Starting phenix.real_space_refine on Sun May 3 15:04:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ujf_64214/05_2026/9ujf_64214.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ujf_64214/05_2026/9ujf_64214.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ujf_64214/05_2026/9ujf_64214.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ujf_64214/05_2026/9ujf_64214.map" model { file = "/net/cci-nas-00/data/ceres_data/9ujf_64214/05_2026/9ujf_64214.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ujf_64214/05_2026/9ujf_64214.cif" } resolution = 2.01 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= -0.002 sd= 0.152 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: 6 Type Number sf(0) Gaussians Zn 10 6.06 5 P 30 5.49 5 S 70 5.16 5 C 8618 2.51 5 N 2370 2.21 5 O 2685 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13783 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 1334 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1331 Classifications: {'peptide': 173} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 166} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Conformer: "B" Number of residues, atoms: 173, 1331 Classifications: {'peptide': 173} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 166} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 bond proxies already assigned to first conformer: 1355 Chain: "B" Number of atoms: 1329 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1326 Classifications: {'peptide': 173} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 166} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Conformer: "B" Number of residues, atoms: 173, 1326 Classifications: {'peptide': 173} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 166} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 bond proxies already assigned to first conformer: 1350 Chain: "C" Number of atoms: 1333 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1330 Classifications: {'peptide': 173} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 166} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Conformer: "B" Number of residues, atoms: 173, 1330 Classifications: {'peptide': 173} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 166} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 bond proxies already assigned to first conformer: 1354 Chain: "D" Number of atoms: 1326 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1323 Classifications: {'peptide': 173} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 10} Link IDs: {'PTRANS': 6, 'TRANS': 166} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 36 Conformer: "B" Number of residues, atoms: 173, 1323 Classifications: {'peptide': 173} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 10} Link IDs: {'PTRANS': 6, 'TRANS': 166} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 36 bond proxies already assigned to first conformer: 1347 Chain: "E" Number of atoms: 1334 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1331 Classifications: {'peptide': 173} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 166} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Conformer: "B" Number of residues, atoms: 173, 1331 Classifications: {'peptide': 173} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 166} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 bond proxies already assigned to first conformer: 1355 Chain: "F" Number of atoms: 1332 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1329 Classifications: {'peptide': 173} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 10} Link IDs: {'PTRANS': 6, 'TRANS': 166} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 30 Conformer: "B" Number of residues, atoms: 173, 1329 Classifications: {'peptide': 173} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 10} Link IDs: {'PTRANS': 6, 'TRANS': 166} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 30 bond proxies already assigned to first conformer: 1353 Chain: "G" Number of atoms: 1333 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1330 Classifications: {'peptide': 173} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 166} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Conformer: "B" Number of residues, atoms: 173, 1330 Classifications: {'peptide': 173} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 166} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 bond proxies already assigned to first conformer: 1354 Chain: "H" Number of atoms: 1335 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1332 Classifications: {'peptide': 173} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 166} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 27 Conformer: "B" Number of residues, atoms: 173, 1332 Classifications: {'peptide': 173} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 166} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 27 bond proxies already assigned to first conformer: 1356 Chain: "I" Number of atoms: 1331 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1328 Classifications: {'peptide': 173} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 166} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Conformer: "B" Number of residues, atoms: 173, 1328 Classifications: {'peptide': 173} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 166} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 bond proxies already assigned to first conformer: 1352 Chain: "J" Number of atoms: 1331 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1328 Classifications: {'peptide': 173} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 166} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Conformer: "B" Number of residues, atoms: 173, 1328 Classifications: {'peptide': 173} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 166} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 bond proxies already assigned to first conformer: 1352 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' ZN': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' ZN': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Unusual residues: {' ZN': 1, 'GTP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' ZN': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Unusual residues: {' ZN': 1, 'GTP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Unusual residues: {' ZN': 1, 'GTP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' ZN': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "F" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "G" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "I" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "J" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1129 SG CYS A 145 43.341 83.553 47.188 1.00 18.97 S ATOM 572 SG BCYS A 74 39.562 84.548 48.868 0.71 19.02 S ATOM 2458 SG CYS B 145 77.326 76.525 47.149 1.00 23.70 S ATOM 1901 SG BCYS B 74 77.473 80.510 48.520 0.67 21.17 S ATOM 3231 SG ACYS C 74 85.292 43.030 48.316 0.67 17.98 S ATOM 3791 SG CYS C 145 81.391 41.743 47.185 1.00 19.62 S ATOM 5117 SG CYS D 145 49.625 27.390 47.178 1.00 22.99 S ATOM 4560 SG BCYS D 74 52.070 24.068 48.372 0.70 19.27 S ATOM 6451 SG CYS E 145 26.162 53.076 47.200 1.00 23.07 S ATOM 5894 SG BCYS E 74 23.738 49.873 48.569 0.67 20.27 S ATOM 7783 SG CYS F 145 29.793 41.666 32.504 1.00 19.40 S ATOM 7226 SG BCYS F 74 26.008 43.029 30.970 0.70 17.91 S ATOM 9116 SG CYS G 145 33.607 76.363 32.456 1.00 21.96 S ATOM 8559 SG BCYS G 74 33.732 80.492 31.080 0.64 21.32 S ATOM 10451 SG CYS H 145 85.114 53.197 32.431 1.00 19.64 S ATOM 9894 SG BCYS H 74 87.503 49.866 31.381 0.71 17.83 S ATOM 11782 SG CYS I 145 67.989 83.417 32.506 1.00 21.12 S ATOM 11225 SG BCYS I 74 71.814 84.706 31.409 0.67 21.79 S ATOM 13113 SG CYS J 145 61.466 27.390 32.544 1.00 21.87 S ATOM 12556 SG BCYS J 74 59.164 24.046 31.196 0.68 18.08 S Time building chain proxies: 5.38, per 1000 atoms: 0.39 Number of scatterers: 13783 At special positions: 0 Unit cell: (112.05, 107.9, 80.51, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 10 29.99 S 70 16.00 P 30 15.00 O 2685 8.00 N 2370 7.00 C 8618 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 201 " pdb="ZN ZN A 201 " - pdb=" SG BCYS A 74 " pdb="ZN ZN A 201 " - pdb=" ND1 HIS A 77 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 145 " pdb=" ZN B 201 " pdb="ZN ZN B 201 " - pdb=" SG BCYS B 74 " pdb="ZN ZN B 201 " - pdb=" ND1 HIS B 77 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 145 " pdb=" ZN C 201 " pdb="ZN ZN C 201 " - pdb=" ND1 HIS C 77 " pdb="ZN ZN C 201 " - pdb=" SG ACYS C 74 " pdb="ZN ZN C 201 " - pdb=" SG CYS C 145 " pdb=" ZN D 202 " pdb="ZN ZN D 202 " - pdb=" ND1 HIS D 77 " pdb="ZN ZN D 202 " - pdb=" SG BCYS D 74 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 145 " pdb=" ZN E 202 " pdb="ZN ZN E 202 " - pdb=" ND1 HIS E 77 " pdb="ZN ZN E 202 " - pdb=" SG BCYS E 74 " pdb="ZN ZN E 202 " - pdb=" SG CYS E 145 " pdb=" ZN F 201 " pdb="ZN ZN F 201 " - pdb=" ND1 HIS F 77 " pdb="ZN ZN F 201 " - pdb=" SG BCYS F 74 " pdb="ZN ZN F 201 " - pdb=" SG CYS F 145 " pdb=" ZN G 202 " pdb="ZN ZN G 202 " - pdb=" SG BCYS G 74 " pdb="ZN ZN G 202 " - pdb=" ND1 HIS G 77 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 145 " pdb=" ZN H 202 " pdb="ZN ZN H 202 " - pdb=" SG BCYS H 74 " pdb="ZN ZN H 202 " - pdb=" ND1 HIS H 77 " pdb="ZN ZN H 202 " - pdb=" SG CYS H 145 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG BCYS I 74 " pdb="ZN ZN I 201 " - pdb=" ND1 HIS I 77 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 145 " pdb=" ZN J 202 " pdb="ZN ZN J 202 " - pdb=" ND1 HIS J 77 " pdb="ZN ZN J 202 " - pdb=" SG BCYS J 74 " pdb="ZN ZN J 202 " - pdb=" SG CYS J 145 " 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3200 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 12 sheets defined 45.5% alpha, 26.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 Processing helix chain 'A' and resid 14 through 19 Processing helix chain 'A' and resid 20 through 22 No H-bonds generated for 'chain 'A' and resid 20 through 22' Processing helix chain 'A' and resid 25 through 38 Processing helix chain 'A' and resid 39 through 43 Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 114 through 129 Processing helix chain 'A' and resid 144 through 148 Processing helix chain 'A' and resid 166 through 173 removed outlier: 3.808A pdb=" N LEU A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 11 Processing helix chain 'B' and resid 14 through 19 Processing helix chain 'B' and resid 20 through 22 No H-bonds generated for 'chain 'B' and resid 20 through 22' Processing helix chain 'B' and resid 25 through 38 Processing helix chain 'B' and resid 39 through 43 Processing helix chain 'B' and resid 99 through 110 Processing helix chain 'B' and resid 114 through 129 Processing helix chain 'B' and resid 144 through 148 Processing helix chain 'B' and resid 166 through 173 removed outlier: 3.825A pdb=" N LEU B 170 " --> pdb=" O ASP B 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 11 Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 20 through 22 No H-bonds generated for 'chain 'C' and resid 20 through 22' Processing helix chain 'C' and resid 25 through 38 Processing helix chain 'C' and resid 39 through 43 Processing helix chain 'C' and resid 99 through 110 removed outlier: 3.502A pdb=" N ARG C 103 " --> pdb=" O GLY C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 129 Processing helix chain 'C' and resid 144 through 148 Processing helix chain 'C' and resid 166 through 173 removed outlier: 3.772A pdb=" N LEU C 170 " --> pdb=" O ASP C 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 11 Processing helix chain 'D' and resid 14 through 19 Processing helix chain 'D' and resid 20 through 22 No H-bonds generated for 'chain 'D' and resid 20 through 22' Processing helix chain 'D' and resid 25 through 38 Processing helix chain 'D' and resid 39 through 43 Processing helix chain 'D' and resid 99 through 110 Processing helix chain 'D' and resid 114 through 129 Processing helix chain 'D' and resid 144 through 148 Processing helix chain 'D' and resid 166 through 173 removed outlier: 3.877A pdb=" N LEU D 170 " --> pdb=" O ASP D 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 11 Processing helix chain 'E' and resid 14 through 19 Processing helix chain 'E' and resid 20 through 22 No H-bonds generated for 'chain 'E' and resid 20 through 22' Processing helix chain 'E' and resid 25 through 38 Processing helix chain 'E' and resid 39 through 43 Processing helix chain 'E' and resid 44 through 48 removed outlier: 3.718A pdb=" N ILE E 48 " --> pdb=" O THR E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 110 Processing helix chain 'E' and resid 114 through 129 Processing helix chain 'E' and resid 144 through 148 Processing helix chain 'E' and resid 166 through 173 removed outlier: 3.815A pdb=" N LEU E 170 " --> pdb=" O ASP E 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 11 Processing helix chain 'F' and resid 14 through 19 Processing helix chain 'F' and resid 20 through 22 No H-bonds generated for 'chain 'F' and resid 20 through 22' Processing helix chain 'F' and resid 25 through 38 Processing helix chain 'F' and resid 39 through 43 Processing helix chain 'F' and resid 99 through 110 Processing helix chain 'F' and resid 114 through 129 Processing helix chain 'F' and resid 144 through 148 Processing helix chain 'F' and resid 166 through 173 removed outlier: 3.847A pdb=" N LEU F 170 " --> pdb=" O ASP F 166 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 11 Processing helix chain 'G' and resid 14 through 19 Processing helix chain 'G' and resid 20 through 22 No H-bonds generated for 'chain 'G' and resid 20 through 22' Processing helix chain 'G' and resid 25 through 38 Processing helix chain 'G' and resid 39 through 43 Processing helix chain 'G' and resid 44 through 48 removed outlier: 3.675A pdb=" N ILE G 48 " --> pdb=" O THR G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 110 Processing helix chain 'G' and resid 114 through 129 Processing helix chain 'G' and resid 144 through 148 Processing helix chain 'G' and resid 166 through 173 removed outlier: 3.874A pdb=" N LEU G 170 " --> pdb=" O ASP G 166 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 11 Processing helix chain 'H' and resid 14 through 19 Processing helix chain 'H' and resid 20 through 22 No H-bonds generated for 'chain 'H' and resid 20 through 22' Processing helix chain 'H' and resid 25 through 38 Processing helix chain 'H' and resid 39 through 43 Processing helix chain 'H' and resid 99 through 110 removed outlier: 3.527A pdb=" N ARG H 103 " --> pdb=" O GLY H 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 129 Processing helix chain 'H' and resid 144 through 148 Processing helix chain 'H' and resid 166 through 173 removed outlier: 3.900A pdb=" N LEU H 170 " --> pdb=" O ASP H 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 11 Processing helix chain 'I' and resid 14 through 19 Processing helix chain 'I' and resid 25 through 38 Processing helix chain 'I' and resid 39 through 43 Processing helix chain 'I' and resid 99 through 110 Processing helix chain 'I' and resid 114 through 131 Processing helix chain 'I' and resid 144 through 148 Processing helix chain 'I' and resid 166 through 173 removed outlier: 3.858A pdb=" N LEU I 170 " --> pdb=" O ASP I 166 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 11 Processing helix chain 'J' and resid 14 through 19 Processing helix chain 'J' and resid 25 through 38 Processing helix chain 'J' and resid 39 through 43 Processing helix chain 'J' and resid 99 through 110 removed outlier: 3.546A pdb=" N ARG J 103 " --> pdb=" O GLY J 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 129 Processing helix chain 'J' and resid 144 through 148 Processing helix chain 'J' and resid 166 through 173 removed outlier: 3.782A pdb=" N LEU J 170 " --> pdb=" O ASP J 166 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.817A pdb=" N VAL A 53 " --> pdb=" O ILE A 95 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 74 removed outlier: 5.359A pdb=" N ARG A 64 " --> pdb=" O TYR A 89 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N TYR A 89 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ARG A 66 " --> pdb=" O ILE A 87 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE A 87 " --> pdb=" O ARG A 66 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA A 134 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ARG B 64 " --> pdb=" O TYR B 89 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N TYR B 89 " --> pdb=" O ARG B 64 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ARG B 66 " --> pdb=" O ILE B 87 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE B 87 " --> pdb=" O ARG B 66 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B 84 " --> pdb=" O SER B 140 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA B 134 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ARG C 64 " --> pdb=" O TYR C 89 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N TYR C 89 " --> pdb=" O ARG C 64 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N ARG C 66 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE C 87 " --> pdb=" O ARG C 66 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA C 134 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ARG D 64 " --> pdb=" O TYR D 89 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N TYR D 89 " --> pdb=" O ARG D 64 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ARG D 66 " --> pdb=" O ILE D 87 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE D 87 " --> pdb=" O ARG D 66 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA D 134 " --> pdb=" O VAL D 90 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ARG E 64 " --> pdb=" O TYR E 89 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N TYR E 89 " --> pdb=" O ARG E 64 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ARG E 66 " --> pdb=" O ILE E 87 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE E 87 " --> pdb=" O ARG E 66 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA E 134 " --> pdb=" O VAL E 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 51 through 54 removed outlier: 6.808A pdb=" N ILE B 95 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 51 through 54 removed outlier: 6.841A pdb=" N ILE C 95 " --> pdb=" O THR C 52 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 51 through 54 removed outlier: 6.805A pdb=" N ILE D 95 " --> pdb=" O THR D 52 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 51 through 54 removed outlier: 6.876A pdb=" N ILE E 95 " --> pdb=" O THR E 52 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 51 through 54 removed outlier: 6.821A pdb=" N ILE F 95 " --> pdb=" O THR F 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 63 through 74 removed outlier: 5.356A pdb=" N ARG F 64 " --> pdb=" O TYR F 89 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N TYR F 89 " --> pdb=" O ARG F 64 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ARG F 66 " --> pdb=" O ILE F 87 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE F 87 " --> pdb=" O ARG F 66 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA F 134 " --> pdb=" O VAL F 90 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ARG J 64 " --> pdb=" O TYR J 89 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N TYR J 89 " --> pdb=" O ARG J 64 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ARG J 66 " --> pdb=" O ILE J 87 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE J 87 " --> pdb=" O ARG J 66 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA J 134 " --> pdb=" O VAL J 90 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ARG H 64 " --> pdb=" O TYR H 89 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N TYR H 89 " --> pdb=" O ARG H 64 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ARG H 66 " --> pdb=" O ILE H 87 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE H 87 " --> pdb=" O ARG H 66 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS H 84 " --> pdb=" O SER H 140 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA H 134 " --> pdb=" O VAL H 90 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ARG I 64 " --> pdb=" O TYR I 89 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N TYR I 89 " --> pdb=" O ARG I 64 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ARG I 66 " --> pdb=" O ILE I 87 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE I 87 " --> pdb=" O ARG I 66 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS I 84 " --> pdb=" O SER I 140 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA I 134 " --> pdb=" O VAL I 90 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ARG G 64 " --> pdb=" O TYR G 89 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N TYR G 89 " --> pdb=" O ARG G 64 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ARG G 66 " --> pdb=" O ILE G 87 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE G 87 " --> pdb=" O ARG G 66 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA G 134 " --> pdb=" O VAL G 90 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 51 through 54 removed outlier: 6.791A pdb=" N ILE G 95 " --> pdb=" O THR G 52 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 51 through 54 removed outlier: 6.816A pdb=" N ILE H 95 " --> pdb=" O THR H 52 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 51 through 54 removed outlier: 3.853A pdb=" N VAL I 53 " --> pdb=" O ILE I 95 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 51 through 54 removed outlier: 3.757A pdb=" N VAL J 53 " --> pdb=" O ILE J 95 " (cutoff:3.500A) 729 hydrogen bonds defined for protein. 2051 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: 2.29 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4346 1.34 - 1.46: 3221 1.46 - 1.58: 6231 1.58 - 1.70: 50 1.70 - 1.82: 100 Bond restraints: 13948 Sorted by residual: bond pdb=" CE1 HIS I 76 " pdb=" NE2 HIS I 76 " ideal model delta sigma weight residual 1.321 1.333 -0.012 1.00e-02 1.00e+04 1.43e+00 bond pdb=" CD2 HIS G 76 " pdb=" NE2 HIS G 76 " ideal model delta sigma weight residual 1.374 1.361 0.013 1.10e-02 8.26e+03 1.36e+00 bond pdb=" CD2 HIS B 76 " pdb=" NE2 HIS B 76 " ideal model delta sigma weight residual 1.374 1.361 0.013 1.10e-02 8.26e+03 1.32e+00 bond pdb=" CE1 HIS B 76 " pdb=" NE2 HIS B 76 " ideal model delta sigma weight residual 1.321 1.332 -0.011 1.00e-02 1.00e+04 1.20e+00 bond pdb=" CB MET E 127 " pdb=" CG MET E 127 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.19e+00 ... (remaining 13943 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 18634 1.94 - 3.88: 332 3.88 - 5.81: 52 5.81 - 7.75: 15 7.75 - 9.69: 11 Bond angle restraints: 19044 Sorted by residual: angle pdb=" C1' GTP J 201 " pdb=" C2' GTP J 201 " pdb=" C3' GTP J 201 " ideal model delta sigma weight residual 111.00 101.31 9.69 3.00e+00 1.11e-01 1.04e+01 angle pdb=" C1' GTP B 202 " pdb=" C2' GTP B 202 " pdb=" C3' GTP B 202 " ideal model delta sigma weight residual 111.00 101.33 9.67 3.00e+00 1.11e-01 1.04e+01 angle pdb=" C1' GTP H 201 " pdb=" C2' GTP H 201 " pdb=" C3' GTP H 201 " ideal model delta sigma weight residual 111.00 101.42 9.58 3.00e+00 1.11e-01 1.02e+01 angle pdb=" C1' GTP D 201 " pdb=" C2' GTP D 201 " pdb=" C3' GTP D 201 " ideal model delta sigma weight residual 111.00 101.55 9.45 3.00e+00 1.11e-01 9.93e+00 angle pdb=" C1' GTP G 201 " pdb=" C2' GTP G 201 " pdb=" C3' GTP G 201 " ideal model delta sigma weight residual 111.00 101.68 9.32 3.00e+00 1.11e-01 9.65e+00 ... (remaining 19039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.04: 7879 33.04 - 66.08: 266 66.08 - 99.12: 26 99.12 - 132.15: 15 132.15 - 165.19: 16 Dihedral angle restraints: 8202 sinusoidal: 3172 harmonic: 5030 Sorted by residual: dihedral pdb=" C8 GTP H 203 " pdb=" C1' GTP H 203 " pdb=" N9 GTP H 203 " pdb=" O4' GTP H 203 " ideal model delta sinusoidal sigma weight residual 104.59 -90.21 -165.19 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" C8 GTP E 201 " pdb=" C1' GTP E 201 " pdb=" N9 GTP E 201 " pdb=" O4' GTP E 201 " ideal model delta sinusoidal sigma weight residual 104.59 -90.51 -164.90 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" C8 GTP D 201 " pdb=" C1' GTP D 201 " pdb=" N9 GTP D 201 " pdb=" O4' GTP D 201 " ideal model delta sinusoidal sigma weight residual 104.59 -90.79 -164.62 1 2.00e+01 2.50e-03 4.71e+01 ... (remaining 8199 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1060 0.031 - 0.063: 695 0.063 - 0.094: 240 0.094 - 0.125: 142 0.125 - 0.156: 45 Chirality restraints: 2182 Sorted by residual: chirality pdb=" C3' GTP B 202 " pdb=" C2' GTP B 202 " pdb=" C4' GTP B 202 " pdb=" O3' GTP B 202 " both_signs ideal model delta sigma weight residual False -2.47 -2.63 0.16 2.00e-01 2.50e+01 6.11e-01 chirality pdb=" CA ILE J 87 " pdb=" N ILE J 87 " pdb=" C ILE J 87 " pdb=" CB ILE J 87 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.58e-01 chirality pdb=" CA ILE D 157 " pdb=" N ILE D 157 " pdb=" C ILE D 157 " pdb=" CB ILE D 157 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.56e-01 ... (remaining 2179 not shown) Planarity restraints: 2344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE F 101 " 0.030 5.00e-02 4.00e+02 4.56e-02 3.33e+00 pdb=" N PRO F 102 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO F 102 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 102 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 81 " -0.013 2.00e-02 2.50e+03 1.06e-02 1.96e+00 pdb=" CG PHE F 81 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE F 81 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE F 81 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE F 81 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE F 81 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE F 81 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS H 76 " -0.015 2.00e-02 2.50e+03 1.10e-02 1.80e+00 pdb=" CG HIS H 76 " 0.016 2.00e-02 2.50e+03 pdb=" ND1 HIS H 76 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 HIS H 76 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 HIS H 76 " -0.007 2.00e-02 2.50e+03 pdb=" NE2 HIS H 76 " -0.009 2.00e-02 2.50e+03 ... (remaining 2341 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 5101 2.88 - 3.39: 13471 3.39 - 3.89: 26003 3.89 - 4.40: 30377 4.40 - 4.90: 49481 Nonbonded interactions: 124433 Sorted by model distance: nonbonded pdb=" SG BCYS J 74 " pdb=" O HOH J 303 " model vdw 2.376 3.400 nonbonded pdb="ZN ZN I 201 " pdb=" O HOH I 301 " model vdw 2.438 2.230 nonbonded pdb=" SG BCYS E 74 " pdb=" O HOH E 301 " model vdw 2.442 3.400 nonbonded pdb=" SG BCYS A 74 " pdb=" O HOH A 305 " model vdw 2.471 3.400 nonbonded pdb="ZN ZN G 202 " pdb=" O HOH G 308 " model vdw 2.519 2.230 ... (remaining 124428 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 24 or (resid 25 and (name N or name \ CA or name C or name O or name CB )) or resid 26 through 35 or (resid 36 and (n \ ame N or name CA or name C or name O or name CB or name CG )) or resid 37 throug \ h 41 or (resid 42 and (name N or name CA or name C or name O or name CB or name \ CG )) or resid 43 or (resid 44 and (name N or name CA or name C or name O or nam \ e CB )) or resid 45 through 73 or resid 75 through 174)) selection = (chain 'B' and (resid 2 through 21 or (resid 22 through 23 and (name N or name C \ A or name C or name O or name CB )) or resid 24 or (resid 25 and (name N or name \ CA or name C or name O or name CB )) or resid 26 through 35 or (resid 36 and (n \ ame N or name CA or name C or name O or name CB or name CG )) or resid 37 throug \ h 73 or resid 75 through 174)) selection = (chain 'C' and (resid 2 through 22 or (resid 23 and (name N or name CA or name C \ or name O or name CB )) or resid 24 through 35 or (resid 36 and (name N or name \ CA or name C or name O or name CB or name CG )) or resid 37 through 41 or (resi \ d 42 and (name N or name CA or name C or name O or name CB or name CG )) or resi \ d 43 or (resid 44 and (name N or name CA or name C or name O or name CB )) or re \ sid 45 through 73 or resid 75 through 174)) selection = (chain 'D' and (resid 2 through 43 or (resid 44 and (name N or name CA or name C \ or name O or name CB )) or resid 45 through 73 or resid 75 through 174)) selection = (chain 'E' and (resid 2 through 22 or (resid 23 and (name N or name CA or name C \ or name O or name CB )) or resid 24 or (resid 25 and (name N or name CA or name \ C or name O or name CB )) or resid 26 through 35 or (resid 36 and (name N or na \ me CA or name C or name O or name CB or name CG )) or resid 37 through 41 or (re \ sid 42 and (name N or name CA or name C or name O or name CB or name CG )) or re \ sid 43 or (resid 44 and (name N or name CA or name C or name O or name CB )) or \ resid 45 through 73 or resid 75 through 174)) selection = (chain 'F' and (resid 2 through 35 or (resid 36 and (name N or name CA or name C \ or name O or name CB or name CG )) or resid 37 through 41 or (resid 42 and (nam \ e N or name CA or name C or name O or name CB or name CG )) or resid 43 or (resi \ d 44 and (name N or name CA or name C or name O or name CB )) or resid 45 throug \ h 73 or resid 75 through 174)) selection = (chain 'G' and (resid 2 through 22 or (resid 23 and (name N or name CA or name C \ or name O or name CB )) or resid 24 through 35 or (resid 36 and (name N or name \ CA or name C or name O or name CB or name CG )) or resid 37 through 41 or (resi \ d 42 and (name N or name CA or name C or name O or name CB or name CG )) or resi \ d 43 or (resid 44 and (name N or name CA or name C or name O or name CB )) or re \ sid 45 through 73 or resid 75 through 174)) selection = (chain 'H' and (resid 2 through 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB )) or resid 6 through 22 or (resid 23 and (name N or name CA \ or name C or name O or name CB )) or resid 24 or (resid 25 and (name N or name \ CA or name C or name O or name CB )) or resid 26 through 35 or (resid 36 and (na \ me N or name CA or name C or name O or name CB or name CG )) or resid 37 through \ 41 or (resid 42 and (name N or name CA or name C or name O or name CB or name C \ G )) or resid 43 or (resid 44 and (name N or name CA or name C or name O or name \ CB )) or resid 45 through 73 or resid 75 through 174)) selection = (chain 'I' and (resid 2 through 21 or (resid 22 through 23 and (name N or name C \ A or name C or name O or name CB )) or resid 24 through 35 or (resid 36 and (nam \ e N or name CA or name C or name O or name CB or name CG )) or resid 37 through \ 43 or (resid 44 and (name N or name CA or name C or name O or name CB )) or resi \ d 45 through 73 or resid 75 through 174)) selection = (chain 'J' and (resid 2 through 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB )) or resid 6 through 24 or (resid 25 and (name N or name CA \ or name C or name O or name CB )) or resid 26 through 35 or (resid 36 and (name \ N or name CA or name C or name O or name CB or name CG )) or resid 37 through 4 \ 3 or (resid 44 and (name N or name CA or name C or name O or name CB )) or resid \ 45 through 73 or resid 75 through 174)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.29 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: 3.030 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.130 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 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:6.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13978 Z= 0.167 Angle : 0.703 9.688 19044 Z= 0.353 Chirality : 0.050 0.156 2182 Planarity : 0.004 0.046 2344 Dihedral : 19.785 165.193 5002 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.70 % Allowed : 11.43 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.20), residues: 1720 helix: 0.01 (0.20), residues: 690 sheet: 0.14 (0.24), residues: 460 loop : -1.14 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 64 TYR 0.017 0.002 TYR G 34 PHE 0.024 0.002 PHE F 81 TRP 0.008 0.001 TRP C 20 HIS 0.006 0.001 HIS H 117 Details of bonding type rmsd covalent geometry : bond 0.00332 (13948) covalent geometry : angle 0.70311 (19044) hydrogen bonds : bond 0.08733 ( 729) hydrogen bonds : angle 5.91155 ( 2051) metal coordination : bond 0.00559 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 295 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: C 50 LYS cc_start: 0.8168 (mttp) cc_final: 0.7917 (mtmt) REVERT: H 50 LYS cc_start: 0.8230 (mtpt) cc_final: 0.7649 (mttp) REVERT: I 149 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.7573 (ppp-140) outliers start: 14 outliers final: 12 residues processed: 307 average time/residue: 0.5480 time to fit residues: 185.4464 Evaluate side-chains 306 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 293 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 149 ARG Chi-restraints excluded: chain J residue 51 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.0010 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN B 113 GLN B 115 GLN C 10 ASN C 69 ASN F 8 GLN F 76 HIS F 115 GLN G 8 GLN I 115 GLN J 8 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.162244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.141680 restraints weight = 25057.896| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.27 r_work: 0.3488 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3373 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3372 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.0380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13978 Z= 0.149 Angle : 0.678 9.816 19044 Z= 0.331 Chirality : 0.050 0.161 2182 Planarity : 0.004 0.041 2344 Dihedral : 20.198 163.663 2099 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.84 % Allowed : 10.47 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.20), residues: 1720 helix: 0.13 (0.20), residues: 690 sheet: 0.26 (0.24), residues: 460 loop : -1.04 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 64 TYR 0.018 0.002 TYR B 34 PHE 0.020 0.002 PHE E 81 TRP 0.006 0.001 TRP C 20 HIS 0.005 0.001 HIS H 117 Details of bonding type rmsd covalent geometry : bond 0.00311 (13948) covalent geometry : angle 0.67780 (19044) hydrogen bonds : bond 0.05233 ( 729) hydrogen bonds : angle 5.33771 ( 2051) metal coordination : bond 0.00624 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 303 time to evaluate : 0.550 Fit side-chains revert: symmetry clash REVERT: B 36 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8051 (mt-10) REVERT: H 50 LYS cc_start: 0.8245 (mtpt) cc_final: 0.7635 (mttp) REVERT: I 149 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.7397 (ppp-140) outliers start: 16 outliers final: 12 residues processed: 316 average time/residue: 0.5480 time to fit residues: 191.0986 Evaluate side-chains 310 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 297 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 149 ARG Chi-restraints excluded: chain J residue 51 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 83 optimal weight: 0.3980 chunk 9 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 chunk 165 optimal weight: 0.6980 chunk 102 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 104 optimal weight: 0.4980 chunk 156 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 GLN F 8 GLN I 76 HIS J 8 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.164646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.143583 restraints weight = 31199.851| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.53 r_work: 0.3495 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3387 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3387 r_free = 0.3387 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3387 r_free = 0.3387 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3387 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.0589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13978 Z= 0.116 Angle : 0.618 9.066 19044 Z= 0.302 Chirality : 0.048 0.143 2182 Planarity : 0.004 0.040 2344 Dihedral : 19.851 163.654 2098 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.14 % Allowed : 10.18 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.20), residues: 1720 helix: 0.30 (0.20), residues: 690 sheet: 0.31 (0.24), residues: 460 loop : -1.07 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 64 TYR 0.014 0.001 TYR C 34 PHE 0.018 0.002 PHE E 81 TRP 0.005 0.001 TRP C 20 HIS 0.003 0.000 HIS H 117 Details of bonding type rmsd covalent geometry : bond 0.00240 (13948) covalent geometry : angle 0.61791 (19044) hydrogen bonds : bond 0.04456 ( 729) hydrogen bonds : angle 5.11740 ( 2051) metal coordination : bond 0.00286 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 315 time to evaluate : 0.486 Fit side-chains revert: symmetry clash REVERT: C 50 LYS cc_start: 0.8373 (mtpt) cc_final: 0.7874 (mttp) REVERT: H 50 LYS cc_start: 0.8273 (mtpt) cc_final: 0.7692 (mttp) REVERT: I 149 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.7321 (ppp-140) outliers start: 20 outliers final: 13 residues processed: 331 average time/residue: 0.5270 time to fit residues: 192.6427 Evaluate side-chains 319 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 305 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 149 ARG Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 51 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 114 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 36 optimal weight: 0.3980 chunk 61 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS B 76 HIS ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 GLN I 76 HIS J 8 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.160516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.140622 restraints weight = 21247.163| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.15 r_work: 0.3476 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3364 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3364 r_free = 0.3364 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3364 r_free = 0.3364 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3364 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.0643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13978 Z= 0.189 Angle : 0.725 10.022 19044 Z= 0.355 Chirality : 0.051 0.162 2182 Planarity : 0.005 0.042 2344 Dihedral : 20.524 164.819 2097 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.21 % Allowed : 9.66 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.20), residues: 1720 helix: 0.12 (0.20), residues: 690 sheet: 0.28 (0.24), residues: 460 loop : -0.98 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 64 TYR 0.020 0.002 TYR B 34 PHE 0.020 0.003 PHE E 81 TRP 0.005 0.001 TRP C 20 HIS 0.003 0.001 HIS H 117 Details of bonding type rmsd covalent geometry : bond 0.00399 (13948) covalent geometry : angle 0.72482 (19044) hydrogen bonds : bond 0.05837 ( 729) hydrogen bonds : angle 5.36290 ( 2051) metal coordination : bond 0.01062 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 303 time to evaluate : 0.560 Fit side-chains REVERT: I 149 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.7486 (ppp-140) outliers start: 21 outliers final: 16 residues processed: 319 average time/residue: 0.5471 time to fit residues: 192.3177 Evaluate side-chains 312 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 295 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 149 ARG Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 51 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 79 optimal weight: 0.7980 chunk 33 optimal weight: 7.9990 chunk 82 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 152 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS B 76 HIS B 113 GLN F 8 GLN G 8 GLN I 76 HIS J 8 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.161678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.140865 restraints weight = 26329.730| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.30 r_work: 0.3474 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3360 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3360 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.0585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13978 Z= 0.155 Angle : 0.681 9.780 19044 Z= 0.333 Chirality : 0.050 0.162 2182 Planarity : 0.004 0.037 2344 Dihedral : 20.359 164.994 2097 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.14 % Allowed : 9.22 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.20), residues: 1720 helix: 0.15 (0.20), residues: 690 sheet: 0.31 (0.24), residues: 460 loop : -1.05 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 64 TYR 0.017 0.002 TYR D 34 PHE 0.019 0.002 PHE E 81 TRP 0.005 0.001 TRP C 20 HIS 0.004 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00322 (13948) covalent geometry : angle 0.68141 (19044) hydrogen bonds : bond 0.05299 ( 729) hydrogen bonds : angle 5.27607 ( 2051) metal coordination : bond 0.00687 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 305 time to evaluate : 0.526 Fit side-chains revert: symmetry clash REVERT: B 36 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8038 (mt-10) REVERT: C 50 LYS cc_start: 0.8339 (mtpt) cc_final: 0.7815 (mttp) REVERT: H 50 LYS cc_start: 0.8261 (mtpt) cc_final: 0.7660 (mttp) REVERT: I 149 ARG cc_start: 0.9058 (OUTLIER) cc_final: 0.7404 (ppp-140) outliers start: 20 outliers final: 17 residues processed: 321 average time/residue: 0.5431 time to fit residues: 191.9920 Evaluate side-chains 317 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 299 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 149 ARG Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 51 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 19 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 154 optimal weight: 6.9990 chunk 7 optimal weight: 0.0970 chunk 14 optimal weight: 0.8980 chunk 110 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 GLN I 76 HIS J 8 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.159571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.138763 restraints weight = 24607.776| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.26 r_work: 0.3450 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3336 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3336 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.0750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13978 Z= 0.212 Angle : 0.757 10.126 19044 Z= 0.372 Chirality : 0.052 0.166 2182 Planarity : 0.005 0.049 2344 Dihedral : 20.942 164.931 2097 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.21 % Allowed : 9.07 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.20), residues: 1720 helix: -0.02 (0.20), residues: 690 sheet: 0.26 (0.24), residues: 460 loop : -0.96 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 64 TYR 0.022 0.003 TYR D 34 PHE 0.021 0.003 PHE C 81 TRP 0.005 0.002 TRP C 20 HIS 0.003 0.001 HIS C 117 Details of bonding type rmsd covalent geometry : bond 0.00448 (13948) covalent geometry : angle 0.75651 (19044) hydrogen bonds : bond 0.06215 ( 729) hydrogen bonds : angle 5.46759 ( 2051) metal coordination : bond 0.01192 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 299 time to evaluate : 0.574 Fit side-chains REVERT: G 127 MET cc_start: 0.7930 (mmm) cc_final: 0.7707 (mmp) REVERT: I 149 ARG cc_start: 0.9062 (OUTLIER) cc_final: 0.7450 (ppp-140) outliers start: 21 outliers final: 17 residues processed: 316 average time/residue: 0.5419 time to fit residues: 188.7730 Evaluate side-chains 310 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 292 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 149 ARG Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 51 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 123 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 165 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 129 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS B 76 HIS ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 GLN G 8 GLN I 76 HIS J 8 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.160002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.139410 restraints weight = 24520.676| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.28 r_work: 0.3449 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3334 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3334 r_free = 0.3334 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3334 r_free = 0.3334 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3334 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.0710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13978 Z= 0.197 Angle : 0.742 10.146 19044 Z= 0.365 Chirality : 0.051 0.168 2182 Planarity : 0.005 0.044 2344 Dihedral : 20.991 164.999 2097 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.36 % Allowed : 9.00 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.20), residues: 1720 helix: -0.03 (0.20), residues: 690 sheet: 0.26 (0.24), residues: 460 loop : -1.02 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 64 TYR 0.020 0.002 TYR D 34 PHE 0.022 0.003 PHE C 81 TRP 0.005 0.002 TRP C 20 HIS 0.002 0.001 HIS H 143 Details of bonding type rmsd covalent geometry : bond 0.00415 (13948) covalent geometry : angle 0.74156 (19044) hydrogen bonds : bond 0.05986 ( 729) hydrogen bonds : angle 5.44188 ( 2051) metal coordination : bond 0.01050 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 297 time to evaluate : 0.561 Fit side-chains REVERT: B 36 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8100 (mt-10) REVERT: H 50 LYS cc_start: 0.8280 (mtpt) cc_final: 0.7668 (mttp) REVERT: I 149 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.7491 (ppp-140) REVERT: J 127 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7898 (mmp) outliers start: 23 outliers final: 17 residues processed: 314 average time/residue: 0.5464 time to fit residues: 189.2068 Evaluate side-chains 312 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 293 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 149 ARG Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 127 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 119 optimal weight: 0.9990 chunk 156 optimal weight: 0.1980 chunk 115 optimal weight: 9.9990 chunk 92 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 96 optimal weight: 0.8980 chunk 22 optimal weight: 9.9990 chunk 49 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS B 76 HIS B 113 GLN F 8 GLN I 76 HIS J 8 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.163363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.143549 restraints weight = 32973.898| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.40 r_work: 0.3492 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3381 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3381 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.0701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13978 Z= 0.125 Angle : 0.644 9.349 19044 Z= 0.315 Chirality : 0.048 0.147 2182 Planarity : 0.004 0.037 2344 Dihedral : 20.147 164.572 2097 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.14 % Allowed : 8.85 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.20), residues: 1720 helix: 0.22 (0.21), residues: 690 sheet: 0.33 (0.24), residues: 460 loop : -1.07 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 133 TYR 0.015 0.001 TYR C 34 PHE 0.020 0.002 PHE C 81 TRP 0.004 0.001 TRP C 20 HIS 0.002 0.000 HIS H 117 Details of bonding type rmsd covalent geometry : bond 0.00257 (13948) covalent geometry : angle 0.64386 (19044) hydrogen bonds : bond 0.04723 ( 729) hydrogen bonds : angle 5.15349 ( 2051) metal coordination : bond 0.00296 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 308 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: C 50 LYS cc_start: 0.8329 (mtpt) cc_final: 0.7837 (mttp) REVERT: F 50 LYS cc_start: 0.8303 (mtpt) cc_final: 0.7765 (mttp) REVERT: H 50 LYS cc_start: 0.8316 (mtpt) cc_final: 0.7746 (mttp) REVERT: I 149 ARG cc_start: 0.9045 (OUTLIER) cc_final: 0.7275 (ppp-140) REVERT: J 127 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7896 (mmp) outliers start: 20 outliers final: 16 residues processed: 324 average time/residue: 0.5359 time to fit residues: 191.7546 Evaluate side-chains 316 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 298 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 149 ARG Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 127 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 74 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 156 optimal weight: 6.9990 chunk 86 optimal weight: 8.9990 chunk 68 optimal weight: 10.0000 chunk 7 optimal weight: 0.2980 chunk 89 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 HIS ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 GLN I 76 HIS J 8 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.160251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.139025 restraints weight = 27561.606| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.34 r_work: 0.3449 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3336 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3336 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.0715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13978 Z= 0.189 Angle : 0.733 10.125 19044 Z= 0.360 Chirality : 0.051 0.167 2182 Planarity : 0.005 0.041 2344 Dihedral : 20.775 164.899 2097 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.99 % Allowed : 9.73 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.20), residues: 1720 helix: 0.04 (0.20), residues: 690 sheet: 0.26 (0.24), residues: 460 loop : -0.99 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 64 TYR 0.020 0.002 TYR D 34 PHE 0.022 0.003 PHE C 81 TRP 0.005 0.001 TRP C 20 HIS 0.004 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00397 (13948) covalent geometry : angle 0.73268 (19044) hydrogen bonds : bond 0.05876 ( 729) hydrogen bonds : angle 5.36577 ( 2051) metal coordination : bond 0.00995 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 294 time to evaluate : 0.431 Fit side-chains REVERT: C 50 LYS cc_start: 0.8307 (mtpt) cc_final: 0.7820 (mttp) REVERT: F 50 LYS cc_start: 0.8293 (mtpt) cc_final: 0.7799 (mttp) REVERT: I 149 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.7548 (ppp-140) REVERT: J 127 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7898 (mmp) outliers start: 18 outliers final: 16 residues processed: 310 average time/residue: 0.5485 time to fit residues: 187.1967 Evaluate side-chains 309 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 291 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 149 ARG Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 127 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 162 optimal weight: 4.9990 chunk 120 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 130 optimal weight: 0.5980 chunk 135 optimal weight: 0.0970 chunk 161 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 87 optimal weight: 0.0570 chunk 102 optimal weight: 0.9990 chunk 146 optimal weight: 0.0870 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 GLN F 8 GLN J 8 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.166674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.146268 restraints weight = 28592.400| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 1.35 r_work: 0.3540 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3430 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3430 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13978 Z= 0.106 Angle : 0.605 8.565 19044 Z= 0.297 Chirality : 0.047 0.138 2182 Planarity : 0.004 0.039 2344 Dihedral : 19.738 164.065 2097 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.06 % Allowed : 9.96 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.20), residues: 1720 helix: 0.20 (0.20), residues: 700 sheet: 0.32 (0.24), residues: 460 loop : -0.97 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 133 TYR 0.013 0.001 TYR C 34 PHE 0.018 0.002 PHE H 81 TRP 0.004 0.001 TRP C 20 HIS 0.002 0.000 HIS B 143 Details of bonding type rmsd covalent geometry : bond 0.00217 (13948) covalent geometry : angle 0.60499 (19044) hydrogen bonds : bond 0.04063 ( 729) hydrogen bonds : angle 5.01949 ( 2051) metal coordination : bond 0.00179 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 317 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8234 (mt-10) cc_final: 0.8018 (tt0) REVERT: B 36 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7813 (mt-10) REVERT: C 50 LYS cc_start: 0.8326 (mtpt) cc_final: 0.7802 (mttp) REVERT: E 50 LYS cc_start: 0.8348 (mtpt) cc_final: 0.7737 (mttp) REVERT: F 50 LYS cc_start: 0.8320 (mtpt) cc_final: 0.7813 (mttp) REVERT: H 50 LYS cc_start: 0.8338 (mtpt) cc_final: 0.7772 (mttp) REVERT: I 149 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.7165 (ppp-140) outliers start: 19 outliers final: 13 residues processed: 331 average time/residue: 0.5317 time to fit residues: 194.4511 Evaluate side-chains 315 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 301 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 149 ARG Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 51 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 135 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 21 optimal weight: 0.0970 chunk 39 optimal weight: 9.9990 chunk 120 optimal weight: 0.9990 chunk 134 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 137 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 HIS ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 HIS I 76 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.161059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.139765 restraints weight = 28340.455| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.37 r_work: 0.3459 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3345 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3345 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.0685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13978 Z= 0.174 Angle : 0.716 10.091 19044 Z= 0.351 Chirality : 0.051 0.162 2182 Planarity : 0.005 0.037 2344 Dihedral : 20.402 164.988 2097 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.84 % Allowed : 10.40 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.20), residues: 1720 helix: 0.13 (0.20), residues: 690 sheet: 0.30 (0.24), residues: 460 loop : -0.96 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 64 TYR 0.019 0.002 TYR D 34 PHE 0.021 0.003 PHE C 81 TRP 0.004 0.001 TRP E 20 HIS 0.004 0.001 HIS G 76 Details of bonding type rmsd covalent geometry : bond 0.00364 (13948) covalent geometry : angle 0.71565 (19044) hydrogen bonds : bond 0.05633 ( 729) hydrogen bonds : angle 5.27801 ( 2051) metal coordination : bond 0.00896 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7199.04 seconds wall clock time: 123 minutes 6.08 seconds (7386.08 seconds total)