2.025 3.760 nonbonded pdb=" SG CYS B 511 " pdb=" SG CYS B 556 " model vdw 2.026 3.760 nonbonded pdb=" SG CYS D 601 " pdb=" SG CYS D 608 " model vdw 2.043 3.760 ... (remaining 107283 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: 0.04 Found NCS groups: ncs_group { reference = chain 'Z' selection = chain 'Y' selection = chain 'L' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'D' } ncs_group { reference = chain 'H' selection = chain 'W' selection = chain 'Q' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.940 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 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 : 0.015 0.137 14508 Z= 0.615 Angle : 1.687 19.160 19764 Z= 0.893 Chirality : 0.085 0.287 2235 Planarity : 0.011 0.071 2517 Dihedral : 16.533 101.024 5325 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.69 % Favored : 92.80 % Rotamer: Outliers : 3.96 % Allowed : 8.05 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.00 (0.17), residues: 1749 helix: 0.77 (0.32), residues: 186 sheet: -0.70 (0.21), residues: 498 loop : -2.13 (0.16), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.003 ARG B 559 TYR 0.026 0.005 TYR W 54 PHE 0.058 0.007 PHE C 252 TRP 0.049 0.006 TRP C 104 HIS 0.008 0.003 HIS F 516 Details of bonding type rmsd covalent geometry : bond 0.01462 (14487) covalent geometry : angle 1.66678 (19710) SS BOND : bond 0.00561 ( 9) SS BOND : angle 2.67662 ( 18) hydrogen bonds : bond 0.15358 ( 474) hydrogen bonds : angle 8.26303 ( 1341) link_BETA1-4 : bond 0.00304 ( 6) link_BETA1-4 : angle 4.46350 ( 18) link_NAG-ASN : bond 0.01278 ( 6) link_NAG-ASN : angle 7.55022 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 212 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 103 LYS cc_start: 0.6613 (mptt) cc_final: 0.6096 (tttp) REVERT: H 35 TRP cc_start: 0.8165 (m100) cc_final: 0.7482 (m100) REVERT: E 56 LYS cc_start: 0.8316 (mmtp) cc_final: 0.8100 (mmtp) REVERT: W 54 TYR cc_start: 0.6568 (p90) cc_final: 0.6308 (p90) REVERT: Q 54 TYR cc_start: 0.7033 (p90) cc_final: 0.6785 (p90) REVERT: Q 60 TYR cc_start: 0.7694 (m-80) cc_final: 0.7367 (m-80) outliers start: 60 outliers final: 18 residues processed: 267 average time/residue: 0.1319 time to fit residues: 50.6308 Evaluate side-chains 170 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain B residue 620 THR Chi-restraints excluded: chain B residue 627 ILE Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain E residue 258 GLU Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain F residue 627 ILE Chi-restraints excluded: chain D residue 620 THR Chi-restraints excluded: chain D residue 627 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 40.0000 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.2980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 93 ASN A 257 ASN Y 53 ASN Y 93 ASN B 550 ASN L 53 ASN H 3 GLN H 61 ASN C 257 ASN E 257 ASN W 3 GLN W 61 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.239797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.186481 restraints weight = 17049.842| |-----------------------------------------------------------------------------| r_work (start): 0.4211 rms_B_bonded: 3.94 r_work: 0.3898 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14508 Z= 0.169 Angle : 0.823 12.127 19764 Z= 0.413 Chirality : 0.049 0.213 2235 Planarity : 0.006 0.056 2517 Dihedral : 10.972 101.561 2221 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.55 % Favored : 94.28 % Rotamer: Outliers : 2.84 % Allowed : 12.94 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.57 (0.18), residues: 1749 helix: 0.93 (0.35), residues: 213 sheet: -0.39 (0.21), residues: 519 loop : -1.93 (0.17), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 54 TYR 0.023 0.002 TYR A 232 PHE 0.020 0.002 PHE C 252 TRP 0.020 0.002 TRP H 48 HIS 0.007 0.001 HIS D 516 Details of bonding type rmsd covalent geometry : bond 0.00367 (14487) covalent geometry : angle 0.79818 (19710) SS BOND : bond 0.00248 ( 9) SS BOND : angle 2.02046 ( 18) hydrogen bonds : bond 0.04687 ( 474) hydrogen bonds : angle 6.51883 ( 1341) link_BETA1-4 : bond 0.00252 ( 6) link_BETA1-4 : angle 2.61718 ( 18) link_NAG-ASN : bond 0.00549 ( 6) link_NAG-ASN : angle 5.97193 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 163 time to evaluate : 0.529 Fit side-chains revert: symmetry clash REVERT: A 137 TYR cc_start: 0.7496 (m-80) cc_final: 0.7167 (m-80) REVERT: A 163 ASP cc_start: 0.8111 (t70) cc_final: 0.7884 (t0) REVERT: B 548 MET cc_start: 0.7026 (ttt) cc_final: 0.6813 (ttt) REVERT: H 35 TRP cc_start: 0.8382 (m100) cc_final: 0.7675 (m100) REVERT: C 56 LYS cc_start: 0.8396 (mmtp) cc_final: 0.8083 (mmtp) REVERT: E 56 LYS cc_start: 0.8488 (mmtp) cc_final: 0.8080 (mmtp) REVERT: E 136 ARG cc_start: 0.6823 (mpt-90) cc_final: 0.6512 (mpt-90) REVERT: Q 60 TYR cc_start: 0.7618 (m-80) cc_final: 0.7124 (m-80) outliers start: 43 outliers final: 23 residues processed: 191 average time/residue: 0.1340 time to fit residues: 36.5149 Evaluate side-chains 168 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 2 ILE Chi-restraints excluded: chain Z residue 37 GLN Chi-restraints excluded: chain Z residue 93 ASN Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain Y residue 12 SER Chi-restraints excluded: chain Y residue 31 THR Chi-restraints excluded: chain Y residue 37 GLN Chi-restraints excluded: chain Y residue 69 THR Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 627 ILE Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain F residue 591 ASP Chi-restraints excluded: chain F residue 627 ILE Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 627 ILE Chi-restraints excluded: chain W residue 11 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 44 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 165 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 121 optimal weight: 0.0000 chunk 40 optimal weight: 8.9990 chunk 62 optimal weight: 0.0980 chunk 136 optimal weight: 7.9990 chunk 61 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 53 ASN A 257 ASN H 3 GLN C 257 ASN E 257 ASN F 550 ASN W 3 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.240004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.187705 restraints weight = 17148.656| |-----------------------------------------------------------------------------| r_work (start): 0.4227 rms_B_bonded: 3.56 r_work: 0.3922 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14508 Z= 0.142 Angle : 0.735 12.878 19764 Z= 0.365 Chirality : 0.048 0.272 2235 Planarity : 0.005 0.056 2517 Dihedral : 7.230 43.984 2195 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.06 % Favored : 93.77 % Rotamer: Outliers : 2.77 % Allowed : 13.86 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.45 (0.18), residues: 1749 helix: 0.80 (0.34), residues: 213 sheet: -0.42 (0.21), residues: 555 loop : -1.74 (0.17), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Z 96 TYR 0.025 0.002 TYR W 60 PHE 0.012 0.002 PHE E 132 TRP 0.019 0.001 TRP H 48 HIS 0.002 0.000 HIS E 139 Details of bonding type rmsd covalent geometry : bond 0.00316 (14487) covalent geometry : angle 0.71388 (19710) SS BOND : bond 0.00433 ( 9) SS BOND : angle 1.32747 ( 18) hydrogen bonds : bond 0.03931 ( 474) hydrogen bonds : angle 5.94899 ( 1341) link_BETA1-4 : bond 0.00267 ( 6) link_BETA1-4 : angle 2.73019 ( 18) link_NAG-ASN : bond 0.00595 ( 6) link_NAG-ASN : angle 5.05248 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 157 time to evaluate : 0.549 Fit side-chains REVERT: A 111 LEU cc_start: 0.6764 (mp) cc_final: 0.6524 (mp) REVERT: Y 55 GLN cc_start: 0.7061 (OUTLIER) cc_final: 0.6615 (tt0) REVERT: L 55 GLN cc_start: 0.7315 (OUTLIER) cc_final: 0.6987 (tt0) REVERT: H 35 TRP cc_start: 0.8239 (m100) cc_final: 0.7713 (m100) REVERT: C 56 LYS cc_start: 0.8573 (mmtp) cc_final: 0.8236 (mmtp) REVERT: E 56 LYS cc_start: 0.8499 (mmtp) cc_final: 0.7979 (mmtm) REVERT: E 136 ARG cc_start: 0.6800 (mpt-90) cc_final: 0.6386 (mpt-90) REVERT: D 596 ARG cc_start: 0.7355 (ttt90) cc_final: 0.7132 (ttt90) REVERT: Q 60 TYR cc_start: 0.7687 (m-80) cc_final: 0.7287 (m-80) outliers start: 42 outliers final: 25 residues processed: 182 average time/residue: 0.1399 time to fit residues: 36.6734 Evaluate side-chains 174 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 2 ILE Chi-restraints excluded: chain Z residue 37 GLN Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 48 ILE Chi-restraints excluded: chain Z residue 58 VAL Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain Y residue 3 GLN Chi-restraints excluded: chain Y residue 55 GLN Chi-restraints excluded: chain Y residue 69 THR Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 55 GLN Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 591 ASP Chi-restraints excluded: chain W residue 2 VAL Chi-restraints excluded: chain W residue 36 THR Chi-restraints excluded: chain Q residue 36 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 164 optimal weight: 0.0870 chunk 84 optimal weight: 0.3980 chunk 140 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 42 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 chunk 158 optimal weight: 5.9990 chunk 86 optimal weight: 0.1980 chunk 82 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.5160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 GLN D 550 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.241229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.188945 restraints weight = 17028.533| |-----------------------------------------------------------------------------| r_work (start): 0.4241 rms_B_bonded: 3.60 r_work: 0.3916 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14508 Z= 0.120 Angle : 0.660 10.770 19764 Z= 0.330 Chirality : 0.045 0.159 2235 Planarity : 0.005 0.054 2517 Dihedral : 5.902 41.307 2187 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.77 % Allowed : 14.32 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.20 (0.18), residues: 1749 helix: 1.15 (0.35), residues: 213 sheet: -0.33 (0.21), residues: 558 loop : -1.56 (0.17), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 136 TYR 0.023 0.001 TYR Q 54 PHE 0.009 0.001 PHE B 572 TRP 0.024 0.001 TRP C 104 HIS 0.003 0.000 HIS F 549 Details of bonding type rmsd covalent geometry : bond 0.00260 (14487) covalent geometry : angle 0.64303 (19710) SS BOND : bond 0.00382 ( 9) SS BOND : angle 1.03837 ( 18) hydrogen bonds : bond 0.03400 ( 474) hydrogen bonds : angle 5.51087 ( 1341) link_BETA1-4 : bond 0.00241 ( 6) link_BETA1-4 : angle 2.21274 ( 18) link_NAG-ASN : bond 0.00712 ( 6) link_NAG-ASN : angle 4.41700 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 155 time to evaluate : 0.604 Fit side-chains REVERT: A 111 LEU cc_start: 0.6768 (OUTLIER) cc_final: 0.6523 (mp) REVERT: H 35 TRP cc_start: 0.8091 (m100) cc_final: 0.7665 (m100) REVERT: C 56 LYS cc_start: 0.8577 (mmtp) cc_final: 0.8230 (mmtp) REVERT: E 56 LYS cc_start: 0.8590 (mmtp) cc_final: 0.8038 (mmtm) REVERT: E 84 LYS cc_start: 0.7908 (mttt) cc_final: 0.7693 (mmtp) REVERT: E 136 ARG cc_start: 0.6777 (mpt-90) cc_final: 0.6261 (mpt-90) REVERT: D 548 MET cc_start: 0.7356 (mmm) cc_final: 0.6417 (mtp) REVERT: Q 60 TYR cc_start: 0.7776 (m-80) cc_final: 0.7372 (m-80) outliers start: 42 outliers final: 29 residues processed: 182 average time/residue: 0.1240 time to fit residues: 33.0205 Evaluate side-chains 171 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 2 ILE Chi-restraints excluded: chain Z residue 11 LEU Chi-restraints excluded: chain Z residue 31 THR Chi-restraints excluded: chain Z residue 37 GLN Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 58 VAL Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain Y residue 3 GLN Chi-restraints excluded: chain Y residue 37 GLN Chi-restraints excluded: chain Y residue 69 THR Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain F residue 540 GLU Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 591 ASP Chi-restraints excluded: chain W residue 2 VAL Chi-restraints excluded: chain W residue 36 THR Chi-restraints excluded: chain Q residue 36 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 101 optimal weight: 520.0000 chunk 85 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 chunk 123 optimal weight: 40.0000 chunk 66 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 98 optimal weight: 8.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 74 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.236475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.183760 restraints weight = 17126.420| |-----------------------------------------------------------------------------| r_work (start): 0.4250 rms_B_bonded: 3.33 r_work: 0.3956 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14508 Z= 0.166 Angle : 0.724 15.073 19764 Z= 0.354 Chirality : 0.047 0.187 2235 Planarity : 0.005 0.056 2517 Dihedral : 6.099 39.906 2187 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 3.37 % Allowed : 14.98 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.26 (0.18), residues: 1749 helix: 0.84 (0.34), residues: 213 sheet: -0.38 (0.21), residues: 558 loop : -1.53 (0.17), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 136 TYR 0.021 0.002 TYR Q 54 PHE 0.016 0.002 PHE A 132 TRP 0.018 0.002 TRP Q 48 HIS 0.005 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00388 (14487) covalent geometry : angle 0.70810 (19710) SS BOND : bond 0.00544 ( 9) SS BOND : angle 2.26853 ( 18) hydrogen bonds : bond 0.03746 ( 474) hydrogen bonds : angle 5.62363 ( 1341) link_BETA1-4 : bond 0.00116 ( 6) link_BETA1-4 : angle 2.09939 ( 18) link_NAG-ASN : bond 0.00782 ( 6) link_NAG-ASN : angle 4.13619 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 151 time to evaluate : 0.551 Fit side-chains REVERT: A 111 LEU cc_start: 0.6869 (OUTLIER) cc_final: 0.6618 (mp) REVERT: Y 55 GLN cc_start: 0.7296 (OUTLIER) cc_final: 0.6793 (tt0) REVERT: L 55 GLN cc_start: 0.7474 (OUTLIER) cc_final: 0.7122 (tt0) REVERT: H 35 TRP cc_start: 0.8247 (m100) cc_final: 0.7760 (m100) REVERT: C 56 LYS cc_start: 0.8571 (mmtp) cc_final: 0.7924 (mmtt) REVERT: E 56 LYS cc_start: 0.8629 (mmtp) cc_final: 0.8062 (mmtm) REVERT: E 84 LYS cc_start: 0.8191 (mttt) cc_final: 0.7865 (mmtp) REVERT: E 136 ARG cc_start: 0.6873 (mpt-90) cc_final: 0.6318 (mpt-90) REVERT: F 548 MET cc_start: 0.7588 (tpt) cc_final: 0.6906 (ttp) REVERT: D 548 MET cc_start: 0.7373 (mmm) cc_final: 0.6496 (mtp) REVERT: Q 60 TYR cc_start: 0.7910 (m-80) cc_final: 0.7584 (m-80) outliers start: 51 outliers final: 34 residues processed: 186 average time/residue: 0.1320 time to fit residues: 35.5047 Evaluate side-chains 178 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 141 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 2 ILE Chi-restraints excluded: chain Z residue 37 GLN Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain Y residue 12 SER Chi-restraints excluded: chain Y residue 37 GLN Chi-restraints excluded: chain Y residue 55 GLN Chi-restraints excluded: chain Y residue 69 THR Chi-restraints excluded: chain Y residue 83 PHE Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 55 GLN Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain F residue 540 GLU Chi-restraints excluded: chain F residue 591 ASP Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 591 ASP Chi-restraints excluded: chain D residue 604 LEU Chi-restraints excluded: chain W residue 2 VAL Chi-restraints excluded: chain W residue 36 THR Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 36 THR Chi-restraints excluded: chain Q residue 72 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 79 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 168 optimal weight: 0.7980 chunk 130 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 166 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 chunk 128 optimal weight: 0.0980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.227885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.173710 restraints weight = 17250.142| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 3.74 r_work: 0.3756 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14508 Z= 0.175 Angle : 0.712 15.202 19764 Z= 0.352 Chirality : 0.047 0.209 2235 Planarity : 0.005 0.056 2517 Dihedral : 6.093 40.974 2187 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 3.63 % Allowed : 15.91 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.34 (0.18), residues: 1749 helix: 0.30 (0.33), residues: 231 sheet: -0.13 (0.22), residues: 513 loop : -1.64 (0.17), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 136 TYR 0.021 0.002 TYR Q 54 PHE 0.016 0.002 PHE E 132 TRP 0.022 0.002 TRP Q 48 HIS 0.003 0.001 HIS D 516 Details of bonding type rmsd covalent geometry : bond 0.00412 (14487) covalent geometry : angle 0.69846 (19710) SS BOND : bond 0.00468 ( 9) SS BOND : angle 1.87743 ( 18) hydrogen bonds : bond 0.03746 ( 474) hydrogen bonds : angle 5.63874 ( 1341) link_BETA1-4 : bond 0.00127 ( 6) link_BETA1-4 : angle 1.92057 ( 18) link_NAG-ASN : bond 0.00805 ( 6) link_NAG-ASN : angle 3.91121 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 150 time to evaluate : 0.538 Fit side-chains REVERT: Z 81 GLU cc_start: 0.8478 (tp30) cc_final: 0.8275 (tp30) REVERT: A 56 LYS cc_start: 0.8245 (mmtp) cc_final: 0.7822 (mmtp) REVERT: A 111 LEU cc_start: 0.6968 (OUTLIER) cc_final: 0.6737 (mp) REVERT: A 136 ARG cc_start: 0.6596 (mtt-85) cc_final: 0.6292 (mtt-85) REVERT: Y 55 GLN cc_start: 0.7325 (OUTLIER) cc_final: 0.6766 (tt0) REVERT: L 37 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.7425 (tt0) REVERT: H 35 TRP cc_start: 0.8198 (m100) cc_final: 0.7691 (m100) REVERT: H 96 CYS cc_start: 0.7228 (p) cc_final: 0.6816 (p) REVERT: C 56 LYS cc_start: 0.8503 (mmtp) cc_final: 0.7792 (mmtt) REVERT: E 56 LYS cc_start: 0.8627 (mmtp) cc_final: 0.8292 (mmtp) REVERT: E 84 LYS cc_start: 0.8348 (mttt) cc_final: 0.8011 (mmtp) REVERT: E 136 ARG cc_start: 0.7009 (mpt-90) cc_final: 0.6154 (mmp80) REVERT: F 548 MET cc_start: 0.7853 (tpt) cc_final: 0.7340 (ttp) REVERT: D 548 MET cc_start: 0.7436 (mmm) cc_final: 0.6616 (mtp) REVERT: W 4 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8096 (mt) REVERT: Q 60 TYR cc_start: 0.7995 (m-80) cc_final: 0.7693 (m-80) outliers start: 55 outliers final: 33 residues processed: 187 average time/residue: 0.1354 time to fit residues: 36.6581 Evaluate side-chains 175 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 138 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 2 ILE Chi-restraints excluded: chain Z residue 37 GLN Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain Y residue 12 SER Chi-restraints excluded: chain Y residue 37 GLN Chi-restraints excluded: chain Y residue 55 GLN Chi-restraints excluded: chain Y residue 69 THR Chi-restraints excluded: chain Y residue 83 PHE Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain F residue 540 GLU Chi-restraints excluded: chain F residue 591 ASP Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 591 ASP Chi-restraints excluded: chain W residue 2 VAL Chi-restraints excluded: chain W residue 4 LEU Chi-restraints excluded: chain W residue 36 THR Chi-restraints excluded: chain Q residue 11 LEU Chi-restraints excluded: chain Q residue 36 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 114 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 96 optimal weight: 20.0000 chunk 52 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 97 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 42 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.226591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.171439 restraints weight = 17307.985| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 3.72 r_work: 0.3729 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14508 Z= 0.204 Angle : 0.743 14.946 19764 Z= 0.366 Chirality : 0.048 0.174 2235 Planarity : 0.005 0.057 2517 Dihedral : 6.237 44.418 2187 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 3.04 % Allowed : 17.16 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.40 (0.18), residues: 1749 helix: 0.12 (0.33), residues: 231 sheet: -0.14 (0.22), residues: 501 loop : -1.66 (0.17), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 136 TYR 0.022 0.002 TYR W 60 PHE 0.016 0.002 PHE E 132 TRP 0.022 0.002 TRP Q 48 HIS 0.003 0.001 HIS F 516 Details of bonding type rmsd covalent geometry : bond 0.00490 (14487) covalent geometry : angle 0.72994 (19710) SS BOND : bond 0.00603 ( 9) SS BOND : angle 2.03566 ( 18) hydrogen bonds : bond 0.03934 ( 474) hydrogen bonds : angle 5.70581 ( 1341) link_BETA1-4 : bond 0.00107 ( 6) link_BETA1-4 : angle 1.99466 ( 18) link_NAG-ASN : bond 0.00821 ( 6) link_NAG-ASN : angle 3.85582 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 137 time to evaluate : 0.359 Fit side-chains REVERT: Z 81 GLU cc_start: 0.8526 (tp30) cc_final: 0.8319 (tp30) REVERT: A 56 LYS cc_start: 0.8318 (mmtp) cc_final: 0.7881 (mmtp) REVERT: A 111 LEU cc_start: 0.7147 (OUTLIER) cc_final: 0.6851 (mp) REVERT: A 162 TYR cc_start: 0.8372 (m-80) cc_final: 0.7318 (m-80) REVERT: Y 55 GLN cc_start: 0.7450 (OUTLIER) cc_final: 0.6904 (tt0) REVERT: L 37 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.7363 (tt0) REVERT: H 35 TRP cc_start: 0.8257 (m100) cc_final: 0.7760 (m100) REVERT: H 96 CYS cc_start: 0.7314 (p) cc_final: 0.6896 (p) REVERT: C 56 LYS cc_start: 0.8560 (mmtp) cc_final: 0.7863 (mmtt) REVERT: E 56 LYS cc_start: 0.8671 (mmtp) cc_final: 0.8258 (mmtp) REVERT: E 84 LYS cc_start: 0.8373 (mttt) cc_final: 0.8037 (mmtp) REVERT: E 136 ARG cc_start: 0.6940 (mpt-90) cc_final: 0.6393 (mpt-90) REVERT: D 548 MET cc_start: 0.7413 (mmm) cc_final: 0.6631 (mtp) REVERT: W 67 ARG cc_start: 0.7322 (ptt180) cc_final: 0.7106 (ptt90) REVERT: Q 60 TYR cc_start: 0.8025 (m-80) cc_final: 0.7776 (m-80) outliers start: 46 outliers final: 29 residues processed: 163 average time/residue: 0.1312 time to fit residues: 30.6953 Evaluate side-chains 166 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 2 ILE Chi-restraints excluded: chain Z residue 37 GLN Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain Y residue 12 SER Chi-restraints excluded: chain Y residue 37 GLN Chi-restraints excluded: chain Y residue 55 GLN Chi-restraints excluded: chain Y residue 69 THR Chi-restraints excluded: chain Y residue 83 PHE Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain F residue 540 GLU Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 591 ASP Chi-restraints excluded: chain F residue 604 LEU Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 591 ASP Chi-restraints excluded: chain W residue 2 VAL Chi-restraints excluded: chain W residue 36 THR Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 36 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 138 optimal weight: 8.9990 chunk 47 optimal weight: 0.8980 chunk 120 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 165 optimal weight: 2.9990 chunk 121 optimal weight: 50.0000 chunk 136 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 109 optimal weight: 3.9990 chunk 86 optimal weight: 0.3980 chunk 89 optimal weight: 0.0470 overall best weight: 0.9880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.228759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.174547 restraints weight = 17221.555| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 4.11 r_work: 0.3755 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14508 Z= 0.143 Angle : 0.671 14.406 19764 Z= 0.333 Chirality : 0.046 0.155 2235 Planarity : 0.005 0.056 2517 Dihedral : 5.898 39.496 2187 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.51 % Allowed : 18.02 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.34 (0.19), residues: 1749 helix: 0.32 (0.34), residues: 231 sheet: -0.34 (0.22), residues: 546 loop : -1.55 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 136 TYR 0.018 0.001 TYR Q 54 PHE 0.012 0.001 PHE E 132 TRP 0.021 0.002 TRP Q 48 HIS 0.002 0.001 HIS D 516 Details of bonding type rmsd covalent geometry : bond 0.00334 (14487) covalent geometry : angle 0.65980 (19710) SS BOND : bond 0.00408 ( 9) SS BOND : angle 1.54754 ( 18) hydrogen bonds : bond 0.03431 ( 474) hydrogen bonds : angle 5.43727 ( 1341) link_BETA1-4 : bond 0.00117 ( 6) link_BETA1-4 : angle 1.77837 ( 18) link_NAG-ASN : bond 0.00746 ( 6) link_NAG-ASN : angle 3.57397 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 143 time to evaluate : 0.530 Fit side-chains REVERT: A 56 LYS cc_start: 0.8289 (mmtp) cc_final: 0.7854 (mmtp) REVERT: A 111 LEU cc_start: 0.7038 (OUTLIER) cc_final: 0.6828 (mp) REVERT: Y 55 GLN cc_start: 0.7386 (OUTLIER) cc_final: 0.6839 (tt0) REVERT: L 37 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.7289 (tt0) REVERT: H 35 TRP cc_start: 0.8099 (m100) cc_final: 0.7764 (m100) REVERT: H 96 CYS cc_start: 0.7208 (p) cc_final: 0.6803 (p) REVERT: C 56 LYS cc_start: 0.8523 (mmtp) cc_final: 0.7846 (mmtt) REVERT: E 56 LYS cc_start: 0.8638 (mmtp) cc_final: 0.8210 (mmtp) REVERT: E 84 LYS cc_start: 0.8363 (mttt) cc_final: 0.7993 (mmtp) REVERT: E 136 ARG cc_start: 0.6924 (mpt-90) cc_final: 0.6340 (mpt-90) REVERT: W 4 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8007 (mp) outliers start: 38 outliers final: 28 residues processed: 167 average time/residue: 0.1279 time to fit residues: 31.0895 Evaluate side-chains 171 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 2 ILE Chi-restraints excluded: chain Z residue 37 GLN Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain Y residue 12 SER Chi-restraints excluded: chain Y residue 37 GLN Chi-restraints excluded: chain Y residue 55 GLN Chi-restraints excluded: chain Y residue 69 THR Chi-restraints excluded: chain Y residue 83 PHE Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain F residue 540 GLU Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 591 ASP Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain W residue 2 VAL Chi-restraints excluded: chain W residue 4 LEU Chi-restraints excluded: chain W residue 36 THR Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 36 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 52 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 123 optimal weight: 10.0000 chunk 109 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 159 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 163 optimal weight: 6.9990 chunk 92 optimal weight: 0.8980 chunk 56 optimal weight: 20.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.225368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.175093 restraints weight = 17361.078| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 2.85 r_work: 0.3753 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 14508 Z= 0.231 Angle : 0.761 13.401 19764 Z= 0.378 Chirality : 0.048 0.199 2235 Planarity : 0.005 0.059 2517 Dihedral : 6.343 45.879 2187 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 2.71 % Allowed : 18.09 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.49 (0.19), residues: 1749 helix: -0.00 (0.33), residues: 231 sheet: -0.23 (0.22), residues: 501 loop : -1.67 (0.17), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 136 TYR 0.027 0.002 TYR H 54 PHE 0.017 0.002 PHE C 132 TRP 0.022 0.002 TRP W 48 HIS 0.002 0.001 HIS A 154 Details of bonding type rmsd covalent geometry : bond 0.00557 (14487) covalent geometry : angle 0.74788 (19710) SS BOND : bond 0.00579 ( 9) SS BOND : angle 2.11040 ( 18) hydrogen bonds : bond 0.04177 ( 474) hydrogen bonds : angle 5.75431 ( 1341) link_BETA1-4 : bond 0.00165 ( 6) link_BETA1-4 : angle 1.99249 ( 18) link_NAG-ASN : bond 0.00848 ( 6) link_NAG-ASN : angle 3.77045 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 142 time to evaluate : 0.531 Fit side-chains revert: symmetry clash REVERT: A 56 LYS cc_start: 0.8364 (mmtp) cc_final: 0.8014 (mmtp) REVERT: Y 55 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.6956 (tt0) REVERT: L 37 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.7434 (tt0) REVERT: H 35 TRP cc_start: 0.8227 (m100) cc_final: 0.7763 (m100) REVERT: H 96 CYS cc_start: 0.7279 (p) cc_final: 0.6890 (p) REVERT: C 56 LYS cc_start: 0.8583 (mmtp) cc_final: 0.7949 (mmtt) REVERT: E 56 LYS cc_start: 0.8644 (mmtp) cc_final: 0.8224 (mmtp) REVERT: E 84 LYS cc_start: 0.8292 (mttt) cc_final: 0.8047 (mmtp) REVERT: E 136 ARG cc_start: 0.6918 (mpt-90) cc_final: 0.6369 (mpt-90) REVERT: D 545 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7350 (mm-30) REVERT: W 4 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8075 (mt) outliers start: 41 outliers final: 30 residues processed: 168 average time/residue: 0.1382 time to fit residues: 33.2277 Evaluate side-chains 170 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 2 ILE Chi-restraints excluded: chain Z residue 11 LEU Chi-restraints excluded: chain Z residue 37 GLN Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain Y residue 12 SER Chi-restraints excluded: chain Y residue 37 GLN Chi-restraints excluded: chain Y residue 55 GLN Chi-restraints excluded: chain Y residue 69 THR Chi-restraints excluded: chain Y residue 83 PHE Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain F residue 540 GLU Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain W residue 2 VAL Chi-restraints excluded: chain W residue 4 LEU Chi-restraints excluded: chain W residue 36 THR Chi-restraints excluded: chain W residue 110 THR Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 36 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 114 optimal weight: 0.8980 chunk 160 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 chunk 32 optimal weight: 30.0000 chunk 0 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 135 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 146 optimal weight: 0.1980 chunk 93 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 89 GLN Y 93 ASN F 516 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.225885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.175446 restraints weight = 17052.234| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 2.98 r_work: 0.3751 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14508 Z= 0.162 Angle : 0.687 12.805 19764 Z= 0.344 Chirality : 0.046 0.187 2235 Planarity : 0.005 0.057 2517 Dihedral : 6.042 39.896 2187 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 2.24 % Allowed : 18.75 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.33 (0.19), residues: 1749 helix: 0.19 (0.34), residues: 231 sheet: -0.19 (0.23), residues: 513 loop : -1.57 (0.18), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 136 TYR 0.029 0.002 TYR H 54 PHE 0.013 0.002 PHE E 132 TRP 0.022 0.002 TRP W 48 HIS 0.002 0.001 HIS D 602 Details of bonding type rmsd covalent geometry : bond 0.00384 (14487) covalent geometry : angle 0.67603 (19710) SS BOND : bond 0.00476 ( 9) SS BOND : angle 1.59400 ( 18) hydrogen bonds : bond 0.03612 ( 474) hydrogen bonds : angle 5.50275 ( 1341) link_BETA1-4 : bond 0.00072 ( 6) link_BETA1-4 : angle 1.86153 ( 18) link_NAG-ASN : bond 0.00745 ( 6) link_NAG-ASN : angle 3.53808 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 142 time to evaluate : 0.526 Fit side-chains revert: symmetry clash REVERT: A 56 LYS cc_start: 0.8385 (mmtp) cc_final: 0.7921 (mmtp) REVERT: Y 55 GLN cc_start: 0.7477 (OUTLIER) cc_final: 0.6935 (tt0) REVERT: L 37 GLN cc_start: 0.7747 (OUTLIER) cc_final: 0.7318 (tt0) REVERT: H 35 TRP cc_start: 0.8134 (m100) cc_final: 0.7701 (m100) REVERT: H 96 CYS cc_start: 0.7239 (p) cc_final: 0.6865 (p) REVERT: C 56 LYS cc_start: 0.8594 (mmtp) cc_final: 0.7945 (mmtt) REVERT: C 106 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7235 (mm-30) REVERT: C 136 ARG cc_start: 0.7086 (mpt180) cc_final: 0.6841 (mpt-90) REVERT: E 56 LYS cc_start: 0.8633 (mmtp) cc_final: 0.8199 (mmtp) REVERT: E 84 LYS cc_start: 0.8316 (mttt) cc_final: 0.8067 (mmtp) REVERT: E 136 ARG cc_start: 0.7070 (mpt-90) cc_final: 0.6772 (mpt-90) REVERT: F 548 MET cc_start: 0.7623 (ttt) cc_final: 0.7377 (ttp) REVERT: D 545 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7297 (mm-30) REVERT: W 4 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8060 (mp) outliers start: 34 outliers final: 31 residues processed: 163 average time/residue: 0.1334 time to fit residues: 31.5738 Evaluate side-chains 173 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 139 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 2 ILE Chi-restraints excluded: chain Z residue 11 LEU Chi-restraints excluded: chain Z residue 37 GLN Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain Y residue 12 SER Chi-restraints excluded: chain Y residue 37 GLN Chi-restraints excluded: chain Y residue 55 GLN Chi-restraints excluded: chain Y residue 69 THR Chi-restraints excluded: chain Y residue 83 PHE Chi-restraints excluded: chain Y residue 93 ASN Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain F residue 540 GLU Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain W residue 2 VAL Chi-restraints excluded: chain W residue 4 LEU Chi-restraints excluded: chain W residue 36 THR Chi-restraints excluded: chain W residue 110 THR Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 36 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 105 optimal weight: 2.9990 chunk 153 optimal weight: 6.9990 chunk 110 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 164 optimal weight: 3.9990 chunk 157 optimal weight: 0.7980 chunk 166 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 150 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.226167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.175347 restraints weight = 16994.068| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 3.14 r_work: 0.3748 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.146 14508 Z= 0.188 Angle : 0.882 59.196 19764 Z= 0.488 Chirality : 0.050 0.929 2235 Planarity : 0.005 0.057 2517 Dihedral : 6.042 39.890 2187 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 2.44 % Allowed : 18.75 % Favored : 78.81 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 6.45 % 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: -1.33 (0.19), residues: 1749 helix: 0.21 (0.34), residues: 231 sheet: -0.19 (0.23), residues: 513 loop : -1.57 (0.18), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG B 596 TYR 0.028 0.002 TYR H 54 PHE 0.012 0.001 PHE E 132 TRP 0.032 0.002 TRP E 104 HIS 0.043 0.001 HIS F 516 Details of bonding type rmsd covalent geometry : bond 0.00413 (14487) covalent geometry : angle 0.87332 (19710) SS BOND : bond 0.00488 ( 9) SS BOND : angle 1.57814 ( 18) hydrogen bonds : bond 0.03590 ( 474) hydrogen bonds : angle 5.50326 ( 1341) link_BETA1-4 : bond 0.00224 ( 6) link_BETA1-4 : angle 1.88700 ( 18) link_NAG-ASN : bond 0.00749 ( 6) link_NAG-ASN : angle 3.52897 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3817.26 seconds wall clock time: 66 minutes 9.07 seconds (3969.07 seconds total)