Starting phenix.real_space_refine (version: dev) on Tue Dec 13 03:00:00 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4p_13812/12_2022/7q4p_13812_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4p_13812/12_2022/7q4p_13812.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4p_13812/12_2022/7q4p_13812_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4p_13812/12_2022/7q4p_13812_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4p_13812/12_2022/7q4p_13812_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4p_13812/12_2022/7q4p_13812.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4p_13812/12_2022/7q4p_13812.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4p_13812/12_2022/7q4p_13812_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4p_13812/12_2022/7q4p_13812_updated.pdb" } resolution = 2.15 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "1 GLU 66": "OE1" <-> "OE2" Residue "9 TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 428": "OE1" <-> "OE2" Residue "9 GLU 453": "OE1" <-> "OE2" Residue "9 GLU 476": "OE1" <-> "OE2" Residue "9 TYR 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 480": "OE1" <-> "OE2" Residue "A ARG 1053": "NH1" <-> "NH2" Residue "A ARG 1057": "NH1" <-> "NH2" Residue "A PHE 1060": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1061": "OE1" <-> "OE2" Residue "A GLU 1064": "OE1" <-> "OE2" Residue "A ARG 1074": "NH1" <-> "NH2" Residue "A GLU 1105": "OE1" <-> "OE2" Residue "A ARG 1109": "NH1" <-> "NH2" Residue "A GLU 1140": "OE1" <-> "OE2" Residue "A ARG 1180": "NH1" <-> "NH2" Residue "A GLU 1221": "OE1" <-> "OE2" Residue "A ARG 1245": "NH1" <-> "NH2" Residue "A ARG 1262": "NH1" <-> "NH2" Residue "B ASP 473": "OD1" <-> "OD2" Residue "B ARG 495": "NH1" <-> "NH2" Residue "B PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 530": "NH1" <-> "NH2" Residue "B TYR 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 593": "OE1" <-> "OE2" Residue "C GLU 29": "OE1" <-> "OE2" Residue "C GLU 39": "OE1" <-> "OE2" Residue "C PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "C GLU 100": "OE1" <-> "OE2" Residue "C GLU 136": "OE1" <-> "OE2" Residue "C GLU 159": "OE1" <-> "OE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C ARG 222": "NH1" <-> "NH2" Residue "C TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 229": "OE1" <-> "OE2" Residue "C GLU 230": "OE1" <-> "OE2" Residue "C GLU 253": "OE1" <-> "OE2" Residue "C ARG 274": "NH1" <-> "NH2" Residue "C ARG 275": "NH1" <-> "NH2" Residue "C PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 326": "NH1" <-> "NH2" Residue "C PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 370": "OE1" <-> "OE2" Residue "C GLU 372": "OE1" <-> "OE2" Residue "C GLU 380": "OE1" <-> "OE2" Residue "C ARG 429": "NH1" <-> "NH2" Residue "C GLU 821": "OE1" <-> "OE2" Residue "C GLU 825": "OE1" <-> "OE2" Residue "C GLU 833": "OE1" <-> "OE2" Residue "C GLU 849": "OE1" <-> "OE2" Residue "C PHE 896": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 901": "OE1" <-> "OE2" Residue "C GLU 946": "OE1" <-> "OE2" Residue "C GLU 947": "OE1" <-> "OE2" Residue "C TYR 989": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1004": "OD1" <-> "OD2" Residue "C ARG 1013": "NH1" <-> "NH2" Residue "C GLU 1018": "OE1" <-> "OE2" Residue "C PHE 1024": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1064": "OD1" <-> "OD2" Residue "C GLU 1065": "OE1" <-> "OE2" Residue "C ASP 1067": "OD1" <-> "OD2" Residue "C GLU 1068": "OE1" <-> "OE2" Residue "C GLU 1136": "OE1" <-> "OE2" Residue "C GLU 1151": "OE1" <-> "OE2" Residue "C GLU 1195": "OE1" <-> "OE2" Residue "C TYR 1215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 30": "OE1" <-> "OE2" Residue "E ASP 48": "OD1" <-> "OD2" Residue "E GLU 57": "OE1" <-> "OE2" Residue "E GLU 59": "OE1" <-> "OE2" Residue "E GLU 70": "OE1" <-> "OE2" Residue "G GLU 24": "OE1" <-> "OE2" Residue "G GLU 48": "OE1" <-> "OE2" Residue "G ARG 57": "NH1" <-> "NH2" Residue "G GLU 74": "OE1" <-> "OE2" Residue "G GLU 79": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 13451 Number of models: 1 Model: "" Number of chains: 17 Chain: "1" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 308 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "2" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 952 Classifications: {'RNA': 45} Modifications used: {'rna2p': 1, 'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p': 13, 'rna3p_pur': 15, 'rna3p_pyr': 12} Link IDs: {'rna2p': 5, 'rna3p': 39} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 5 Chain: "9" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 838 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "A" Number of atoms: 2043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2043 Classifications: {'peptide': 254} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 243} Chain: "B" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 985 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 9, 'TRANS': 107} Chain breaks: 2 Chain: "C" Number of atoms: 6926 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 878, 6920 Classifications: {'peptide': 878} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 43, 'TRANS': 831} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 878, 6920 Classifications: {'peptide': 878} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 43, 'TRANS': 831} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 7063 Chain: "E" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 524 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 3, 'TRANS': 60} Chain: "G" Number of atoms: 629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 629 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "9" 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "2" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "C" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 148 Classifications: {'water': 148} Link IDs: {None: 147} Chain: "E" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "G" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 110 SG CYS 1 56 38.100 53.118 16.480 1.00 92.44 S ATOM 133 SG CYS 1 59 41.800 51.954 15.349 1.00 88.93 S ATOM 1410 SG CYS 9 408 63.904 29.933 34.254 1.00 78.29 S ATOM 1433 SG CYS 9 411 61.215 27.973 31.965 1.00 83.68 S ATOM 12747 SG CYS G 30 45.324 81.582 54.021 1.00 53.40 S ATOM 12768 SG CYS G 33 44.082 78.851 51.695 1.00 55.13 S ATOM 13063 SG CYS G 72 42.872 78.799 54.982 1.00 41.79 S ATOM 13087 SG CYS G 75 46.413 78.059 54.405 1.00 42.12 S ATOM 12609 SG CYS G 11 61.031 87.619 54.014 1.00 75.17 S ATOM 12872 SG CYS G 46 59.992 90.187 56.957 1.00 61.94 S ATOM 12895 SG CYS G 49 58.850 91.203 54.259 1.00 80.04 S ATOM 13166 SG CYS G 85 57.120 88.509 55.982 1.00 59.20 S ATOM 12696 SG CYS G 23 44.364 94.843 47.799 1.00 73.73 S ATOM 12720 SG CYS G 26 45.153 91.007 47.017 1.00 77.15 S ATOM 12967 SG CYS G 58 47.484 93.005 49.901 1.00 82.21 S ATOM 12988 SG CYS G 61 47.969 93.965 46.251 1.00 80.99 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ASER C 290 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER C 290 " occ=0.50 Time building chain proxies: 10.63, per 1000 atoms: 0.79 Number of scatterers: 13451 At special positions: 0 Unit cell: (106.88, 111.36, 124.16, 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 5 29.99 S 71 16.00 P 45 15.00 O 2822 8.00 N 2268 7.00 C 8240 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 - 3.50 Amino acid : False - 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: 5.58 Conformation dependent library (CDL) restraints added in 2.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 1 501 " pdb="ZN ZN 1 501 " - pdb=" SG CYS 1 56 " pdb="ZN ZN 1 501 " - pdb=" NE2 HIS 1 72 " pdb="ZN ZN 1 501 " - pdb=" ND1 HIS 1 78 " pdb="ZN ZN 1 501 " - pdb=" SG CYS 1 59 " pdb=" ZN 9 601 " pdb="ZN ZN 9 601 " - pdb=" ND1 HIS 9 431 " pdb="ZN ZN 9 601 " - pdb=" SG CYS 9 408 " pdb="ZN ZN 9 601 " - pdb=" SG CYS 9 411 " pdb=" ZN G 201 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 33 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 72 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 75 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 30 " pdb=" ZN G 202 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 46 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 49 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 11 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 85 " pdb=" ZN G 203 " pdb="ZN ZN G 203 " - pdb=" SG CYS G 61 " pdb="ZN ZN G 203 " - pdb=" SG CYS G 23 " pdb="ZN ZN G 203 " - pdb=" SG CYS G 26 " pdb="ZN ZN G 203 " - pdb=" SG CYS G 58 " Number of angles added : 19 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2868 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 18 sheets defined 28.7% alpha, 23.0% beta 5 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 5.38 Creating SS restraints... Processing helix chain '1' and resid 66 through 73 Processing helix chain '1' and resid 76 through 80 Processing helix chain '9' and resid 394 through 399 Processing helix chain '9' and resid 419 through 427 removed outlier: 4.340A pdb=" N PHE 9 426 " --> pdb=" O PHE 9 422 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ALA 9 427 " --> pdb=" O GLN 9 423 " (cutoff:3.500A) Processing helix chain '9' and resid 429 through 438 Processing helix chain '9' and resid 444 through 446 No H-bonds generated for 'chain '9' and resid 444 through 446' Processing helix chain '9' and resid 452 through 467 Processing helix chain 'A' and resid 1052 through 1062 Processing helix chain 'A' and resid 1071 through 1087 removed outlier: 3.694A pdb=" N GLY A1082 " --> pdb=" O VAL A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1101 removed outlier: 3.706A pdb=" N LEU A1101 " --> pdb=" O LEU A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1122 removed outlier: 3.569A pdb=" N CYS A1111 " --> pdb=" O GLN A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1135 Proline residue: A1130 - end of helix Processing helix chain 'A' and resid 1141 through 1177 removed outlier: 3.595A pdb=" N GLY A1159 " --> pdb=" O PHE A1155 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N GLU A1160 " --> pdb=" O GLU A1156 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N MET A1161 " --> pdb=" O TYR A1157 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N GLY A1162 " --> pdb=" O ILE A1158 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LYS A1163 " --> pdb=" O GLY A1159 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ASP A1164 " --> pdb=" O GLU A1160 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N TYR A1165 " --> pdb=" O MET A1161 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N TYR A1167 " --> pdb=" O LYS A1163 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ALA A1168 " --> pdb=" O ASP A1164 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL A1169 " --> pdb=" O TYR A1165 " (cutoff:3.500A) Proline residue: A1171 - end of helix Processing helix chain 'A' and resid 1182 through 1198 Processing helix chain 'A' and resid 1205 through 1220 removed outlier: 3.939A pdb=" N TYR A1214 " --> pdb=" O HIS A1210 " (cutoff:3.500A) Proline residue: A1217 - end of helix removed outlier: 5.130A pdb=" N PHE A1220 " --> pdb=" O TRP A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1224 through 1241 removed outlier: 3.619A pdb=" N VAL A1239 " --> pdb=" O GLU A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1243 through 1253 removed outlier: 5.154A pdb=" N GLN A1252 " --> pdb=" O GLN A1248 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N GLY A1253 " --> pdb=" O TYR A1249 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1276 removed outlier: 4.210A pdb=" N VAL A1264 " --> pdb=" O LYS A1260 " (cutoff:3.500A) Processing helix chain 'A' and resid 1279 through 1283 Processing helix chain 'A' and resid 1298 through 1301 Processing helix chain 'B' and resid 462 through 468 removed outlier: 3.681A pdb=" N GLN B 467 " --> pdb=" O ALA B 463 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B 468 " --> pdb=" O GLU B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 481 Processing helix chain 'B' and resid 485 through 493 Processing helix chain 'B' and resid 502 through 504 No H-bonds generated for 'chain 'B' and resid 502 through 504' Processing helix chain 'B' and resid 526 through 529 No H-bonds generated for 'chain 'B' and resid 526 through 529' Processing helix chain 'B' and resid 569 through 576 removed outlier: 4.228A pdb=" N PHE B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 202 No H-bonds generated for 'chain 'C' and resid 199 through 202' Processing helix chain 'C' and resid 430 through 432 No H-bonds generated for 'chain 'C' and resid 430 through 432' Processing helix chain 'C' and resid 809 through 825 Processing helix chain 'C' and resid 834 through 844 Processing helix chain 'C' and resid 849 through 852 No H-bonds generated for 'chain 'C' and resid 849 through 852' Processing helix chain 'C' and resid 1074 through 1077 No H-bonds generated for 'chain 'C' and resid 1074 through 1077' Processing helix chain 'C' and resid 1135 through 1151 removed outlier: 3.717A pdb=" N SER C1150 " --> pdb=" O MET C1146 " (cutoff:3.500A) Processing helix chain 'C' and resid 1160 through 1164 Processing helix chain 'C' and resid 1176 through 1184 removed outlier: 3.970A pdb=" N GLN C1181 " --> pdb=" O ASP C1177 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE C1182 " --> pdb=" O LEU C1178 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ASN C1183 " --> pdb=" O CYS C1179 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N SER C1184 " --> pdb=" O GLU C1180 " (cutoff:3.500A) Processing helix chain 'C' and resid 1187 through 1197 Processing helix chain 'C' and resid 1201 through 1215 removed outlier: 3.580A pdb=" N TYR C1215 " --> pdb=" O ILE C1211 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 45 Processing helix chain 'E' and resid 47 through 57 Processing helix chain 'E' and resid 61 through 71 Processing helix chain 'G' and resid 47 through 49 No H-bonds generated for 'chain 'G' and resid 47 through 49' Processing helix chain 'G' and resid 52 through 54 No H-bonds generated for 'chain 'G' and resid 52 through 54' Processing helix chain 'G' and resid 73 through 77 Processing helix chain 'G' and resid 80 through 82 No H-bonds generated for 'chain 'G' and resid 80 through 82' Processing sheet with id= A, first strand: chain '1' and resid 46 through 48 removed outlier: 3.646A pdb=" N THR 1 61 " --> pdb=" O CYS 1 56 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '9' and resid 405 through 408 Processing sheet with id= C, first strand: chain 'C' and resid 1173 through 1175 removed outlier: 6.739A pdb=" N LEU C 3 " --> pdb=" O ILE C1174 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE C1126 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N GLU C1115 " --> pdb=" O PRO C1131 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER C1103 " --> pdb=" O THR C1120 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 16 through 20 removed outlier: 3.542A pdb=" N PHE C 16 " --> pdb=" O SER C 33 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU C 54 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ARG C 42 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N THR C 52 " --> pdb=" O ARG C 42 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASP C 44 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N VAL C 50 " --> pdb=" O ASP C 44 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 62 through 68 removed outlier: 6.542A pdb=" N GLY C 81 " --> pdb=" O ARG C 63 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU C 65 " --> pdb=" O VAL C 79 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL C 79 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ALA C 67 " --> pdb=" O TYR C 77 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N TYR C 77 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N SER C 82 " --> pdb=" O ARG C 86 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ARG C 86 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N HIS C 103 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLU C 91 " --> pdb=" O LYS C 101 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N LYS C 101 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLN C 93 " --> pdb=" O PHE C 99 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N PHE C 99 " --> pdb=" O GLN C 93 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 120 through 123 Processing sheet with id= G, first strand: chain 'C' and resid 144 through 146 Processing sheet with id= H, first strand: chain 'C' and resid 165 through 173 removed outlier: 6.533A pdb=" N LEU C 185 " --> pdb=" O TYR C 168 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL C 170 " --> pdb=" O ALA C 183 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ALA C 183 " --> pdb=" O VAL C 170 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLY C 172 " --> pdb=" O MET C 181 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N MET C 181 " --> pdb=" O GLY C 172 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLU C 212 " --> pdb=" O ARG C 222 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N ARG C 222 " --> pdb=" O GLU C 212 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASP C 214 " --> pdb=" O VAL C 220 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N VAL C 220 " --> pdb=" O ASP C 214 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 267 through 270 removed outlier: 3.545A pdb=" N TYR C 255 " --> pdb=" O SER C 252 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE C 234 " --> pdb=" O CYS C 251 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 287 through 294 removed outlier: 6.757A pdb=" N GLN C 304 " --> pdb=" O VAL C 288 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASER C 290 " --> pdb=" O LEU C 302 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU C 302 " --> pdb=" O ASER C 290 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N THR C 292 " --> pdb=" O PHE C 300 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N PHE C 300 " --> pdb=" O THR C 292 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N PHE C 299 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LEU C 315 " --> pdb=" O PHE C 299 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASP C 309 " --> pdb=" O THR C 305 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LYS C 312 " --> pdb=" O TYR C 329 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N TYR C 329 " --> pdb=" O LYS C 312 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N THR C 314 " --> pdb=" O LEU C 327 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LEU C 327 " --> pdb=" O THR C 314 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N GLU C 316 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE C 325 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 336 through 342 removed outlier: 6.928A pdb=" N ALA C 350 " --> pdb=" O ALA C 337 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N MET C 339 " --> pdb=" O PHE C 348 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE C 348 " --> pdb=" O MET C 339 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N VAL C 341 " --> pdb=" O PHE C 346 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N PHE C 346 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N GLN C 360 " --> pdb=" O LEU C 397 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N LEU C 397 " --> pdb=" O GLN C 360 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 774 through 780 Processing sheet with id= M, first strand: chain 'C' and resid 785 through 790 removed outlier: 6.977A pdb=" N ILE C 800 " --> pdb=" O ARG C 786 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N PHE C 788 " --> pdb=" O ILE C 798 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE C 798 " --> pdb=" O PHE C 788 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 886 through 895 removed outlier: 6.430A pdb=" N GLY C 908 " --> pdb=" O PHE C 889 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL C 891 " --> pdb=" O LEU C 906 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU C 906 " --> pdb=" O VAL C 891 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N VAL C 893 " --> pdb=" O TYR C 904 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N TYR C 904 " --> pdb=" O VAL C 893 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N TRP C 903 " --> pdb=" O LEU C 930 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N HIS C 941 " --> pdb=" O THR C 927 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N LYS C 929 " --> pdb=" O PHE C 939 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N PHE C 939 " --> pdb=" O LYS C 929 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL C 931 " --> pdb=" O LEU C 937 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N LEU C 937 " --> pdb=" O VAL C 931 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 949 through 955 removed outlier: 6.709A pdb=" N GLY C 962 " --> pdb=" O ALA C 950 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE C 952 " --> pdb=" O LEU C 960 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU C 960 " --> pdb=" O ILE C 952 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARG C 958 " --> pdb=" O PRO C 954 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS C 981 " --> pdb=" O VAL C 969 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ASP C 971 " --> pdb=" O ARG C 979 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ARG C 979 " --> pdb=" O ASP C 971 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 990 through 996 removed outlier: 6.318A pdb=" N SER C1003 " --> pdb=" O SER C 991 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ILE C 993 " --> pdb=" O ILE C1001 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE C1001 " --> pdb=" O ILE C 993 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N THR C 995 " --> pdb=" O ARG C 999 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ARG C 999 " --> pdb=" O THR C 995 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ARG C1013 " --> pdb=" O ILE C1023 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ILE C1023 " --> pdb=" O ARG C1013 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N LYS C1015 " --> pdb=" O LEU C1021 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N LEU C1021 " --> pdb=" O LYS C1015 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 1033 through 1038 removed outlier: 6.845A pdb=" N ALA C1047 " --> pdb=" O THR C1034 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA C1036 " --> pdb=" O ALA C1045 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ALA C1045 " --> pdb=" O ALA C1036 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N LEU C1038 " --> pdb=" O THR C1043 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N THR C1043 " --> pdb=" O LEU C1038 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASN C1052 " --> pdb=" O ASP C1048 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ARG C1057 " --> pdb=" O VAL C1091 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N VAL C1091 " --> pdb=" O ARG C1057 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'G' and resid 39 through 42 removed outlier: 6.028A pdb=" N TYR G 71 " --> pdb=" O CYS G 40 " (cutoff:3.500A) 405 hydrogen bonds defined for protein. 1164 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 13 hydrogen bonds 26 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 5.53 Time building geometry restraints manager: 6.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 2118 1.31 - 1.44: 3952 1.44 - 1.58: 7335 1.58 - 1.71: 88 1.71 - 1.85: 102 Bond restraints: 13595 Sorted by residual: bond pdb=" C5 OMU 2 47 " pdb=" C6 OMU 2 47 " ideal model delta sigma weight residual 1.480 1.344 0.136 2.00e-02 2.50e+03 4.64e+01 bond pdb=" C2 OMC 2 61 " pdb=" N3 OMC 2 61 " ideal model delta sigma weight residual 1.490 1.358 0.132 2.00e-02 2.50e+03 4.34e+01 bond pdb=" C2 OMC 2 40 " pdb=" N3 OMC 2 40 " ideal model delta sigma weight residual 1.490 1.359 0.131 2.00e-02 2.50e+03 4.27e+01 bond pdb=" N3 OMG 2 11 " pdb=" C4 OMG 2 11 " ideal model delta sigma weight residual 1.492 1.363 0.129 2.00e-02 2.50e+03 4.17e+01 bond pdb=" N3 OMG 2 10 " pdb=" C4 OMG 2 10 " ideal model delta sigma weight residual 1.492 1.363 0.129 2.00e-02 2.50e+03 4.16e+01 ... (remaining 13590 not shown) Histogram of bond angle deviations from ideal: 91.11 - 100.11: 18 100.11 - 109.10: 2312 109.10 - 118.10: 8464 118.10 - 127.09: 7617 127.09 - 136.08: 203 Bond angle restraints: 18614 Sorted by residual: angle pdb=" N ARG C 34 " pdb=" CA ARG C 34 " pdb=" C ARG C 34 " ideal model delta sigma weight residual 110.53 91.11 19.42 1.29e+00 6.01e-01 2.27e+02 angle pdb=" C ALA C 857 " pdb=" N GLY C 858 " pdb=" CA GLY C 858 " ideal model delta sigma weight residual 122.04 108.06 13.98 1.44e+00 4.82e-01 9.42e+01 angle pdb=" CB GLU G 79 " pdb=" CG GLU G 79 " pdb=" CD GLU G 79 " ideal model delta sigma weight residual 112.60 125.49 -12.89 1.70e+00 3.46e-01 5.75e+01 angle pdb=" CA ASP C1064 " pdb=" CB ASP C1064 " pdb=" CG ASP C1064 " ideal model delta sigma weight residual 112.60 119.78 -7.18 1.00e+00 1.00e+00 5.16e+01 angle pdb=" CA ASP B 479 " pdb=" CB ASP B 479 " pdb=" CG ASP B 479 " ideal model delta sigma weight residual 112.60 119.71 -7.11 1.00e+00 1.00e+00 5.05e+01 ... (remaining 18609 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.52: 7739 35.52 - 71.03: 256 71.03 - 106.55: 19 106.55 - 142.06: 0 142.06 - 177.58: 5 Dihedral angle restraints: 8019 sinusoidal: 3558 harmonic: 4461 Sorted by residual: dihedral pdb=" O4' C 2 9 " pdb=" C1' C 2 9 " pdb=" N1 C 2 9 " pdb=" C2 C 2 9 " ideal model delta sinusoidal sigma weight residual -128.00 43.16 -171.16 1 1.70e+01 3.46e-03 6.60e+01 dihedral pdb=" O4* PSU 2 58 " pdb=" C1* PSU 2 58 " pdb=" C5 PSU 2 58 " pdb=" C4 PSU 2 58 " ideal model delta sinusoidal sigma weight residual -160.00 17.58 -177.58 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O4* PSU 2 39 " pdb=" C1* PSU 2 39 " pdb=" C5 PSU 2 39 " pdb=" C4 PSU 2 39 " ideal model delta sinusoidal sigma weight residual 200.00 33.31 166.69 1 2.00e+01 2.50e-03 4.74e+01 ... (remaining 8016 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 1384 0.123 - 0.246: 567 0.246 - 0.369: 85 0.369 - 0.492: 10 0.492 - 0.615: 5 Chirality restraints: 2051 Sorted by residual: chirality pdb=" CA SER C1008 " pdb=" N SER C1008 " pdb=" C SER C1008 " pdb=" CB SER C1008 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.45e+00 chirality pdb=" P G 2 20 " pdb=" OP1 G 2 20 " pdb=" OP2 G 2 20 " pdb=" O5' G 2 20 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.21e+00 chirality pdb=" P U 2 8 " pdb=" OP1 U 2 8 " pdb=" OP2 U 2 8 " pdb=" O5' U 2 8 " both_signs ideal model delta sigma weight residual True 2.41 2.98 -0.57 2.00e-01 2.50e+01 8.14e+00 ... (remaining 2048 not shown) Planarity restraints: 2254 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMG 2 10 " -0.153 2.00e-02 2.50e+03 5.34e-01 6.41e+03 pdb=" C4' OMG 2 10 " 0.457 2.00e-02 2.50e+03 pdb=" O4' OMG 2 10 " 0.837 2.00e-02 2.50e+03 pdb=" C3' OMG 2 10 " -0.543 2.00e-02 2.50e+03 pdb=" O3' OMG 2 10 " -0.342 2.00e-02 2.50e+03 pdb=" C2' OMG 2 10 " -0.318 2.00e-02 2.50e+03 pdb=" O2' OMG 2 10 " 0.623 2.00e-02 2.50e+03 pdb=" C1' OMG 2 10 " 0.255 2.00e-02 2.50e+03 pdb=" N9 OMG 2 10 " -0.816 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC 2 61 " -0.090 2.00e-02 2.50e+03 5.16e-01 6.00e+03 pdb=" C4' OMC 2 61 " 0.429 2.00e-02 2.50e+03 pdb=" O4' OMC 2 61 " 0.664 2.00e-02 2.50e+03 pdb=" C3' OMC 2 61 " -0.553 2.00e-02 2.50e+03 pdb=" O3' OMC 2 61 " -0.404 2.00e-02 2.50e+03 pdb=" C2' OMC 2 61 " -0.262 2.00e-02 2.50e+03 pdb=" O2' OMC 2 61 " 0.744 2.00e-02 2.50e+03 pdb=" C1' OMC 2 61 " 0.253 2.00e-02 2.50e+03 pdb=" N1 OMC 2 61 " -0.782 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC 2 40 " 0.165 2.00e-02 2.50e+03 5.10e-01 5.85e+03 pdb=" C4' OMC 2 40 " -0.435 2.00e-02 2.50e+03 pdb=" O4' OMC 2 40 " -0.768 2.00e-02 2.50e+03 pdb=" C3' OMC 2 40 " 0.549 2.00e-02 2.50e+03 pdb=" O3' OMC 2 40 " 0.314 2.00e-02 2.50e+03 pdb=" C2' OMC 2 40 " 0.313 2.00e-02 2.50e+03 pdb=" O2' OMC 2 40 " -0.634 2.00e-02 2.50e+03 pdb=" C1' OMC 2 40 " -0.258 2.00e-02 2.50e+03 pdb=" N1 OMC 2 40 " 0.753 2.00e-02 2.50e+03 ... (remaining 2251 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 505 2.69 - 3.24: 12174 3.24 - 3.79: 23859 3.79 - 4.35: 32709 4.35 - 4.90: 50323 Nonbonded interactions: 119570 Sorted by model distance: nonbonded pdb=" N ARG C 34 " pdb=" O ARG C 34 " model vdw 2.134 2.496 nonbonded pdb=" O GLU A1156 " pdb=" NH1 ARG G 38 " model vdw 2.293 2.520 nonbonded pdb=" O ALA C 857 " pdb=" CA GLY C 858 " model vdw 2.386 2.752 nonbonded pdb=" O ALA C 200 " pdb=" OG1 THR C 204 " model vdw 2.396 2.440 nonbonded pdb=" NE2 GLN C 304 " pdb=" O PRO C 334 " model vdw 2.412 2.520 ... (remaining 119565 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 5 6.06 5 P 45 5.49 5 S 71 5.16 5 C 8240 2.51 5 N 2268 2.21 5 O 2822 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 13.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 53.860 Check model and map are aligned: 0.290 Convert atoms to be neutral: 0.120 Process input model: 48.650 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:13.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 130.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9029 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 : 0.012 0.136 13595 Z= 0.752 Angle : 1.856 19.417 18614 Z= 1.214 Chirality : 0.126 0.615 2051 Planarity : 0.026 0.534 2254 Dihedral : 17.430 177.575 5151 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer Outliers : 1.95 % Cbeta Deviations : 2.86 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.18), residues: 1514 helix: -2.29 (0.19), residues: 439 sheet: 0.16 (0.25), residues: 369 loop : -1.12 (0.19), residues: 706 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 311 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 3 residues processed: 326 average time/residue: 1.3783 time to fit residues: 488.2689 Evaluate side-chains 218 residues out of total 1331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 215 time to evaluate : 1.552 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.1252 time to fit residues: 2.3348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.7980 chunk 116 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 139 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 9 442 ASN A1144 GLN B 569 GLN ** C 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 GLN C 203 ASN C1181 GLN G 78 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9053 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 13595 Z= 0.226 Angle : 0.822 13.872 18614 Z= 0.482 Chirality : 0.049 0.604 2051 Planarity : 0.007 0.127 2254 Dihedral : 14.892 179.231 2192 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.20), residues: 1514 helix: 0.00 (0.24), residues: 427 sheet: 0.61 (0.26), residues: 373 loop : -0.61 (0.21), residues: 714 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 243 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 5 residues processed: 254 average time/residue: 1.3345 time to fit residues: 373.4675 Evaluate side-chains 216 residues out of total 1331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 211 time to evaluate : 1.549 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 2 average time/residue: 0.2019 time to fit residues: 2.7009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 chunk 116 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 140 optimal weight: 2.9990 chunk 151 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 81 ASN 9 413 ASN 9 442 ASN A1079 ASN A1228 GLN B 458 ASN B 496 ASN ** C 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 411 GLN C 805 ASN G 78 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9092 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 13595 Z= 0.225 Angle : 0.761 12.989 18614 Z= 0.455 Chirality : 0.046 0.430 2051 Planarity : 0.007 0.126 2254 Dihedral : 14.444 172.951 2192 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.21), residues: 1514 helix: 0.97 (0.25), residues: 431 sheet: 0.54 (0.26), residues: 378 loop : -0.35 (0.21), residues: 705 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 211 time to evaluate : 1.906 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 7 residues processed: 224 average time/residue: 1.2937 time to fit residues: 318.3871 Evaluate side-chains 203 residues out of total 1331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 196 time to evaluate : 1.551 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.2017 time to fit residues: 2.6533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 140 optimal weight: 0.0060 chunk 148 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 133 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 9 425 HIS 9 442 ASN ** 9 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1107 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9090 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 13595 Z= 0.210 Angle : 0.749 13.207 18614 Z= 0.449 Chirality : 0.045 0.453 2051 Planarity : 0.007 0.122 2254 Dihedral : 14.271 174.997 2192 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer Outliers : 1.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.21), residues: 1514 helix: 1.27 (0.25), residues: 433 sheet: 0.55 (0.26), residues: 381 loop : -0.26 (0.22), residues: 700 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 205 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 5 residues processed: 213 average time/residue: 1.2803 time to fit residues: 298.6966 Evaluate side-chains 208 residues out of total 1331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 203 time to evaluate : 1.704 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 2.1817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 110 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 76 optimal weight: 0.7980 chunk 133 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 9 442 ASN A1100 ASN A1228 GLN B 458 ASN C 93 GLN C 818 GLN G 50 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9119 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 13595 Z= 0.288 Angle : 0.769 12.859 18614 Z= 0.457 Chirality : 0.046 0.450 2051 Planarity : 0.007 0.125 2254 Dihedral : 14.211 174.005 2192 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer Outliers : 1.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.21), residues: 1514 helix: 1.36 (0.25), residues: 432 sheet: 0.48 (0.26), residues: 381 loop : -0.22 (0.22), residues: 701 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 203 time to evaluate : 1.626 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 211 average time/residue: 1.4176 time to fit residues: 325.9228 Evaluate side-chains 209 residues out of total 1331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 198 time to evaluate : 1.414 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 6 residues processed: 5 average time/residue: 0.4984 time to fit residues: 5.1437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1228 GLN C 818 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9120 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 13595 Z= 0.291 Angle : 0.769 13.011 18614 Z= 0.458 Chirality : 0.046 0.446 2051 Planarity : 0.007 0.124 2254 Dihedral : 14.170 174.743 2192 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.21), residues: 1514 helix: 1.41 (0.26), residues: 425 sheet: 0.45 (0.26), residues: 381 loop : -0.18 (0.22), residues: 708 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 203 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 11 residues processed: 214 average time/residue: 1.3810 time to fit residues: 322.9411 Evaluate side-chains 212 residues out of total 1331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 201 time to evaluate : 1.375 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 6 residues processed: 5 average time/residue: 0.3314 time to fit residues: 4.2516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 148 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 91 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1228 GLN B 458 ASN C 818 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9098 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 13595 Z= 0.197 Angle : 0.744 13.170 18614 Z= 0.446 Chirality : 0.044 0.453 2051 Planarity : 0.007 0.122 2254 Dihedral : 14.110 175.963 2192 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer Outliers : 0.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.21), residues: 1514 helix: 1.59 (0.26), residues: 423 sheet: 0.44 (0.26), residues: 383 loop : -0.14 (0.22), residues: 708 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 206 time to evaluate : 1.578 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 4 residues processed: 215 average time/residue: 1.3619 time to fit residues: 319.5471 Evaluate side-chains 201 residues out of total 1331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 197 time to evaluate : 1.533 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 2.0784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 13 optimal weight: 0.3980 chunk 116 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 81 ASN A1228 GLN B 458 ASN C 805 ASN C 818 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9133 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 13595 Z= 0.353 Angle : 0.788 12.971 18614 Z= 0.466 Chirality : 0.047 0.455 2051 Planarity : 0.007 0.124 2254 Dihedral : 14.252 176.594 2192 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer Outliers : 1.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.21), residues: 1514 helix: 1.44 (0.25), residues: 426 sheet: 0.46 (0.26), residues: 381 loop : -0.16 (0.22), residues: 707 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 204 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 212 average time/residue: 1.4079 time to fit residues: 325.2371 Evaluate side-chains 211 residues out of total 1331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 203 time to evaluate : 1.599 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 0.1287 time to fit residues: 2.3810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 124 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 81 ASN B 458 ASN C 805 ASN C 818 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9117 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 13595 Z= 0.260 Angle : 0.769 13.161 18614 Z= 0.456 Chirality : 0.046 0.483 2051 Planarity : 0.007 0.122 2254 Dihedral : 14.210 178.001 2192 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.21), residues: 1514 helix: 1.53 (0.26), residues: 426 sheet: 0.48 (0.26), residues: 381 loop : -0.16 (0.22), residues: 707 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 200 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 207 average time/residue: 1.3944 time to fit residues: 315.5338 Evaluate side-chains 207 residues out of total 1331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 199 time to evaluate : 1.569 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 0.2750 time to fit residues: 2.4890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 69 optimal weight: 0.0980 chunk 101 optimal weight: 0.7980 chunk 153 optimal weight: 0.4980 chunk 141 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 94 optimal weight: 0.4980 chunk 74 optimal weight: 0.0000 chunk 97 optimal weight: 1.9990 overall best weight: 0.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 81 ASN 9 423 GLN B 458 ASN C 818 GLN C1192 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9078 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 13595 Z= 0.164 Angle : 0.739 13.259 18614 Z= 0.443 Chirality : 0.044 0.494 2051 Planarity : 0.006 0.120 2254 Dihedral : 14.059 179.740 2192 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer Outliers : 0.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.21), residues: 1514 helix: 1.69 (0.26), residues: 424 sheet: 0.48 (0.27), residues: 383 loop : -0.09 (0.22), residues: 707 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 203 time to evaluate : 1.591 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 208 average time/residue: 1.3471 time to fit residues: 306.4646 Evaluate side-chains 205 residues out of total 1331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 198 time to evaluate : 1.732 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.6905 time to fit residues: 4.5614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.1980 chunk 37 optimal weight: 0.9990 chunk 112 optimal weight: 0.5980 chunk 18 optimal weight: 0.0670 chunk 33 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 107 optimal weight: 0.0870 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 81 ASN 9 448 ASN C 818 GLN G 78 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.102872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.067971 restraints weight = 38292.899| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 2.67 r_work: 0.2680 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2548 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3465 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3465 r_free = 0.3465 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3465 r_free = 0.3465 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3465 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9147 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 13595 Z= 0.166 Angle : 0.743 13.304 18614 Z= 0.444 Chirality : 0.044 0.485 2051 Planarity : 0.006 0.119 2254 Dihedral : 13.965 179.225 2192 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.21), residues: 1514 helix: 1.79 (0.26), residues: 419 sheet: 0.55 (0.27), residues: 369 loop : 0.02 (0.22), residues: 726 =============================================================================== Job complete usr+sys time: 6993.19 seconds wall clock time: 124 minutes 21.51 seconds (7461.51 seconds total)