Starting phenix.real_space_refine on Sun Mar 17 15:03:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wxu_21963/03_2024/6wxu_21963_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wxu_21963/03_2024/6wxu_21963.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wxu_21963/03_2024/6wxu_21963_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wxu_21963/03_2024/6wxu_21963_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wxu_21963/03_2024/6wxu_21963_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wxu_21963/03_2024/6wxu_21963.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wxu_21963/03_2024/6wxu_21963.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wxu_21963/03_2024/6wxu_21963_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wxu_21963/03_2024/6wxu_21963_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.027 sd= 0.126 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 Fe 4 7.16 5 P 4 5.49 5 S 74 5.16 5 C 11828 2.51 5 N 3014 2.21 5 O 3232 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 43": "NH1" <-> "NH2" Residue "A ARG 50": "NH1" <-> "NH2" Residue "A ARG 84": "NH1" <-> "NH2" Residue "A ARG 93": "NH1" <-> "NH2" Residue "A ARG 150": "NH1" <-> "NH2" Residue "A ARG 241": "NH1" <-> "NH2" Residue "A ARG 282": "NH1" <-> "NH2" Residue "A ARG 362": "NH1" <-> "NH2" Residue "A ARG 377": "NH1" <-> "NH2" Residue "A GLU 394": "OE1" <-> "OE2" Residue "A ARG 395": "NH1" <-> "NH2" Residue "A ARG 428": "NH1" <-> "NH2" Residue "A ARG 507": "NH1" <-> "NH2" Residue "A ARG 520": "NH1" <-> "NH2" Residue "A ARG 618": "NH1" <-> "NH2" Residue "A ARG 1042": "NH1" <-> "NH2" Residue "A ARG 1043": "NH1" <-> "NH2" Residue "A ARG 1216": "NH1" <-> "NH2" Residue "A ARG 1248": "NH1" <-> "NH2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ARG 50": "NH1" <-> "NH2" Residue "C ARG 84": "NH1" <-> "NH2" Residue "C ARG 93": "NH1" <-> "NH2" Residue "C ARG 150": "NH1" <-> "NH2" Residue "C ARG 241": "NH1" <-> "NH2" Residue "C ARG 282": "NH1" <-> "NH2" Residue "C ARG 362": "NH1" <-> "NH2" Residue "C ARG 377": "NH1" <-> "NH2" Residue "C GLU 394": "OE1" <-> "OE2" Residue "C ARG 395": "NH1" <-> "NH2" Residue "C ARG 428": "NH1" <-> "NH2" Residue "C ARG 507": "NH1" <-> "NH2" Residue "C ARG 520": "NH1" <-> "NH2" Residue "C ARG 618": "NH1" <-> "NH2" Residue "C ARG 1042": "NH1" <-> "NH2" Residue "C ARG 1043": "NH1" <-> "NH2" Residue "C ARG 1216": "NH1" <-> "NH2" Residue "C ARG 1248": "NH1" <-> "NH2" Residue "D ARG 237": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18156 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 6624 Classifications: {'peptide': 834} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 53, 'TRANS': 779} Chain breaks: 2 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 4, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 43 Chain: "B" Number of atoms: 2093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2093 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 258} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 6624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 6624 Classifications: {'peptide': 834} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 53, 'TRANS': 779} Chain breaks: 2 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 4, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 43 Chain: "D" Number of atoms: 2093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2093 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 258} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "F" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "A" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 164 Unusual residues: {'HEC': 2, 'NAG': 3, 'PX2': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 70 Unusual residues: {'NAG': 2, 'PLC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 164 Unusual residues: {'HEC': 2, 'NAG': 3, 'PX2': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 70 Unusual residues: {'NAG': 2, 'PLC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 9.51, per 1000 atoms: 0.52 Number of scatterers: 18156 At special positions: 0 Unit cell: (117.72, 96.12, 122.04, 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) Fe 4 26.01 S 74 16.00 P 4 15.00 O 3232 8.00 N 3014 7.00 C 11828 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A1165 " distance=2.03 Simple disulfide: pdb=" SG CYS A 345 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 364 " - pdb=" SG CYS A 579 " distance=2.03 Simple disulfide: pdb=" SG CYS B 167 " - pdb=" SG CYS B 234 " distance=2.03 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C1165 " distance=2.03 Simple disulfide: pdb=" SG CYS C 345 " - pdb=" SG CYS C 565 " distance=2.03 Simple disulfide: pdb=" SG CYS C 364 " - pdb=" SG CYS C 579 " distance=2.03 Simple disulfide: pdb=" SG CYS D 167 " - pdb=" SG CYS D 234 " distance=2.03 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=4, symmetry=0 Links applied ALPHA1-2 " MAN E 4 " - " MAN E 5 " " MAN E 5 " - " MAN E 6 " " MAN E 8 " - " MAN E 9 " " MAN E 10 " - " MAN E 11 " " MAN F 4 " - " MAN F 5 " " MAN F 5 " - " MAN F 6 " " MAN F 8 " - " MAN F 9 " " MAN F 10 " - " MAN F 11 " ALPHA1-3 " BMA E 3 " - " MAN E 4 " " MAN E 7 " - " MAN E 8 " " BMA F 3 " - " MAN F 4 " " MAN F 7 " - " MAN F 8 " ALPHA1-6 " BMA E 3 " - " MAN E 7 " " MAN E 7 " - " MAN E 10 " " BMA F 3 " - " MAN F 7 " " MAN F 7 " - " MAN F 10 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG A1601 " - " ASN A 94 " " NAG A1602 " - " ASN A 342 " " NAG A1603 " - " ASN A 534 " " NAG B 401 " - " ASN B 84 " " NAG B 413 " - " ASN B 121 " " NAG C1601 " - " ASN C 94 " " NAG C1602 " - " ASN C 342 " " NAG C1603 " - " ASN C 534 " " NAG D 401 " - " ASN D 84 " " NAG D 413 " - " ASN D 121 " " NAG E 1 " - " ASN B 109 " " NAG F 1 " - " ASN D 109 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.56 Conformation dependent library (CDL) restraints added in 3.4 seconds 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4092 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 86 helices and 2 sheets defined 47.5% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.83 Creating SS restraints... Processing helix chain 'A' and resid 75 through 78 No H-bonds generated for 'chain 'A' and resid 75 through 78' Processing helix chain 'A' and resid 97 through 110 Processing helix chain 'A' and resid 183 through 188 removed outlier: 3.688A pdb=" N THR A 188 " --> pdb=" O SER A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 266 removed outlier: 4.030A pdb=" N LEU A 248 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS A 256 " --> pdb=" O TRP A 252 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG A 261 " --> pdb=" O ASN A 257 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN A 265 " --> pdb=" O ARG A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 293 removed outlier: 3.653A pdb=" N LYS A 281 " --> pdb=" O GLN A 277 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG A 282 " --> pdb=" O HIS A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 299 No H-bonds generated for 'chain 'A' and resid 296 through 299' Processing helix chain 'A' and resid 320 through 326 removed outlier: 3.806A pdb=" N VAL A 324 " --> pdb=" O PRO A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 332 No H-bonds generated for 'chain 'A' and resid 330 through 332' Processing helix chain 'A' and resid 364 through 366 No H-bonds generated for 'chain 'A' and resid 364 through 366' Processing helix chain 'A' and resid 378 through 389 Processing helix chain 'A' and resid 402 through 405 No H-bonds generated for 'chain 'A' and resid 402 through 405' Processing helix chain 'A' and resid 419 through 430 Processing helix chain 'A' and resid 435 through 441 removed outlier: 3.534A pdb=" N GLU A 440 " --> pdb=" O THR A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 460 Processing helix chain 'A' and resid 463 through 472 removed outlier: 3.712A pdb=" N ALA A 467 " --> pdb=" O THR A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 481 through 487 Processing helix chain 'A' and resid 495 through 510 removed outlier: 3.547A pdb=" N THR A 499 " --> pdb=" O PRO A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 533 removed outlier: 3.516A pdb=" N ALA A 530 " --> pdb=" O LYS A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 544 Processing helix chain 'A' and resid 549 through 551 No H-bonds generated for 'chain 'A' and resid 549 through 551' Processing helix chain 'A' and resid 592 through 604 Processing helix chain 'A' and resid 606 through 621 removed outlier: 3.932A pdb=" N LEU A 611 " --> pdb=" O LEU A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 1031 through 1040 Processing helix chain 'A' and resid 1042 through 1068 Processing helix chain 'A' and resid 1081 through 1096 removed outlier: 3.737A pdb=" N THR A1089 " --> pdb=" O LEU A1085 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A1090 " --> pdb=" O SER A1086 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA A1091 " --> pdb=" O ARG A1087 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE A1095 " --> pdb=" O ALA A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1112 Processing helix chain 'A' and resid 1116 through 1119 removed outlier: 3.511A pdb=" N ARG A1119 " --> pdb=" O PHE A1116 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1116 through 1119' Processing helix chain 'A' and resid 1128 through 1136 Processing helix chain 'A' and resid 1138 through 1155 removed outlier: 3.699A pdb=" N LEU A1143 " --> pdb=" O ILE A1139 " (cutoff:3.500A) Processing helix chain 'A' and resid 1160 through 1166 removed outlier: 3.879A pdb=" N CYS A1165 " --> pdb=" O SER A1161 " (cutoff:3.500A) Processing helix chain 'A' and resid 1182 through 1187 Processing helix chain 'A' and resid 1190 through 1208 removed outlier: 3.627A pdb=" N VAL A1196 " --> pdb=" O GLY A1192 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A1197 " --> pdb=" O LEU A1193 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A1207 " --> pdb=" O ALA A1203 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1239 removed outlier: 3.872A pdb=" N HIS A1226 " --> pdb=" O TRP A1222 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LEU A1227 " --> pdb=" O LEU A1223 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N TYR A1228 " --> pdb=" O THR A1224 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ILE A1229 " --> pdb=" O HIS A1225 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N PHE A1230 " --> pdb=" O HIS A1226 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY A1239 " --> pdb=" O LEU A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1269 removed outlier: 4.939A pdb=" N VAL A1255 " --> pdb=" O ILE A1251 " (cutoff:3.500A) Proline residue: A1256 - end of helix removed outlier: 3.743A pdb=" N SER A1269 " --> pdb=" O LEU A1265 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 44 removed outlier: 4.205A pdb=" N ILE B 27 " --> pdb=" O THR B 23 " (cutoff:3.500A) Proline residue: B 43 - end of helix Processing helix chain 'B' and resid 48 through 72 removed outlier: 4.079A pdb=" N LEU B 51 " --> pdb=" O LYS B 48 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU B 55 " --> pdb=" O PHE B 52 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N THR B 59 " --> pdb=" O ARG B 56 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER B 60 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE B 67 " --> pdb=" O GLY B 64 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL B 70 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN B 71 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE B 72 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 147 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 170 through 199 Processing helix chain 'B' and resid 203 through 226 removed outlier: 3.940A pdb=" N LEU B 211 " --> pdb=" O GLY B 207 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA B 212 " --> pdb=" O HIS B 208 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN B 217 " --> pdb=" O THR B 213 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N MET B 226 " --> pdb=" O PHE B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 231 No H-bonds generated for 'chain 'B' and resid 228 through 231' Processing helix chain 'B' and resid 249 through 273 Processing helix chain 'C' and resid 75 through 78 No H-bonds generated for 'chain 'C' and resid 75 through 78' Processing helix chain 'C' and resid 97 through 110 Processing helix chain 'C' and resid 183 through 188 removed outlier: 3.687A pdb=" N THR C 188 " --> pdb=" O SER C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 266 removed outlier: 4.030A pdb=" N LEU C 248 " --> pdb=" O PHE C 244 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY C 249 " --> pdb=" O LEU C 245 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS C 256 " --> pdb=" O TRP C 252 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG C 261 " --> pdb=" O ASN C 257 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA C 264 " --> pdb=" O ALA C 260 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN C 265 " --> pdb=" O ARG C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 293 removed outlier: 3.653A pdb=" N LYS C 281 " --> pdb=" O GLN C 277 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG C 282 " --> pdb=" O HIS C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 299 No H-bonds generated for 'chain 'C' and resid 296 through 299' Processing helix chain 'C' and resid 320 through 326 removed outlier: 3.806A pdb=" N VAL C 324 " --> pdb=" O PRO C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 332 No H-bonds generated for 'chain 'C' and resid 330 through 332' Processing helix chain 'C' and resid 364 through 366 No H-bonds generated for 'chain 'C' and resid 364 through 366' Processing helix chain 'C' and resid 378 through 389 Processing helix chain 'C' and resid 402 through 405 No H-bonds generated for 'chain 'C' and resid 402 through 405' Processing helix chain 'C' and resid 419 through 430 Processing helix chain 'C' and resid 435 through 441 removed outlier: 3.534A pdb=" N GLU C 440 " --> pdb=" O THR C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 460 Processing helix chain 'C' and resid 463 through 472 removed outlier: 3.712A pdb=" N ALA C 467 " --> pdb=" O THR C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 478 No H-bonds generated for 'chain 'C' and resid 476 through 478' Processing helix chain 'C' and resid 481 through 487 Processing helix chain 'C' and resid 495 through 510 removed outlier: 3.547A pdb=" N THR C 499 " --> pdb=" O PRO C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 533 removed outlier: 3.515A pdb=" N ALA C 530 " --> pdb=" O LYS C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 544 Processing helix chain 'C' and resid 549 through 551 No H-bonds generated for 'chain 'C' and resid 549 through 551' Processing helix chain 'C' and resid 592 through 604 Processing helix chain 'C' and resid 606 through 621 removed outlier: 3.933A pdb=" N LEU C 611 " --> pdb=" O LEU C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 1031 through 1040 Processing helix chain 'C' and resid 1042 through 1068 Processing helix chain 'C' and resid 1081 through 1096 removed outlier: 3.737A pdb=" N THR C1089 " --> pdb=" O LEU C1085 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA C1090 " --> pdb=" O SER C1086 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA C1091 " --> pdb=" O ARG C1087 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE C1095 " --> pdb=" O ALA C1091 " (cutoff:3.500A) Processing helix chain 'C' and resid 1106 through 1112 Processing helix chain 'C' and resid 1116 through 1119 removed outlier: 3.512A pdb=" N ARG C1119 " --> pdb=" O PHE C1116 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1116 through 1119' Processing helix chain 'C' and resid 1128 through 1136 Processing helix chain 'C' and resid 1138 through 1155 removed outlier: 3.700A pdb=" N LEU C1143 " --> pdb=" O ILE C1139 " (cutoff:3.500A) Processing helix chain 'C' and resid 1160 through 1166 removed outlier: 3.880A pdb=" N CYS C1165 " --> pdb=" O SER C1161 " (cutoff:3.500A) Processing helix chain 'C' and resid 1182 through 1187 Processing helix chain 'C' and resid 1190 through 1208 removed outlier: 3.626A pdb=" N VAL C1196 " --> pdb=" O GLY C1192 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU C1197 " --> pdb=" O LEU C1193 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL C1207 " --> pdb=" O ALA C1203 " (cutoff:3.500A) Processing helix chain 'C' and resid 1218 through 1239 removed outlier: 3.872A pdb=" N HIS C1226 " --> pdb=" O TRP C1222 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LEU C1227 " --> pdb=" O LEU C1223 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N TYR C1228 " --> pdb=" O THR C1224 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ILE C1229 " --> pdb=" O HIS C1225 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N PHE C1230 " --> pdb=" O HIS C1226 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY C1239 " --> pdb=" O LEU C1235 " (cutoff:3.500A) Processing helix chain 'C' and resid 1249 through 1269 removed outlier: 4.940A pdb=" N VAL C1255 " --> pdb=" O ILE C1251 " (cutoff:3.500A) Proline residue: C1256 - end of helix removed outlier: 3.743A pdb=" N SER C1269 " --> pdb=" O LEU C1265 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 44 removed outlier: 4.205A pdb=" N ILE D 27 " --> pdb=" O THR D 23 " (cutoff:3.500A) Proline residue: D 43 - end of helix Processing helix chain 'D' and resid 48 through 72 removed outlier: 4.079A pdb=" N LEU D 51 " --> pdb=" O LYS D 48 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU D 55 " --> pdb=" O PHE D 52 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N THR D 59 " --> pdb=" O ARG D 56 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER D 60 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE D 67 " --> pdb=" O GLY D 64 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL D 70 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN D 71 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE D 72 " --> pdb=" O ALA D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 147 Processing helix chain 'D' and resid 152 through 159 Processing helix chain 'D' and resid 170 through 199 Processing helix chain 'D' and resid 203 through 226 removed outlier: 3.940A pdb=" N LEU D 211 " --> pdb=" O GLY D 207 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA D 212 " --> pdb=" O HIS D 208 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN D 217 " --> pdb=" O THR D 213 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N MET D 226 " --> pdb=" O PHE D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 231 No H-bonds generated for 'chain 'D' and resid 228 through 231' Processing helix chain 'D' and resid 249 through 273 Processing sheet with id= A, first strand: chain 'B' and resid 245 through 247 Processing sheet with id= B, first strand: chain 'D' and resid 245 through 247 658 hydrogen bonds defined for protein. 1872 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: 5.05 Time building geometry restraints manager: 8.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.37: 6687 1.37 - 1.58: 11887 1.58 - 1.80: 77 1.80 - 2.01: 59 2.01 - 2.22: 4 Bond restraints: 18714 Sorted by residual: bond pdb=" CAC HEC C1604 " pdb=" CBC HEC C1604 " ideal model delta sigma weight residual 1.544 1.308 0.236 2.00e-02 2.50e+03 1.40e+02 bond pdb=" CAC HEC A1604 " pdb=" CBC HEC A1604 " ideal model delta sigma weight residual 1.544 1.308 0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" CAC HEC C1605 " pdb=" CBC HEC C1605 " ideal model delta sigma weight residual 1.544 1.312 0.232 2.00e-02 2.50e+03 1.34e+02 bond pdb=" CAC HEC A1605 " pdb=" CBC HEC A1605 " ideal model delta sigma weight residual 1.544 1.313 0.231 2.00e-02 2.50e+03 1.34e+02 bond pdb=" CAB HEC A1604 " pdb=" CBB HEC A1604 " ideal model delta sigma weight residual 1.544 1.313 0.231 2.00e-02 2.50e+03 1.34e+02 ... (remaining 18709 not shown) Histogram of bond angle deviations from ideal: 81.80 - 101.39: 60 101.39 - 120.99: 20361 120.99 - 140.58: 5115 140.58 - 160.17: 0 160.17 - 179.76: 8 Bond angle restraints: 25544 Sorted by residual: angle pdb=" C3B HEC C1605 " pdb=" CAB HEC C1605 " pdb=" CBB HEC C1605 " ideal model delta sigma weight residual 109.00 122.95 -13.95 3.00e+00 1.11e-01 2.16e+01 angle pdb=" C3B HEC A1605 " pdb=" CAB HEC A1605 " pdb=" CBB HEC A1605 " ideal model delta sigma weight residual 109.00 122.93 -13.93 3.00e+00 1.11e-01 2.16e+01 angle pdb=" C3B HEC A1604 " pdb=" CAB HEC A1604 " pdb=" CBB HEC A1604 " ideal model delta sigma weight residual 109.00 122.64 -13.64 3.00e+00 1.11e-01 2.07e+01 angle pdb=" C3B HEC C1604 " pdb=" CAB HEC C1604 " pdb=" CBB HEC C1604 " ideal model delta sigma weight residual 109.00 122.64 -13.64 3.00e+00 1.11e-01 2.07e+01 angle pdb=" C3C HEC C1605 " pdb=" CAC HEC C1605 " pdb=" CBC HEC C1605 " ideal model delta sigma weight residual 109.00 122.15 -13.15 3.00e+00 1.11e-01 1.92e+01 ... (remaining 25539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.71: 10486 20.71 - 41.43: 532 41.43 - 62.14: 132 62.14 - 82.85: 38 82.85 - 103.57: 26 Dihedral angle restraints: 11214 sinusoidal: 4828 harmonic: 6386 Sorted by residual: dihedral pdb=" C2B HEC C1604 " pdb=" C3B HEC C1604 " pdb=" CAB HEC C1604 " pdb=" CBB HEC C1604 " ideal model delta sinusoidal sigma weight residual -120.00 -32.91 -87.09 2 1.00e+01 1.00e-02 4.79e+01 dihedral pdb=" C2B HEC A1604 " pdb=" C3B HEC A1604 " pdb=" CAB HEC A1604 " pdb=" CBB HEC A1604 " ideal model delta sinusoidal sigma weight residual -120.00 -32.94 -87.06 2 1.00e+01 1.00e-02 4.79e+01 dihedral pdb=" C2B HEC C1605 " pdb=" C3B HEC C1605 " pdb=" CAB HEC C1605 " pdb=" CBB HEC C1605 " ideal model delta sinusoidal sigma weight residual -120.00 -39.66 -80.34 2 1.00e+01 1.00e-02 4.66e+01 ... (remaining 11211 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 2663 0.088 - 0.175: 183 0.175 - 0.263: 7 0.263 - 0.351: 1 0.351 - 0.438: 2 Chirality restraints: 2856 Sorted by residual: chirality pdb=" C1 NAG C1602 " pdb=" ND2 ASN C 342 " pdb=" C2 NAG C1602 " pdb=" O5 NAG C1602 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.80e+00 chirality pdb=" C1 NAG A1602 " pdb=" ND2 ASN A 342 " pdb=" C2 NAG A1602 " pdb=" O5 NAG A1602 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.76e+00 chirality pdb=" CA ARG C1131 " pdb=" N ARG C1131 " pdb=" C ARG C1131 " pdb=" CB ARG C1131 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 2853 not shown) Planarity restraints: 3174 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A1129 " 0.014 2.00e-02 2.50e+03 2.80e-02 7.82e+00 pdb=" C PHE A1129 " -0.048 2.00e-02 2.50e+03 pdb=" O PHE A1129 " 0.018 2.00e-02 2.50e+03 pdb=" N HIS A1130 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C1129 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.81e+00 pdb=" C PHE C1129 " 0.048 2.00e-02 2.50e+03 pdb=" O PHE C1129 " -0.018 2.00e-02 2.50e+03 pdb=" N HIS C1130 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A1130 " 0.017 2.00e-02 2.50e+03 1.88e-02 5.30e+00 pdb=" CG HIS A1130 " -0.037 2.00e-02 2.50e+03 pdb=" ND1 HIS A1130 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 HIS A1130 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 HIS A1130 " -0.008 2.00e-02 2.50e+03 pdb=" NE2 HIS A1130 " 0.016 2.00e-02 2.50e+03 ... (remaining 3171 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1635 2.73 - 3.28: 17598 3.28 - 3.82: 28878 3.82 - 4.36: 37082 4.36 - 4.90: 63279 Nonbonded interactions: 148472 Sorted by model distance: nonbonded pdb=" O TRP C 151 " pdb=" NH1 ARG C 153 " model vdw 2.193 2.520 nonbonded pdb=" O TRP A 151 " pdb=" NH1 ARG A 153 " model vdw 2.193 2.520 nonbonded pdb=" OG SER C 91 " pdb=" OE2 GLU C 396 " model vdw 2.230 2.440 nonbonded pdb=" OG SER A 91 " pdb=" OE2 GLU A 396 " model vdw 2.230 2.440 nonbonded pdb=" NH1 ARG C 76 " pdb=" OD2 ASP C 418 " model vdw 2.234 2.520 ... (remaining 148467 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.490 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 49.410 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.140 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:11.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 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 : 0.011 0.296 18714 Z= 0.730 Angle : 0.895 13.948 25544 Z= 0.403 Chirality : 0.049 0.438 2856 Planarity : 0.005 0.057 3162 Dihedral : 14.659 103.567 7098 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.85 % Allowed : 4.67 % Favored : 93.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 1.47 % 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: -3.08 (0.16), residues: 2198 helix: -1.63 (0.13), residues: 1122 sheet: -1.83 (0.52), residues: 92 loop : -2.51 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 252 HIS 0.021 0.001 HIS A1130 PHE 0.014 0.002 PHE C1129 TYR 0.018 0.002 TYR C 64 ARG 0.003 0.001 ARG A 507 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 198 time to evaluate : 1.968 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8690 (mtpp) cc_final: 0.8367 (mttp) REVERT: A 142 VAL cc_start: 0.8450 (OUTLIER) cc_final: 0.8230 (t) REVERT: A 215 MET cc_start: 0.9239 (mmm) cc_final: 0.8952 (mmt) REVERT: A 451 GLN cc_start: 0.7963 (mp10) cc_final: 0.7728 (mp10) REVERT: A 1040 ASN cc_start: 0.8262 (m-40) cc_final: 0.7960 (m110) REVERT: A 1263 ASP cc_start: 0.7904 (t0) cc_final: 0.7697 (t0) REVERT: B 274 MET cc_start: 0.7235 (mtp) cc_final: 0.6610 (pp-130) REVERT: C 68 LYS cc_start: 0.8679 (mtpp) cc_final: 0.8344 (mttp) REVERT: C 142 VAL cc_start: 0.8451 (OUTLIER) cc_final: 0.8227 (t) REVERT: C 215 MET cc_start: 0.9203 (mmm) cc_final: 0.8933 (mmt) REVERT: C 451 GLN cc_start: 0.7948 (mp10) cc_final: 0.7713 (mp10) REVERT: D 98 ASP cc_start: 0.8180 (m-30) cc_final: 0.7963 (m-30) REVERT: D 136 ARG cc_start: 0.8366 (mmm-85) cc_final: 0.8097 (mmm-85) REVERT: D 219 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.8028 (tp) REVERT: D 274 MET cc_start: 0.7235 (mtp) cc_final: 0.6780 (pp-130) outliers start: 34 outliers final: 13 residues processed: 229 average time/residue: 1.5788 time to fit residues: 396.7184 Evaluate side-chains 151 residues out of total 1882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 135 time to evaluate : 1.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 1189 THR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 219 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 1.9990 chunk 166 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 172 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 199 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 105 HIS A 165 GLN A 289 ASN A 302 GLN A 328 GLN A 376 GLN A 391 GLN A 504 GLN A1071 HIS ** A1148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1188 GLN B 6 HIS B 119 GLN B 171 ASN C 23 ASN C 105 HIS C 165 GLN C 289 ASN C 302 GLN C 328 GLN C 376 GLN C 391 GLN C 504 GLN C1040 ASN C1071 HIS ** C1148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1188 GLN D 6 HIS D 82 ASN D 119 GLN D 171 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18714 Z= 0.197 Angle : 0.615 15.184 25544 Z= 0.285 Chirality : 0.043 0.374 2856 Planarity : 0.005 0.056 3162 Dihedral : 12.682 82.202 3238 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.66 % Allowed : 9.55 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 1.47 % 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: -1.56 (0.18), residues: 2198 helix: -0.26 (0.16), residues: 1110 sheet: -1.12 (0.56), residues: 92 loop : -1.91 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 252 HIS 0.006 0.001 HIS A 256 PHE 0.014 0.001 PHE A 253 TYR 0.018 0.001 TYR A 64 ARG 0.008 0.000 ARG C 139 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 144 time to evaluate : 1.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8646 (mtpp) cc_final: 0.8307 (mttp) REVERT: A 142 VAL cc_start: 0.8342 (OUTLIER) cc_final: 0.8139 (t) REVERT: A 215 MET cc_start: 0.9170 (mmm) cc_final: 0.8932 (mmt) REVERT: A 346 HIS cc_start: 0.7342 (t-90) cc_final: 0.6582 (m90) REVERT: A 1040 ASN cc_start: 0.8249 (m-40) cc_final: 0.7936 (m110) REVERT: A 1263 ASP cc_start: 0.7866 (t0) cc_final: 0.7620 (t0) REVERT: B 147 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6867 (mt-10) REVERT: B 159 GLU cc_start: 0.8410 (pt0) cc_final: 0.8208 (tt0) REVERT: B 274 MET cc_start: 0.7435 (mtp) cc_final: 0.6587 (pp-130) REVERT: C 68 LYS cc_start: 0.8640 (mtpp) cc_final: 0.8300 (mttp) REVERT: C 142 VAL cc_start: 0.8361 (OUTLIER) cc_final: 0.8157 (t) REVERT: C 215 MET cc_start: 0.9134 (mmm) cc_final: 0.8915 (mmt) REVERT: C 346 HIS cc_start: 0.7331 (t-90) cc_final: 0.6586 (m90) REVERT: D 98 ASP cc_start: 0.8044 (m-30) cc_final: 0.7817 (m-30) REVERT: D 147 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6867 (mt-10) REVERT: D 159 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8184 (tt0) REVERT: D 274 MET cc_start: 0.7361 (mtp) cc_final: 0.6752 (pp-130) outliers start: 49 outliers final: 16 residues processed: 177 average time/residue: 1.5639 time to fit residues: 306.2456 Evaluate side-chains 157 residues out of total 1882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 136 time to evaluate : 1.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain A residue 1215 ARG Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 244 PHE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain C residue 1189 THR Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain D residue 234 CYS Chi-restraints excluded: chain D residue 242 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 111 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 166 optimal weight: 7.9990 chunk 136 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 200 optimal weight: 10.0000 chunk 216 optimal weight: 0.9990 chunk 178 optimal weight: 6.9990 chunk 198 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 160 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A1148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 HIS C 23 ASN C1040 ASN ** C1148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18714 Z= 0.288 Angle : 0.630 12.909 25544 Z= 0.297 Chirality : 0.045 0.355 2856 Planarity : 0.005 0.054 3162 Dihedral : 12.209 89.693 3228 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.71 % Allowed : 9.77 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 1.47 % 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: -1.02 (0.18), residues: 2198 helix: 0.18 (0.16), residues: 1098 sheet: -0.82 (0.57), residues: 92 loop : -1.62 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 559 HIS 0.009 0.001 HIS C1238 PHE 0.014 0.002 PHE A 253 TYR 0.021 0.002 TYR A 64 ARG 0.007 0.000 ARG C 139 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 144 time to evaluate : 2.025 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8669 (mtpp) cc_final: 0.8298 (mttp) REVERT: A 142 VAL cc_start: 0.8383 (OUTLIER) cc_final: 0.8177 (t) REVERT: A 153 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7337 (tpp80) REVERT: A 215 MET cc_start: 0.9128 (mmm) cc_final: 0.8915 (mmt) REVERT: A 346 HIS cc_start: 0.7390 (t-90) cc_final: 0.6754 (m90) REVERT: A 1040 ASN cc_start: 0.8260 (m-40) cc_final: 0.7931 (m110) REVERT: A 1263 ASP cc_start: 0.7966 (t0) cc_final: 0.7716 (t0) REVERT: B 147 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6848 (mt-10) REVERT: B 159 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8211 (tt0) REVERT: B 274 MET cc_start: 0.7505 (mtp) cc_final: 0.6687 (ppp) REVERT: C 68 LYS cc_start: 0.8666 (mtpp) cc_final: 0.8293 (mttp) REVERT: C 142 VAL cc_start: 0.8387 (OUTLIER) cc_final: 0.8177 (t) REVERT: C 215 MET cc_start: 0.9116 (mmm) cc_final: 0.8915 (mmt) REVERT: C 306 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7475 (pt0) REVERT: C 346 HIS cc_start: 0.7440 (t-90) cc_final: 0.6817 (m90) REVERT: D 98 ASP cc_start: 0.8123 (m-30) cc_final: 0.7887 (m-30) REVERT: D 147 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6963 (mt-10) REVERT: D 274 MET cc_start: 0.7352 (mtp) cc_final: 0.6817 (ppp) outliers start: 50 outliers final: 18 residues processed: 178 average time/residue: 1.5207 time to fit residues: 299.9114 Evaluate side-chains 166 residues out of total 1882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 141 time to evaluate : 2.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 244 PHE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 306 GLU Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 1189 THR Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 234 CYS Chi-restraints excluded: chain D residue 242 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 197 optimal weight: 0.5980 chunk 150 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 200 optimal weight: 8.9990 chunk 212 optimal weight: 6.9990 chunk 104 optimal weight: 0.9980 chunk 190 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A1148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 HIS B 171 ASN C 23 ASN C1040 ASN ** C1148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS D 171 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18714 Z= 0.250 Angle : 0.612 12.746 25544 Z= 0.288 Chirality : 0.044 0.345 2856 Planarity : 0.005 0.055 3162 Dihedral : 11.803 84.981 3228 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.15 % Allowed : 9.93 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 1.47 % 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: -0.68 (0.18), residues: 2198 helix: 0.45 (0.16), residues: 1098 sheet: -0.71 (0.57), residues: 92 loop : -1.44 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 559 HIS 0.008 0.001 HIS C1238 PHE 0.015 0.001 PHE A 253 TYR 0.020 0.002 TYR C 64 ARG 0.008 0.000 ARG C 139 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 148 time to evaluate : 2.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8671 (mtpp) cc_final: 0.8300 (mttp) REVERT: A 153 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7431 (tpp80) REVERT: A 176 SER cc_start: 0.6439 (OUTLIER) cc_final: 0.5893 (t) REVERT: A 346 HIS cc_start: 0.7559 (t-90) cc_final: 0.7116 (m90) REVERT: A 1040 ASN cc_start: 0.8262 (m-40) cc_final: 0.7949 (m110) REVERT: A 1263 ASP cc_start: 0.7940 (t70) cc_final: 0.7694 (t0) REVERT: B 147 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6873 (mt-10) REVERT: B 159 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8218 (tt0) REVERT: B 274 MET cc_start: 0.7472 (mtp) cc_final: 0.6902 (ppp) REVERT: C 68 LYS cc_start: 0.8667 (mtpp) cc_final: 0.8313 (mttp) REVERT: C 153 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7337 (tpp80) REVERT: C 176 SER cc_start: 0.6402 (OUTLIER) cc_final: 0.5801 (t) REVERT: C 272 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7483 (t70) REVERT: C 346 HIS cc_start: 0.7543 (t-90) cc_final: 0.7114 (m90) REVERT: C 1215 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7497 (ttm110) REVERT: D 98 ASP cc_start: 0.8135 (m-30) cc_final: 0.7903 (m-30) REVERT: D 147 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6951 (mt-10) REVERT: D 274 MET cc_start: 0.7345 (mtp) cc_final: 0.7010 (ppp) outliers start: 58 outliers final: 28 residues processed: 192 average time/residue: 1.4884 time to fit residues: 318.4610 Evaluate side-chains 174 residues out of total 1882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 137 time to evaluate : 2.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 153 ARG Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 244 PHE Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 1110 THR Chi-restraints excluded: chain C residue 1189 THR Chi-restraints excluded: chain C residue 1215 ARG Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 234 CYS Chi-restraints excluded: chain D residue 242 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 177 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 181 optimal weight: 5.9990 chunk 146 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 108 optimal weight: 8.9990 chunk 190 optimal weight: 7.9990 chunk 53 optimal weight: 0.1980 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 38 ASN ** A1148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 HIS C 23 ASN C 38 ASN C1040 ASN ** C1148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18714 Z= 0.275 Angle : 0.623 12.698 25544 Z= 0.293 Chirality : 0.045 0.339 2856 Planarity : 0.005 0.054 3162 Dihedral : 11.568 83.310 3226 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.04 % Allowed : 11.29 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 1.47 % 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 (0.18), residues: 2198 helix: 0.58 (0.16), residues: 1096 sheet: -0.65 (0.57), residues: 92 loop : -1.36 (0.20), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 559 HIS 0.009 0.001 HIS A1238 PHE 0.015 0.001 PHE A 253 TYR 0.020 0.002 TYR A 64 ARG 0.010 0.000 ARG C 139 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 139 time to evaluate : 2.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8693 (mtpp) cc_final: 0.8313 (mttp) REVERT: A 153 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7445 (tpp80) REVERT: A 176 SER cc_start: 0.6581 (OUTLIER) cc_final: 0.6028 (t) REVERT: A 272 ASP cc_start: 0.7977 (OUTLIER) cc_final: 0.7469 (t70) REVERT: A 346 HIS cc_start: 0.7512 (t-90) cc_final: 0.7118 (m90) REVERT: A 1040 ASN cc_start: 0.8268 (m-40) cc_final: 0.7961 (m110) REVERT: A 1263 ASP cc_start: 0.7965 (t70) cc_final: 0.7712 (t0) REVERT: B 39 ILE cc_start: 0.7568 (mp) cc_final: 0.7363 (mp) REVERT: B 147 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6964 (mt-10) REVERT: B 159 GLU cc_start: 0.8418 (pt0) cc_final: 0.8218 (tt0) REVERT: C 68 LYS cc_start: 0.8693 (mtpp) cc_final: 0.8310 (mttp) REVERT: C 153 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7437 (tpp80) REVERT: C 176 SER cc_start: 0.6618 (OUTLIER) cc_final: 0.6073 (t) REVERT: C 346 HIS cc_start: 0.7557 (t-90) cc_final: 0.7102 (m90) REVERT: C 1215 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7500 (ttm110) REVERT: D 98 ASP cc_start: 0.8151 (m-30) cc_final: 0.7930 (m-30) REVERT: D 147 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6929 (mt-10) outliers start: 56 outliers final: 34 residues processed: 182 average time/residue: 1.4298 time to fit residues: 289.8096 Evaluate side-chains 181 residues out of total 1882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 139 time to evaluate : 1.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 1110 THR Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 153 ARG Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain C residue 1110 THR Chi-restraints excluded: chain C residue 1189 THR Chi-restraints excluded: chain C residue 1215 ARG Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 234 CYS Chi-restraints excluded: chain D residue 242 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 71 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 124 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 212 optimal weight: 5.9990 chunk 176 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A1148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 HIS C 23 ASN ** C1148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18714 Z= 0.201 Angle : 0.589 12.111 25544 Z= 0.277 Chirality : 0.043 0.332 2856 Planarity : 0.005 0.055 3162 Dihedral : 11.175 82.441 3226 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.39 % Allowed : 12.70 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 1.47 % 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: -0.30 (0.18), residues: 2198 helix: 0.81 (0.16), residues: 1094 sheet: -0.82 (0.56), residues: 90 loop : -1.26 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 559 HIS 0.006 0.001 HIS C1238 PHE 0.015 0.001 PHE A 253 TYR 0.019 0.001 TYR C 64 ARG 0.010 0.000 ARG C 139 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 144 time to evaluate : 2.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ASN cc_start: 0.6800 (OUTLIER) cc_final: 0.6483 (p0) REVERT: A 68 LYS cc_start: 0.8658 (mtpp) cc_final: 0.8294 (mttp) REVERT: A 176 SER cc_start: 0.6611 (OUTLIER) cc_final: 0.6094 (t) REVERT: A 346 HIS cc_start: 0.7515 (t-90) cc_final: 0.7081 (m90) REVERT: A 1040 ASN cc_start: 0.8265 (m-40) cc_final: 0.7956 (m110) REVERT: A 1263 ASP cc_start: 0.7957 (t70) cc_final: 0.7703 (t0) REVERT: B 147 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6883 (mt-10) REVERT: B 274 MET cc_start: 0.7389 (mmm) cc_final: 0.6774 (tmt) REVERT: C 23 ASN cc_start: 0.6723 (OUTLIER) cc_final: 0.6471 (OUTLIER) REVERT: C 68 LYS cc_start: 0.8641 (mtpp) cc_final: 0.8283 (mttp) REVERT: C 176 SER cc_start: 0.6654 (OUTLIER) cc_final: 0.6136 (t) REVERT: C 261 ARG cc_start: 0.7564 (ttm110) cc_final: 0.7220 (ttm110) REVERT: C 346 HIS cc_start: 0.7493 (t-90) cc_final: 0.7075 (m90) REVERT: D 98 ASP cc_start: 0.8115 (m-30) cc_final: 0.7895 (m-30) REVERT: D 147 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6904 (mt-10) REVERT: D 274 MET cc_start: 0.7485 (mmm) cc_final: 0.6896 (tmt) outliers start: 44 outliers final: 27 residues processed: 180 average time/residue: 1.4690 time to fit residues: 293.2658 Evaluate side-chains 173 residues out of total 1882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 141 time to evaluate : 1.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 1110 THR Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 1189 THR Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 234 CYS Chi-restraints excluded: chain D residue 242 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 205 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 179 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 212 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 chunk 129 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A1148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 HIS C 23 ASN ** C1148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18714 Z= 0.258 Angle : 0.614 12.417 25544 Z= 0.288 Chirality : 0.044 0.329 2856 Planarity : 0.005 0.053 3162 Dihedral : 11.111 82.622 3226 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.66 % Allowed : 12.43 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 1.47 % 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 (0.18), residues: 2198 helix: 0.90 (0.16), residues: 1080 sheet: -0.78 (0.57), residues: 90 loop : -1.27 (0.20), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 559 HIS 0.008 0.001 HIS A1238 PHE 0.015 0.001 PHE A 253 TYR 0.020 0.002 TYR C 64 ARG 0.012 0.000 ARG C 139 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 143 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8671 (mtpp) cc_final: 0.8303 (mttp) REVERT: A 153 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7472 (tpp80) REVERT: A 176 SER cc_start: 0.6606 (OUTLIER) cc_final: 0.6120 (t) REVERT: A 346 HIS cc_start: 0.7501 (t-90) cc_final: 0.7082 (m90) REVERT: A 1040 ASN cc_start: 0.8269 (m-40) cc_final: 0.7957 (m110) REVERT: A 1215 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.7507 (ttm110) REVERT: A 1263 ASP cc_start: 0.7979 (t70) cc_final: 0.7729 (t0) REVERT: B 39 ILE cc_start: 0.7496 (mp) cc_final: 0.7275 (mp) REVERT: B 147 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6906 (mt-10) REVERT: B 274 MET cc_start: 0.7397 (mmm) cc_final: 0.6953 (tmt) REVERT: C 68 LYS cc_start: 0.8672 (mtpp) cc_final: 0.8298 (mttp) REVERT: C 153 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7449 (tpp80) REVERT: C 176 SER cc_start: 0.6622 (OUTLIER) cc_final: 0.6123 (t) REVERT: C 346 HIS cc_start: 0.7481 (t-90) cc_final: 0.7076 (m90) REVERT: C 1106 ARG cc_start: 0.7949 (mtt-85) cc_final: 0.7573 (mtt90) REVERT: D 98 ASP cc_start: 0.8131 (m-30) cc_final: 0.7920 (m-30) REVERT: D 147 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6931 (mt-10) REVERT: D 274 MET cc_start: 0.7443 (mmm) cc_final: 0.7005 (tmt) outliers start: 49 outliers final: 32 residues processed: 183 average time/residue: 1.4353 time to fit residues: 292.4007 Evaluate side-chains 176 residues out of total 1882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 137 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 1110 THR Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain A residue 1215 ARG Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 153 ARG Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 1110 THR Chi-restraints excluded: chain C residue 1189 THR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 234 CYS Chi-restraints excluded: chain D residue 242 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 131 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 41 optimal weight: 0.0070 chunk 134 optimal weight: 0.0870 chunk 144 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 166 optimal weight: 8.9990 chunk 192 optimal weight: 9.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A1148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 HIS C 23 ASN ** C1148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18714 Z= 0.180 Angle : 0.574 11.729 25544 Z= 0.269 Chirality : 0.042 0.322 2856 Planarity : 0.004 0.054 3162 Dihedral : 10.704 82.682 3226 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.39 % Allowed : 12.65 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 1.47 % 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: 0.01 (0.19), residues: 2198 helix: 1.13 (0.16), residues: 1080 sheet: -0.75 (0.56), residues: 90 loop : -1.15 (0.20), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 559 HIS 0.005 0.001 HIS C1238 PHE 0.015 0.001 PHE A 244 TYR 0.018 0.001 TYR C 64 ARG 0.013 0.000 ARG A 139 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 149 time to evaluate : 2.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8670 (mtpp) cc_final: 0.8324 (mttp) REVERT: A 153 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7459 (tpp80) REVERT: A 176 SER cc_start: 0.6563 (OUTLIER) cc_final: 0.6111 (t) REVERT: A 346 HIS cc_start: 0.7726 (t-90) cc_final: 0.6976 (m90) REVERT: A 1040 ASN cc_start: 0.8264 (m-40) cc_final: 0.7953 (m110) REVERT: A 1263 ASP cc_start: 0.7965 (t70) cc_final: 0.7706 (t0) REVERT: B 38 PHE cc_start: 0.6667 (m-80) cc_final: 0.6262 (m-10) REVERT: B 147 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6858 (mt-10) REVERT: B 274 MET cc_start: 0.7563 (mmm) cc_final: 0.7083 (tmm) REVERT: C 68 LYS cc_start: 0.8671 (mtpp) cc_final: 0.8323 (mttp) REVERT: C 176 SER cc_start: 0.6648 (OUTLIER) cc_final: 0.6185 (t) REVERT: C 346 HIS cc_start: 0.7707 (t-90) cc_final: 0.6969 (m90) REVERT: C 1106 ARG cc_start: 0.7948 (mtt-85) cc_final: 0.7629 (mtt90) REVERT: D 38 PHE cc_start: 0.6739 (m-80) cc_final: 0.6242 (m-10) REVERT: D 98 ASP cc_start: 0.8082 (m-30) cc_final: 0.7856 (m-30) REVERT: D 147 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6921 (mt-10) REVERT: D 274 MET cc_start: 0.7616 (mmm) cc_final: 0.7163 (tmm) outliers start: 44 outliers final: 26 residues processed: 183 average time/residue: 1.4321 time to fit residues: 291.6113 Evaluate side-chains 176 residues out of total 1882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 145 time to evaluate : 2.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 1110 THR Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 1110 THR Chi-restraints excluded: chain C residue 1189 THR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 234 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 203 optimal weight: 2.9990 chunk 185 optimal weight: 5.9990 chunk 197 optimal weight: 0.8980 chunk 118 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 chunk 155 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 178 optimal weight: 0.9990 chunk 186 optimal weight: 4.9990 chunk 196 optimal weight: 0.9980 chunk 129 optimal weight: 8.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A1148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 HIS C 23 ASN ** C1148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18714 Z= 0.237 Angle : 0.604 12.136 25544 Z= 0.283 Chirality : 0.044 0.319 2856 Planarity : 0.004 0.051 3162 Dihedral : 10.758 83.429 3226 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.28 % Allowed : 12.76 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 1.47 % 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: 0.02 (0.18), residues: 2198 helix: 1.12 (0.16), residues: 1080 sheet: -0.55 (0.57), residues: 92 loop : -1.15 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 559 HIS 0.008 0.001 HIS A1238 PHE 0.018 0.001 PHE A 244 TYR 0.020 0.002 TYR A 64 ARG 0.007 0.000 ARG C1215 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 146 time to evaluate : 1.956 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8667 (mtpp) cc_final: 0.8328 (mttp) REVERT: A 153 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.7460 (tpp80) REVERT: A 176 SER cc_start: 0.6631 (OUTLIER) cc_final: 0.6198 (t) REVERT: A 346 HIS cc_start: 0.7697 (t-90) cc_final: 0.7000 (m90) REVERT: A 1040 ASN cc_start: 0.8269 (m-40) cc_final: 0.7957 (m110) REVERT: A 1263 ASP cc_start: 0.7989 (t70) cc_final: 0.7726 (t0) REVERT: B 38 PHE cc_start: 0.6558 (m-80) cc_final: 0.6164 (m-80) REVERT: B 147 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.6934 (mt-10) REVERT: B 274 MET cc_start: 0.7310 (mmm) cc_final: 0.7074 (tmt) REVERT: C 68 LYS cc_start: 0.8668 (mtpp) cc_final: 0.8328 (mttp) REVERT: C 176 SER cc_start: 0.6652 (OUTLIER) cc_final: 0.6201 (t) REVERT: C 346 HIS cc_start: 0.7690 (t-90) cc_final: 0.7000 (m90) REVERT: C 1106 ARG cc_start: 0.8028 (mtt-85) cc_final: 0.7727 (mtt90) REVERT: D 38 PHE cc_start: 0.6697 (m-80) cc_final: 0.6276 (m-10) REVERT: D 98 ASP cc_start: 0.8230 (m-30) cc_final: 0.8008 (m-30) REVERT: D 147 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6939 (mt-10) REVERT: D 274 MET cc_start: 0.7383 (mmm) cc_final: 0.7143 (tmt) outliers start: 42 outliers final: 31 residues processed: 185 average time/residue: 1.4933 time to fit residues: 306.7283 Evaluate side-chains 178 residues out of total 1882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 142 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 1110 THR Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 1110 THR Chi-restraints excluded: chain C residue 1189 THR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 234 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 208 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 chunk 99 optimal weight: 0.9980 chunk 145 optimal weight: 0.9980 chunk 219 optimal weight: 9.9990 chunk 201 optimal weight: 0.9980 chunk 174 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 107 optimal weight: 9.9990 chunk 138 optimal weight: 6.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A1148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 HIS C 23 ASN ** C1148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1211 HIS D 6 HIS D 118 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18714 Z= 0.207 Angle : 0.590 11.719 25544 Z= 0.276 Chirality : 0.043 0.316 2856 Planarity : 0.004 0.052 3162 Dihedral : 10.622 83.426 3226 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.39 % Allowed : 13.03 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 1.47 % 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: 0.12 (0.19), residues: 2198 helix: 1.22 (0.16), residues: 1080 sheet: -0.70 (0.57), residues: 90 loop : -1.10 (0.20), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 559 HIS 0.006 0.001 HIS C1238 PHE 0.020 0.001 PHE A 244 TYR 0.019 0.001 TYR C 64 ARG 0.016 0.000 ARG A 139 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 146 time to evaluate : 1.964 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8666 (mtpp) cc_final: 0.8334 (mttp) REVERT: A 153 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7461 (tpp80) REVERT: A 176 SER cc_start: 0.6607 (OUTLIER) cc_final: 0.6184 (t) REVERT: A 346 HIS cc_start: 0.7622 (t-90) cc_final: 0.6992 (m90) REVERT: A 1040 ASN cc_start: 0.8269 (m-40) cc_final: 0.7957 (m110) REVERT: A 1263 ASP cc_start: 0.8022 (t70) cc_final: 0.7753 (t0) REVERT: B 38 PHE cc_start: 0.6740 (m-80) cc_final: 0.6237 (m-10) REVERT: B 147 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6927 (mt-10) REVERT: B 274 MET cc_start: 0.7272 (mmm) cc_final: 0.7038 (tmt) REVERT: C 68 LYS cc_start: 0.8668 (mtpp) cc_final: 0.8337 (mttp) REVERT: C 153 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7458 (tpp80) REVERT: C 176 SER cc_start: 0.6637 (OUTLIER) cc_final: 0.6190 (t) REVERT: C 346 HIS cc_start: 0.7621 (t-90) cc_final: 0.7008 (m90) REVERT: C 1106 ARG cc_start: 0.8043 (mtt-85) cc_final: 0.7770 (mtt90) REVERT: D 38 PHE cc_start: 0.6580 (m-80) cc_final: 0.6116 (m-10) REVERT: D 98 ASP cc_start: 0.8159 (m-30) cc_final: 0.7946 (m-30) REVERT: D 147 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6934 (mt-10) REVERT: D 274 MET cc_start: 0.7399 (mmm) cc_final: 0.7181 (tmt) outliers start: 44 outliers final: 31 residues processed: 184 average time/residue: 1.4980 time to fit residues: 305.7649 Evaluate side-chains 181 residues out of total 1882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 144 time to evaluate : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 1110 THR Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 153 ARG Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 1110 THR Chi-restraints excluded: chain C residue 1189 THR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 234 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 160 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 174 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 179 optimal weight: 5.9990 chunk 22 optimal weight: 0.0770 chunk 32 optimal weight: 8.9990 chunk 153 optimal weight: 6.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A1148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 HIS C 23 ASN ** C1148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1211 HIS D 6 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.113418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.089757 restraints weight = 24867.781| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.92 r_work: 0.3003 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18714 Z= 0.275 Angle : 0.623 12.272 25544 Z= 0.293 Chirality : 0.045 0.316 2856 Planarity : 0.005 0.052 3162 Dihedral : 10.813 83.280 3226 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.23 % Allowed : 13.19 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 1.47 % 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: 0.01 (0.18), residues: 2198 helix: 1.12 (0.16), residues: 1082 sheet: -0.71 (0.57), residues: 90 loop : -1.15 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 559 HIS 0.008 0.001 HIS C1238 PHE 0.022 0.002 PHE A 244 TYR 0.020 0.002 TYR A 64 ARG 0.004 0.000 ARG C1215 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5565.50 seconds wall clock time: 99 minutes 31.28 seconds (5971.28 seconds total)