Starting phenix.real_space_refine on Mon Sep 14 13:17:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5yke_6831/09_2026/5yke_6831.cif Found real_map, /net/cci-nas-00/data/ceres_data/5yke_6831/09_2026/5yke_6831.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/5yke_6831/09_2026/5yke_6831.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5yke_6831/09_2026/5yke_6831.cif" model { file = "/net/cci-nas-00/data/ceres_data/5yke_6831/09_2026/5yke_6831.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5yke_6831/09_2026/5yke_6831.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5yke_6831/09_2026/5yke_6831.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5yke_6831/09_2026/5yke_6831.map" } resolution = 4.11 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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: 5 Type Number sf(0) Gaussians S 188 5.16 5 Cl 4 4.86 5 C 20196 2.51 5 N 5116 2.21 5 O 5132 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30636 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1028 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 128} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 6598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 845, 6598 Classifications: {'peptide': 845} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 25, 'TRANS': 819} Chain breaks: 8 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 6, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3, 'TYR:plan': 1, 'PHE:plan': 5, 'GLN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 104 Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'GBM': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, E, G, D, F, H Time building chain proxies: 8.86, per 1000 atoms: 0.29 Number of scatterers: 30636 At special positions: 0 Unit cell: (174.075, 174.075, 110.775, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 188 16.00 O 5132 8.00 N 5116 7.00 C 20196 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS E 110 " - pdb=" SG CYS E 142 " distance=2.03 Simple disulfide: pdb=" SG CYS G 110 " - pdb=" SG CYS G 142 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.79 Conformation dependent library (CDL) restraints added in 1.3 seconds 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7472 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 0 sheets defined 87.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 58 through 64 removed outlier: 3.632A pdb=" N LEU A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 98 removed outlier: 3.614A pdb=" N GLY A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 129 removed outlier: 3.618A pdb=" N VAL A 129 " --> pdb=" O ILE A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 172 removed outlier: 3.622A pdb=" N ILE A 146 " --> pdb=" O CYS A 142 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE A 154 " --> pdb=" O ILE A 150 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE A 167 " --> pdb=" O MET A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 178 Processing helix chain 'B' and resid 25 through 52 Proline residue: B 35 - end of helix removed outlier: 3.942A pdb=" N PHE B 44 " --> pdb=" O LEU B 40 " (cutoff:3.500A) Proline residue: B 45 - end of helix Processing helix chain 'B' and resid 70 through 96 Processing helix chain 'B' and resid 104 through 130 Proline residue: B 109 - end of helix removed outlier: 3.757A pdb=" N MET B 115 " --> pdb=" O GLY B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 160 removed outlier: 3.823A pdb=" N ILE B 137 " --> pdb=" O PRO B 133 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS B 160 " --> pdb=" O LYS B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 193 Processing helix chain 'B' and resid 207 through 212 Processing helix chain 'B' and resid 225 through 230 Processing helix chain 'B' and resid 232 through 243 removed outlier: 4.250A pdb=" N PHE B 236 " --> pdb=" O TRP B 232 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS B 242 " --> pdb=" O LYS B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 275 removed outlier: 3.616A pdb=" N ASN B 262 " --> pdb=" O ARG B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 329 removed outlier: 6.309A pdb=" N ARG B 297 " --> pdb=" O HIS B 293 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ARG B 298 " --> pdb=" O ALA B 294 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU B 299 " --> pdb=" O PHE B 295 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE B 300 " --> pdb=" O GLY B 296 " (cutoff:3.500A) Proline residue: B 317 - end of helix Processing helix chain 'B' and resid 355 through 402 removed outlier: 3.630A pdb=" N MET B 400 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N HIS B 401 " --> pdb=" O ASN B 397 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 402 " --> pdb=" O LYS B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 423 Processing helix chain 'B' and resid 423 through 457 Proline residue: B 436 - end of helix removed outlier: 3.536A pdb=" N TRP B 439 " --> pdb=" O CYS B 435 " (cutoff:3.500A) Proline residue: B 442 - end of helix Processing helix chain 'B' and resid 457 through 503 removed outlier: 3.732A pdb=" N LEU B 461 " --> pdb=" O GLY B 457 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE B 462 " --> pdb=" O VAL B 458 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE B 468 " --> pdb=" O ALA B 464 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA B 471 " --> pdb=" O ILE B 467 " (cutoff:3.500A) Proline residue: B 472 - end of helix removed outlier: 3.595A pdb=" N GLU B 501 " --> pdb=" O LYS B 497 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N MET B 502 " --> pdb=" O GLN B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 512 removed outlier: 4.018A pdb=" N TYR B 512 " --> pdb=" O LEU B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 560 removed outlier: 3.655A pdb=" N ARG B 521 " --> pdb=" O ILE B 517 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS B 528 " --> pdb=" O VAL B 524 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA B 535 " --> pdb=" O THR B 531 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR B 548 " --> pdb=" O ILE B 544 " (cutoff:3.500A) Proline residue: B 551 - end of helix removed outlier: 3.554A pdb=" N VAL B 555 " --> pdb=" O PRO B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 615 removed outlier: 3.532A pdb=" N ALA B 576 " --> pdb=" O SER B 572 " (cutoff:3.500A) Proline residue: B 589 - end of helix removed outlier: 4.447A pdb=" N LEU B 592 " --> pdb=" O THR B 588 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 593 " --> pdb=" O PRO B 589 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER B 594 " --> pdb=" O LEU B 590 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER B 595 " --> pdb=" O PHE B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1007 removed outlier: 4.439A pdb=" N CYS B1001 " --> pdb=" O PRO B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1009 through 1039 removed outlier: 3.533A pdb=" N LEU B1013 " --> pdb=" O GLY B1009 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER B1014 " --> pdb=" O ILE B1010 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU B1015 " --> pdb=" O LEU B1011 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER B1019 " --> pdb=" O LEU B1015 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP B1031 " --> pdb=" O LEU B1027 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS B1036 " --> pdb=" O TYR B1032 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASP B1039 " --> pdb=" O ALA B1035 " (cutoff:3.500A) Processing helix chain 'B' and resid 1061 through 1107 removed outlier: 3.541A pdb=" N LEU B1107 " --> pdb=" O ASN B1103 " (cutoff:3.500A) Processing helix chain 'B' and resid 1109 through 1116 Processing helix chain 'B' and resid 1117 through 1127 removed outlier: 3.828A pdb=" N ILE B1121 " --> pdb=" O PRO B1117 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE B1125 " --> pdb=" O ILE B1121 " (cutoff:3.500A) Processing helix chain 'B' and resid 1127 through 1161 Proline residue: B1137 - end of helix removed outlier: 3.575A pdb=" N THR B1161 " --> pdb=" O ILE B1157 " (cutoff:3.500A) Processing helix chain 'B' and resid 1161 through 1210 removed outlier: 3.588A pdb=" N LEU B1165 " --> pdb=" O THR B1161 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL B1166 " --> pdb=" O PRO B1162 " (cutoff:3.500A) Proline residue: B1170 - end of helix removed outlier: 3.539A pdb=" N PHE B1177 " --> pdb=" O VAL B1173 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR B1181 " --> pdb=" O PHE B1177 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE B1182 " --> pdb=" O ILE B1178 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA B1185 " --> pdb=" O TYR B1181 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP B1188 " --> pdb=" O VAL B1184 " (cutoff:3.500A) Proline residue: B1199 - end of helix removed outlier: 3.525A pdb=" N GLY B1210 " --> pdb=" O GLU B1206 " (cutoff:3.500A) Processing helix chain 'B' and resid 1210 through 1218 Processing helix chain 'B' and resid 1219 through 1271 removed outlier: 3.725A pdb=" N ALA B1237 " --> pdb=" O SER B1233 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR B1242 " --> pdb=" O SER B1238 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL B1260 " --> pdb=" O GLY B1256 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER B1269 " --> pdb=" O ALA B1265 " (cutoff:3.500A) Processing helix chain 'B' and resid 1277 through 1289 removed outlier: 4.572A pdb=" N VAL B1281 " --> pdb=" O SER B1277 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY B1282 " --> pdb=" O ALA B1278 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU B1283 " --> pdb=" O GLY B1279 " (cutoff:3.500A) Processing helix chain 'B' and resid 1290 through 1320 removed outlier: 3.639A pdb=" N TYR B1294 " --> pdb=" O MET B1290 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG B1314 " --> pdb=" O GLY B1310 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE B1315 " --> pdb=" O ALA B1311 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS B1316 " --> pdb=" O VAL B1312 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 58 Processing helix chain 'C' and resid 58 through 64 removed outlier: 3.632A pdb=" N LEU C 63 " --> pdb=" O VAL C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 98 removed outlier: 3.614A pdb=" N GLY C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 129 removed outlier: 3.618A pdb=" N VAL C 129 " --> pdb=" O ILE C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 172 removed outlier: 3.622A pdb=" N ILE C 146 " --> pdb=" O CYS C 142 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE C 154 " --> pdb=" O ILE C 150 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE C 167 " --> pdb=" O MET C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 178 Processing helix chain 'D' and resid 25 through 52 Proline residue: D 35 - end of helix removed outlier: 3.942A pdb=" N PHE D 44 " --> pdb=" O LEU D 40 " (cutoff:3.500A) Proline residue: D 45 - end of helix Processing helix chain 'D' and resid 70 through 96 Processing helix chain 'D' and resid 104 through 130 Proline residue: D 109 - end of helix removed outlier: 3.757A pdb=" N MET D 115 " --> pdb=" O GLY D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 160 removed outlier: 3.823A pdb=" N ILE D 137 " --> pdb=" O PRO D 133 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS D 160 " --> pdb=" O LYS D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 193 Processing helix chain 'D' and resid 207 through 212 Processing helix chain 'D' and resid 225 through 230 Processing helix chain 'D' and resid 232 through 243 removed outlier: 4.250A pdb=" N PHE D 236 " --> pdb=" O TRP D 232 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS D 242 " --> pdb=" O LYS D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 275 removed outlier: 3.616A pdb=" N ASN D 262 " --> pdb=" O ARG D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 329 removed outlier: 6.309A pdb=" N ARG D 297 " --> pdb=" O HIS D 293 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ARG D 298 " --> pdb=" O ALA D 294 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU D 299 " --> pdb=" O PHE D 295 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE D 300 " --> pdb=" O GLY D 296 " (cutoff:3.500A) Proline residue: D 317 - end of helix Processing helix chain 'D' and resid 355 through 402 removed outlier: 3.630A pdb=" N MET D 400 " --> pdb=" O TYR D 396 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N HIS D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU D 402 " --> pdb=" O LYS D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 423 Processing helix chain 'D' and resid 423 through 457 Proline residue: D 436 - end of helix removed outlier: 3.536A pdb=" N TRP D 439 " --> pdb=" O CYS D 435 " (cutoff:3.500A) Proline residue: D 442 - end of helix Processing helix chain 'D' and resid 457 through 503 removed outlier: 3.732A pdb=" N LEU D 461 " --> pdb=" O GLY D 457 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE D 462 " --> pdb=" O VAL D 458 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE D 468 " --> pdb=" O ALA D 464 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA D 471 " --> pdb=" O ILE D 467 " (cutoff:3.500A) Proline residue: D 472 - end of helix removed outlier: 3.595A pdb=" N GLU D 501 " --> pdb=" O LYS D 497 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N MET D 502 " --> pdb=" O GLN D 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 512 removed outlier: 4.018A pdb=" N TYR D 512 " --> pdb=" O LEU D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 560 removed outlier: 3.655A pdb=" N ARG D 521 " --> pdb=" O ILE D 517 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS D 528 " --> pdb=" O VAL D 524 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA D 535 " --> pdb=" O THR D 531 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR D 548 " --> pdb=" O ILE D 544 " (cutoff:3.500A) Proline residue: D 551 - end of helix removed outlier: 3.554A pdb=" N VAL D 555 " --> pdb=" O PRO D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 615 removed outlier: 3.532A pdb=" N ALA D 576 " --> pdb=" O SER D 572 " (cutoff:3.500A) Proline residue: D 589 - end of helix removed outlier: 4.447A pdb=" N LEU D 592 " --> pdb=" O THR D 588 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU D 593 " --> pdb=" O PRO D 589 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER D 594 " --> pdb=" O LEU D 590 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER D 595 " --> pdb=" O PHE D 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 997 through 1007 removed outlier: 4.439A pdb=" N CYS D1001 " --> pdb=" O PRO D 997 " (cutoff:3.500A) Processing helix chain 'D' and resid 1009 through 1039 removed outlier: 3.533A pdb=" N LEU D1013 " --> pdb=" O GLY D1009 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER D1014 " --> pdb=" O ILE D1010 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU D1015 " --> pdb=" O LEU D1011 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER D1019 " --> pdb=" O LEU D1015 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP D1031 " --> pdb=" O LEU D1027 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS D1036 " --> pdb=" O TYR D1032 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASP D1039 " --> pdb=" O ALA D1035 " (cutoff:3.500A) Processing helix chain 'D' and resid 1061 through 1107 removed outlier: 3.541A pdb=" N LEU D1107 " --> pdb=" O ASN D1103 " (cutoff:3.500A) Processing helix chain 'D' and resid 1109 through 1116 Processing helix chain 'D' and resid 1117 through 1127 removed outlier: 3.828A pdb=" N ILE D1121 " --> pdb=" O PRO D1117 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE D1125 " --> pdb=" O ILE D1121 " (cutoff:3.500A) Processing helix chain 'D' and resid 1127 through 1161 Proline residue: D1137 - end of helix removed outlier: 3.575A pdb=" N THR D1161 " --> pdb=" O ILE D1157 " (cutoff:3.500A) Processing helix chain 'D' and resid 1161 through 1210 removed outlier: 3.588A pdb=" N LEU D1165 " --> pdb=" O THR D1161 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL D1166 " --> pdb=" O PRO D1162 " (cutoff:3.500A) Proline residue: D1170 - end of helix removed outlier: 3.539A pdb=" N PHE D1177 " --> pdb=" O VAL D1173 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR D1181 " --> pdb=" O PHE D1177 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE D1182 " --> pdb=" O ILE D1178 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA D1185 " --> pdb=" O TYR D1181 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP D1188 " --> pdb=" O VAL D1184 " (cutoff:3.500A) Proline residue: D1199 - end of helix removed outlier: 3.525A pdb=" N GLY D1210 " --> pdb=" O GLU D1206 " (cutoff:3.500A) Processing helix chain 'D' and resid 1210 through 1218 Processing helix chain 'D' and resid 1219 through 1271 removed outlier: 3.725A pdb=" N ALA D1237 " --> pdb=" O SER D1233 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR D1242 " --> pdb=" O SER D1238 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL D1260 " --> pdb=" O GLY D1256 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER D1269 " --> pdb=" O ALA D1265 " (cutoff:3.500A) Processing helix chain 'D' and resid 1277 through 1289 removed outlier: 4.572A pdb=" N VAL D1281 " --> pdb=" O SER D1277 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY D1282 " --> pdb=" O ALA D1278 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU D1283 " --> pdb=" O GLY D1279 " (cutoff:3.500A) Processing helix chain 'D' and resid 1290 through 1320 removed outlier: 3.639A pdb=" N TYR D1294 " --> pdb=" O MET D1290 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG D1314 " --> pdb=" O GLY D1310 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE D1315 " --> pdb=" O ALA D1311 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS D1316 " --> pdb=" O VAL D1312 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 58 Processing helix chain 'E' and resid 58 through 64 removed outlier: 3.632A pdb=" N LEU E 63 " --> pdb=" O VAL E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 98 removed outlier: 3.614A pdb=" N GLY E 98 " --> pdb=" O ALA E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 129 removed outlier: 3.618A pdb=" N VAL E 129 " --> pdb=" O ILE E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 172 removed outlier: 3.622A pdb=" N ILE E 146 " --> pdb=" O CYS E 142 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE E 154 " --> pdb=" O ILE E 150 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE E 167 " --> pdb=" O MET E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 178 Processing helix chain 'F' and resid 25 through 52 Proline residue: F 35 - end of helix removed outlier: 3.942A pdb=" N PHE F 44 " --> pdb=" O LEU F 40 " (cutoff:3.500A) Proline residue: F 45 - end of helix Processing helix chain 'F' and resid 70 through 96 Processing helix chain 'F' and resid 104 through 130 Proline residue: F 109 - end of helix removed outlier: 3.757A pdb=" N MET F 115 " --> pdb=" O GLY F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 160 removed outlier: 3.823A pdb=" N ILE F 137 " --> pdb=" O PRO F 133 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR F 142 " --> pdb=" O ALA F 138 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS F 160 " --> pdb=" O LYS F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 193 Processing helix chain 'F' and resid 207 through 212 Processing helix chain 'F' and resid 225 through 230 Processing helix chain 'F' and resid 232 through 243 removed outlier: 4.250A pdb=" N PHE F 236 " --> pdb=" O TRP F 232 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS F 242 " --> pdb=" O LYS F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 275 removed outlier: 3.616A pdb=" N ASN F 262 " --> pdb=" O ARG F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 329 removed outlier: 6.309A pdb=" N ARG F 297 " --> pdb=" O HIS F 293 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ARG F 298 " --> pdb=" O ALA F 294 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU F 299 " --> pdb=" O PHE F 295 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE F 300 " --> pdb=" O GLY F 296 " (cutoff:3.500A) Proline residue: F 317 - end of helix Processing helix chain 'F' and resid 355 through 402 removed outlier: 3.630A pdb=" N MET F 400 " --> pdb=" O TYR F 396 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N HIS F 401 " --> pdb=" O ASN F 397 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU F 402 " --> pdb=" O LYS F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 423 Processing helix chain 'F' and resid 423 through 457 Proline residue: F 436 - end of helix removed outlier: 3.536A pdb=" N TRP F 439 " --> pdb=" O CYS F 435 " (cutoff:3.500A) Proline residue: F 442 - end of helix Processing helix chain 'F' and resid 457 through 503 removed outlier: 3.732A pdb=" N LEU F 461 " --> pdb=" O GLY F 457 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE F 462 " --> pdb=" O VAL F 458 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE F 468 " --> pdb=" O ALA F 464 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA F 471 " --> pdb=" O ILE F 467 " (cutoff:3.500A) Proline residue: F 472 - end of helix removed outlier: 3.595A pdb=" N GLU F 501 " --> pdb=" O LYS F 497 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N MET F 502 " --> pdb=" O GLN F 498 " (cutoff:3.500A) Processing helix chain 'F' and resid 505 through 512 removed outlier: 4.018A pdb=" N TYR F 512 " --> pdb=" O LEU F 508 " (cutoff:3.500A) Processing helix chain 'F' and resid 514 through 560 removed outlier: 3.655A pdb=" N ARG F 521 " --> pdb=" O ILE F 517 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS F 528 " --> pdb=" O VAL F 524 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA F 535 " --> pdb=" O THR F 531 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR F 548 " --> pdb=" O ILE F 544 " (cutoff:3.500A) Proline residue: F 551 - end of helix removed outlier: 3.554A pdb=" N VAL F 555 " --> pdb=" O PRO F 551 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 615 removed outlier: 3.532A pdb=" N ALA F 576 " --> pdb=" O SER F 572 " (cutoff:3.500A) Proline residue: F 589 - end of helix removed outlier: 4.447A pdb=" N LEU F 592 " --> pdb=" O THR F 588 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU F 593 " --> pdb=" O PRO F 589 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER F 594 " --> pdb=" O LEU F 590 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER F 595 " --> pdb=" O PHE F 591 " (cutoff:3.500A) Processing helix chain 'F' and resid 997 through 1007 removed outlier: 4.439A pdb=" N CYS F1001 " --> pdb=" O PRO F 997 " (cutoff:3.500A) Processing helix chain 'F' and resid 1009 through 1039 removed outlier: 3.533A pdb=" N LEU F1013 " --> pdb=" O GLY F1009 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER F1014 " --> pdb=" O ILE F1010 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU F1015 " --> pdb=" O LEU F1011 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER F1019 " --> pdb=" O LEU F1015 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP F1031 " --> pdb=" O LEU F1027 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS F1036 " --> pdb=" O TYR F1032 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASP F1039 " --> pdb=" O ALA F1035 " (cutoff:3.500A) Processing helix chain 'F' and resid 1061 through 1107 removed outlier: 3.541A pdb=" N LEU F1107 " --> pdb=" O ASN F1103 " (cutoff:3.500A) Processing helix chain 'F' and resid 1109 through 1116 Processing helix chain 'F' and resid 1117 through 1127 removed outlier: 3.828A pdb=" N ILE F1121 " --> pdb=" O PRO F1117 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE F1125 " --> pdb=" O ILE F1121 " (cutoff:3.500A) Processing helix chain 'F' and resid 1127 through 1161 Proline residue: F1137 - end of helix removed outlier: 3.575A pdb=" N THR F1161 " --> pdb=" O ILE F1157 " (cutoff:3.500A) Processing helix chain 'F' and resid 1161 through 1210 removed outlier: 3.588A pdb=" N LEU F1165 " --> pdb=" O THR F1161 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL F1166 " --> pdb=" O PRO F1162 " (cutoff:3.500A) Proline residue: F1170 - end of helix removed outlier: 3.539A pdb=" N PHE F1177 " --> pdb=" O VAL F1173 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR F1181 " --> pdb=" O PHE F1177 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE F1182 " --> pdb=" O ILE F1178 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA F1185 " --> pdb=" O TYR F1181 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP F1188 " --> pdb=" O VAL F1184 " (cutoff:3.500A) Proline residue: F1199 - end of helix removed outlier: 3.525A pdb=" N GLY F1210 " --> pdb=" O GLU F1206 " (cutoff:3.500A) Processing helix chain 'F' and resid 1210 through 1218 Processing helix chain 'F' and resid 1219 through 1271 removed outlier: 3.725A pdb=" N ALA F1237 " --> pdb=" O SER F1233 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR F1242 " --> pdb=" O SER F1238 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL F1260 " --> pdb=" O GLY F1256 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER F1269 " --> pdb=" O ALA F1265 " (cutoff:3.500A) Processing helix chain 'F' and resid 1277 through 1289 removed outlier: 4.572A pdb=" N VAL F1281 " --> pdb=" O SER F1277 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY F1282 " --> pdb=" O ALA F1278 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU F1283 " --> pdb=" O GLY F1279 " (cutoff:3.500A) Processing helix chain 'F' and resid 1290 through 1320 removed outlier: 3.639A pdb=" N TYR F1294 " --> pdb=" O MET F1290 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG F1314 " --> pdb=" O GLY F1310 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE F1315 " --> pdb=" O ALA F1311 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS F1316 " --> pdb=" O VAL F1312 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 58 Processing helix chain 'G' and resid 58 through 64 removed outlier: 3.632A pdb=" N LEU G 63 " --> pdb=" O VAL G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 98 removed outlier: 3.614A pdb=" N GLY G 98 " --> pdb=" O ALA G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 129 removed outlier: 3.618A pdb=" N VAL G 129 " --> pdb=" O ILE G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 172 removed outlier: 3.622A pdb=" N ILE G 146 " --> pdb=" O CYS G 142 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE G 154 " --> pdb=" O ILE G 150 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE G 167 " --> pdb=" O MET G 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 178 Processing helix chain 'H' and resid 25 through 52 Proline residue: H 35 - end of helix removed outlier: 3.942A pdb=" N PHE H 44 " --> pdb=" O LEU H 40 " (cutoff:3.500A) Proline residue: H 45 - end of helix Processing helix chain 'H' and resid 70 through 96 Processing helix chain 'H' and resid 104 through 130 Proline residue: H 109 - end of helix removed outlier: 3.757A pdb=" N MET H 115 " --> pdb=" O GLY H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 160 removed outlier: 3.823A pdb=" N ILE H 137 " --> pdb=" O PRO H 133 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR H 142 " --> pdb=" O ALA H 138 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS H 160 " --> pdb=" O LYS H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 193 Processing helix chain 'H' and resid 207 through 212 Processing helix chain 'H' and resid 225 through 230 Processing helix chain 'H' and resid 232 through 243 removed outlier: 4.250A pdb=" N PHE H 236 " --> pdb=" O TRP H 232 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS H 242 " --> pdb=" O LYS H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 258 through 275 removed outlier: 3.616A pdb=" N ASN H 262 " --> pdb=" O ARG H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 284 through 329 removed outlier: 6.309A pdb=" N ARG H 297 " --> pdb=" O HIS H 293 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ARG H 298 " --> pdb=" O ALA H 294 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU H 299 " --> pdb=" O PHE H 295 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE H 300 " --> pdb=" O GLY H 296 " (cutoff:3.500A) Proline residue: H 317 - end of helix Processing helix chain 'H' and resid 355 through 402 removed outlier: 3.630A pdb=" N MET H 400 " --> pdb=" O TYR H 396 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N HIS H 401 " --> pdb=" O ASN H 397 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU H 402 " --> pdb=" O LYS H 398 " (cutoff:3.500A) Processing helix chain 'H' and resid 412 through 423 Processing helix chain 'H' and resid 423 through 457 Proline residue: H 436 - end of helix removed outlier: 3.536A pdb=" N TRP H 439 " --> pdb=" O CYS H 435 " (cutoff:3.500A) Proline residue: H 442 - end of helix Processing helix chain 'H' and resid 457 through 503 removed outlier: 3.732A pdb=" N LEU H 461 " --> pdb=" O GLY H 457 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE H 462 " --> pdb=" O VAL H 458 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE H 468 " --> pdb=" O ALA H 464 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA H 471 " --> pdb=" O ILE H 467 " (cutoff:3.500A) Proline residue: H 472 - end of helix removed outlier: 3.595A pdb=" N GLU H 501 " --> pdb=" O LYS H 497 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N MET H 502 " --> pdb=" O GLN H 498 " (cutoff:3.500A) Processing helix chain 'H' and resid 505 through 512 removed outlier: 4.018A pdb=" N TYR H 512 " --> pdb=" O LEU H 508 " (cutoff:3.500A) Processing helix chain 'H' and resid 514 through 560 removed outlier: 3.655A pdb=" N ARG H 521 " --> pdb=" O ILE H 517 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS H 528 " --> pdb=" O VAL H 524 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA H 535 " --> pdb=" O THR H 531 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR H 548 " --> pdb=" O ILE H 544 " (cutoff:3.500A) Proline residue: H 551 - end of helix removed outlier: 3.554A pdb=" N VAL H 555 " --> pdb=" O PRO H 551 " (cutoff:3.500A) Processing helix chain 'H' and resid 572 through 615 removed outlier: 3.532A pdb=" N ALA H 576 " --> pdb=" O SER H 572 " (cutoff:3.500A) Proline residue: H 589 - end of helix removed outlier: 4.447A pdb=" N LEU H 592 " --> pdb=" O THR H 588 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU H 593 " --> pdb=" O PRO H 589 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER H 594 " --> pdb=" O LEU H 590 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER H 595 " --> pdb=" O PHE H 591 " (cutoff:3.500A) Processing helix chain 'H' and resid 997 through 1007 removed outlier: 4.439A pdb=" N CYS H1001 " --> pdb=" O PRO H 997 " (cutoff:3.500A) Processing helix chain 'H' and resid 1009 through 1039 removed outlier: 3.533A pdb=" N LEU H1013 " --> pdb=" O GLY H1009 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER H1014 " --> pdb=" O ILE H1010 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU H1015 " --> pdb=" O LEU H1011 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER H1019 " --> pdb=" O LEU H1015 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP H1031 " --> pdb=" O LEU H1027 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS H1036 " --> pdb=" O TYR H1032 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASP H1039 " --> pdb=" O ALA H1035 " (cutoff:3.500A) Processing helix chain 'H' and resid 1061 through 1107 removed outlier: 3.541A pdb=" N LEU H1107 " --> pdb=" O ASN H1103 " (cutoff:3.500A) Processing helix chain 'H' and resid 1109 through 1116 Processing helix chain 'H' and resid 1117 through 1127 removed outlier: 3.828A pdb=" N ILE H1121 " --> pdb=" O PRO H1117 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE H1125 " --> pdb=" O ILE H1121 " (cutoff:3.500A) Processing helix chain 'H' and resid 1127 through 1161 Proline residue: H1137 - end of helix removed outlier: 3.575A pdb=" N THR H1161 " --> pdb=" O ILE H1157 " (cutoff:3.500A) Processing helix chain 'H' and resid 1161 through 1210 removed outlier: 3.588A pdb=" N LEU H1165 " --> pdb=" O THR H1161 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL H1166 " --> pdb=" O PRO H1162 " (cutoff:3.500A) Proline residue: H1170 - end of helix removed outlier: 3.539A pdb=" N PHE H1177 " --> pdb=" O VAL H1173 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR H1181 " --> pdb=" O PHE H1177 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE H1182 " --> pdb=" O ILE H1178 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA H1185 " --> pdb=" O TYR H1181 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP H1188 " --> pdb=" O VAL H1184 " (cutoff:3.500A) Proline residue: H1199 - end of helix removed outlier: 3.525A pdb=" N GLY H1210 " --> pdb=" O GLU H1206 " (cutoff:3.500A) Processing helix chain 'H' and resid 1210 through 1218 Processing helix chain 'H' and resid 1219 through 1271 removed outlier: 3.725A pdb=" N ALA H1237 " --> pdb=" O SER H1233 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR H1242 " --> pdb=" O SER H1238 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL H1260 " --> pdb=" O GLY H1256 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER H1269 " --> pdb=" O ALA H1265 " (cutoff:3.500A) Processing helix chain 'H' and resid 1277 through 1289 removed outlier: 4.572A pdb=" N VAL H1281 " --> pdb=" O SER H1277 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY H1282 " --> pdb=" O ALA H1278 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU H1283 " --> pdb=" O GLY H1279 " (cutoff:3.500A) Processing helix chain 'H' and resid 1290 through 1320 removed outlier: 3.639A pdb=" N TYR H1294 " --> pdb=" O MET H1290 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG H1314 " --> pdb=" O GLY H1310 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE H1315 " --> pdb=" O ALA H1311 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS H1316 " --> pdb=" O VAL H1312 " (cutoff:3.500A) 2472 hydrogen bonds defined for protein. 7392 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: 6.02 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8600 1.34 - 1.46: 6252 1.46 - 1.58: 16160 1.58 - 1.70: 8 1.70 - 1.82: 292 Bond restraints: 31312 Sorted by residual: bond pdb=" C18 GBM B2001 " pdb=" S2 GBM B2001 " ideal model delta sigma weight residual 1.765 1.603 0.162 2.00e-02 2.50e+03 6.56e+01 bond pdb=" C18 GBM D2001 " pdb=" S2 GBM D2001 " ideal model delta sigma weight residual 1.765 1.603 0.162 2.00e-02 2.50e+03 6.56e+01 bond pdb=" C18 GBM F2001 " pdb=" S2 GBM F2001 " ideal model delta sigma weight residual 1.765 1.603 0.162 2.00e-02 2.50e+03 6.56e+01 bond pdb=" C18 GBM H2001 " pdb=" S2 GBM H2001 " ideal model delta sigma weight residual 1.765 1.603 0.162 2.00e-02 2.50e+03 6.56e+01 bond pdb=" C27 GBM F2001 " pdb=" C28 GBM F2001 " ideal model delta sigma weight residual 1.401 1.490 -0.089 2.00e-02 2.50e+03 1.97e+01 ... (remaining 31307 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 41684 2.40 - 4.80: 728 4.80 - 7.20: 140 7.20 - 9.60: 20 9.60 - 12.00: 16 Bond angle restraints: 42588 Sorted by residual: angle pdb=" N THR B 200 " pdb=" CA THR B 200 " pdb=" C THR B 200 " ideal model delta sigma weight residual 109.83 120.85 -11.02 1.27e+00 6.20e-01 7.53e+01 angle pdb=" N THR D 200 " pdb=" CA THR D 200 " pdb=" C THR D 200 " ideal model delta sigma weight residual 109.83 120.85 -11.02 1.27e+00 6.20e-01 7.53e+01 angle pdb=" N THR H 200 " pdb=" CA THR H 200 " pdb=" C THR H 200 " ideal model delta sigma weight residual 109.83 120.85 -11.02 1.27e+00 6.20e-01 7.53e+01 angle pdb=" N THR F 200 " pdb=" CA THR F 200 " pdb=" C THR F 200 " ideal model delta sigma weight residual 109.83 120.85 -11.02 1.27e+00 6.20e-01 7.53e+01 angle pdb=" C SER D 532 " pdb=" N LEU D 533 " pdb=" CA LEU D 533 " ideal model delta sigma weight residual 120.28 130.85 -10.57 1.44e+00 4.82e-01 5.38e+01 ... (remaining 42583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.31: 16812 16.31 - 32.62: 1092 32.62 - 48.93: 348 48.93 - 65.24: 124 65.24 - 81.55: 8 Dihedral angle restraints: 18384 sinusoidal: 6928 harmonic: 11456 Sorted by residual: dihedral pdb=" CA PHE D 295 " pdb=" C PHE D 295 " pdb=" N GLY D 296 " pdb=" CA GLY D 296 " ideal model delta harmonic sigma weight residual 180.00 154.50 25.50 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA PHE B 295 " pdb=" C PHE B 295 " pdb=" N GLY B 296 " pdb=" CA GLY B 296 " ideal model delta harmonic sigma weight residual 180.00 154.50 25.50 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA PHE F 295 " pdb=" C PHE F 295 " pdb=" N GLY F 296 " pdb=" CA GLY F 296 " ideal model delta harmonic sigma weight residual 180.00 154.50 25.50 0 5.00e+00 4.00e-02 2.60e+01 ... (remaining 18381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 4420 0.058 - 0.117: 692 0.117 - 0.175: 44 0.175 - 0.233: 16 0.233 - 0.292: 24 Chirality restraints: 5196 Sorted by residual: chirality pdb=" CA ASP B1133 " pdb=" N ASP B1133 " pdb=" C ASP B1133 " pdb=" CB ASP B1133 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA ASP F1133 " pdb=" N ASP F1133 " pdb=" C ASP F1133 " pdb=" CB ASP F1133 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA ASP D1133 " pdb=" N ASP D1133 " pdb=" C ASP D1133 " pdb=" CB ASP D1133 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 5193 not shown) Planarity restraints: 5116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C25 GBM F2001 " 0.321 2.00e-02 2.50e+03 2.72e-01 9.28e+02 pdb=" C26 GBM F2001 " -0.077 2.00e-02 2.50e+03 pdb=" C27 GBM F2001 " 0.172 2.00e-02 2.50e+03 pdb=" N10 GBM F2001 " -0.478 2.00e-02 2.50e+03 pdb=" O6 GBM F2001 " 0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C25 GBM H2001 " -0.321 2.00e-02 2.50e+03 2.72e-01 9.28e+02 pdb=" C26 GBM H2001 " 0.077 2.00e-02 2.50e+03 pdb=" C27 GBM H2001 " -0.172 2.00e-02 2.50e+03 pdb=" N10 GBM H2001 " 0.478 2.00e-02 2.50e+03 pdb=" O6 GBM H2001 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C25 GBM D2001 " 0.321 2.00e-02 2.50e+03 2.72e-01 9.28e+02 pdb=" C26 GBM D2001 " -0.077 2.00e-02 2.50e+03 pdb=" C27 GBM D2001 " 0.172 2.00e-02 2.50e+03 pdb=" N10 GBM D2001 " -0.478 2.00e-02 2.50e+03 pdb=" O6 GBM D2001 " 0.063 2.00e-02 2.50e+03 ... (remaining 5113 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 6484 2.78 - 3.31: 32596 3.31 - 3.84: 51016 3.84 - 4.37: 55778 4.37 - 4.90: 94232 Nonbonded interactions: 240106 Sorted by model distance: nonbonded pdb=" OD2 ASP B1031 " pdb=" OH TYR B1287 " model vdw 2.246 3.040 nonbonded pdb=" OD2 ASP D1031 " pdb=" OH TYR D1287 " model vdw 2.246 3.040 nonbonded pdb=" OD2 ASP F1031 " pdb=" OH TYR F1287 " model vdw 2.246 3.040 nonbonded pdb=" OD2 ASP H1031 " pdb=" OH TYR H1287 " model vdw 2.246 3.040 nonbonded pdb=" O SER F1126 " pdb=" ND2 ASN F1130 " model vdw 2.276 3.120 ... (remaining 240101 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } 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 group one per residue 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: 2.790 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: 0.030 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 30.120 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 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 : 0.005 0.162 31316 Z= 0.269 Angle : 0.809 12.002 42596 Z= 0.463 Chirality : 0.046 0.292 5196 Planarity : 0.010 0.272 5116 Dihedral : 13.283 81.548 10900 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.65 % Favored : 95.93 % Rotamer: Outliers : 7.60 % Allowed : 10.29 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.12), residues: 3832 helix: -0.74 (0.08), residues: 3168 sheet: None (None), residues: 0 loop : -2.52 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 598 TYR 0.014 0.002 TYR D 378 PHE 0.034 0.002 PHE A 168 TRP 0.010 0.001 TRP B1037 HIS 0.011 0.001 HIS E 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.27 (31312) covalent geometry : angle 0.80886 / 0.46 (42588) SS BOND : bond 0.00324 / 0.16 ( 4) SS BOND : angle 0.10088 / 0.08 ( 8) hydrogen bonds : bond 0.14835 / 10.26 ( 2472) hydrogen bonds : angle 6.13023 / 4.46 ( 7392) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1178 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 248 poor density : 930 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.7945 (tptt) cc_final: 0.6948 (mptt) REVERT: A 91 TRP cc_start: 0.9116 (t60) cc_final: 0.8852 (t-100) REVERT: A 152 GLN cc_start: 0.9195 (OUTLIER) cc_final: 0.8635 (tp40) REVERT: A 176 ARG cc_start: 0.7547 (mmt180) cc_final: 0.7261 (mtt180) REVERT: A 177 ARG cc_start: 0.7961 (mmm-85) cc_final: 0.6760 (ttp-170) REVERT: B 51 TRP cc_start: 0.7652 (t60) cc_final: 0.6544 (m-10) REVERT: B 79 PHE cc_start: 0.8932 (m-80) cc_final: 0.8666 (m-10) REVERT: B 136 LEU cc_start: 0.8058 (mt) cc_final: 0.7533 (pp) REVERT: B 157 PHE cc_start: 0.7468 (t80) cc_final: 0.6641 (t80) REVERT: B 158 TYR cc_start: 0.8838 (t80) cc_final: 0.8618 (t80) REVERT: B 181 MET cc_start: 0.9001 (mtp) cc_final: 0.8524 (mmt) REVERT: B 184 LEU cc_start: 0.9344 (mt) cc_final: 0.8689 (tt) REVERT: B 186 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7760 (tp30) REVERT: B 233 MET cc_start: 0.9260 (mmm) cc_final: 0.9004 (mmm) REVERT: B 382 GLU cc_start: 0.8066 (tt0) cc_final: 0.7681 (tt0) REVERT: B 570 ASP cc_start: 0.7538 (m-30) cc_final: 0.6979 (t70) REVERT: B 1031 ASP cc_start: 0.8796 (m-30) cc_final: 0.8487 (p0) REVERT: B 1064 TYR cc_start: 0.7670 (m-80) cc_final: 0.7443 (m-80) REVERT: B 1168 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8034 (tp) REVERT: B 1171 LEU cc_start: 0.8464 (mt) cc_final: 0.8260 (pp) REVERT: B 1246 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.8780 (mmp80) REVERT: B 1252 MET cc_start: 0.9034 (ttm) cc_final: 0.8720 (mmt) REVERT: C 91 TRP cc_start: 0.9116 (t60) cc_final: 0.8852 (t-100) REVERT: C 131 ILE cc_start: 0.8712 (pt) cc_final: 0.8497 (mt) REVERT: C 152 GLN cc_start: 0.9191 (OUTLIER) cc_final: 0.8629 (tp40) REVERT: C 176 ARG cc_start: 0.7544 (mmt180) cc_final: 0.7261 (mtt180) REVERT: C 177 ARG cc_start: 0.7964 (mmm-85) cc_final: 0.6759 (ttp-170) REVERT: D 51 TRP cc_start: 0.7654 (t60) cc_final: 0.6548 (m-10) REVERT: D 79 PHE cc_start: 0.8932 (m-80) cc_final: 0.8664 (m-10) REVERT: D 136 LEU cc_start: 0.8058 (mt) cc_final: 0.7530 (pp) REVERT: D 157 PHE cc_start: 0.7467 (t80) cc_final: 0.6640 (t80) REVERT: D 158 TYR cc_start: 0.8839 (t80) cc_final: 0.8617 (t80) REVERT: D 181 MET cc_start: 0.9000 (mtp) cc_final: 0.8524 (mmt) REVERT: D 184 LEU cc_start: 0.9346 (mt) cc_final: 0.8691 (tt) REVERT: D 186 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7760 (tp30) REVERT: D 233 MET cc_start: 0.9260 (mmm) cc_final: 0.9007 (mmm) REVERT: D 382 GLU cc_start: 0.8068 (tt0) cc_final: 0.7671 (tt0) REVERT: D 570 ASP cc_start: 0.7538 (m-30) cc_final: 0.6982 (t70) REVERT: D 1031 ASP cc_start: 0.8797 (m-30) cc_final: 0.8485 (p0) REVERT: D 1064 TYR cc_start: 0.7668 (m-80) cc_final: 0.7442 (m-80) REVERT: D 1168 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8032 (tp) REVERT: D 1171 LEU cc_start: 0.8465 (mt) cc_final: 0.8261 (pp) REVERT: D 1246 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.8782 (mmp80) REVERT: D 1252 MET cc_start: 0.9036 (ttm) cc_final: 0.8721 (mmt) REVERT: E 91 TRP cc_start: 0.9119 (t60) cc_final: 0.8853 (t-100) REVERT: E 152 GLN cc_start: 0.9194 (OUTLIER) cc_final: 0.8630 (tp40) REVERT: E 176 ARG cc_start: 0.7543 (mmt180) cc_final: 0.7256 (mtt180) REVERT: E 177 ARG cc_start: 0.7963 (mmm-85) cc_final: 0.6760 (ttp-170) REVERT: F 51 TRP cc_start: 0.7650 (t60) cc_final: 0.6545 (m-10) REVERT: F 79 PHE cc_start: 0.8930 (m-80) cc_final: 0.8663 (m-10) REVERT: F 136 LEU cc_start: 0.8064 (mt) cc_final: 0.7536 (pp) REVERT: F 157 PHE cc_start: 0.7469 (t80) cc_final: 0.6645 (t80) REVERT: F 158 TYR cc_start: 0.8840 (t80) cc_final: 0.8619 (t80) REVERT: F 181 MET cc_start: 0.9000 (mtp) cc_final: 0.8526 (mmt) REVERT: F 184 LEU cc_start: 0.9344 (mt) cc_final: 0.8691 (tt) REVERT: F 186 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7757 (tp30) REVERT: F 233 MET cc_start: 0.9255 (mmm) cc_final: 0.9003 (mmm) REVERT: F 320 ILE cc_start: 0.8992 (mt) cc_final: 0.8791 (mt) REVERT: F 382 GLU cc_start: 0.8068 (tt0) cc_final: 0.7672 (tt0) REVERT: F 570 ASP cc_start: 0.7538 (m-30) cc_final: 0.6982 (t70) REVERT: F 1031 ASP cc_start: 0.8795 (m-30) cc_final: 0.8484 (p0) REVERT: F 1064 TYR cc_start: 0.7668 (m-80) cc_final: 0.7446 (m-80) REVERT: F 1168 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8039 (tp) REVERT: F 1171 LEU cc_start: 0.8465 (mt) cc_final: 0.8262 (pp) REVERT: F 1246 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.8781 (mmp80) REVERT: F 1252 MET cc_start: 0.9033 (ttm) cc_final: 0.8720 (mmt) REVERT: G 91 TRP cc_start: 0.9115 (t60) cc_final: 0.8848 (t-100) REVERT: G 131 ILE cc_start: 0.8714 (pt) cc_final: 0.8507 (mt) REVERT: G 152 GLN cc_start: 0.9193 (OUTLIER) cc_final: 0.8625 (tp40) REVERT: G 176 ARG cc_start: 0.7547 (mmt180) cc_final: 0.7256 (mtt180) REVERT: G 177 ARG cc_start: 0.7960 (mmm-85) cc_final: 0.6760 (ttp-170) REVERT: H 51 TRP cc_start: 0.7653 (t60) cc_final: 0.6546 (m-10) REVERT: H 79 PHE cc_start: 0.8930 (m-80) cc_final: 0.8665 (m-10) REVERT: H 136 LEU cc_start: 0.8063 (mt) cc_final: 0.7538 (pp) REVERT: H 157 PHE cc_start: 0.7469 (t80) cc_final: 0.6642 (t80) REVERT: H 158 TYR cc_start: 0.8839 (t80) cc_final: 0.8617 (t80) REVERT: H 181 MET cc_start: 0.9000 (mtp) cc_final: 0.8524 (mmt) REVERT: H 184 LEU cc_start: 0.9344 (mt) cc_final: 0.8691 (tt) REVERT: H 186 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7759 (tp30) REVERT: H 233 MET cc_start: 0.9257 (mmm) cc_final: 0.9004 (mmm) REVERT: H 382 GLU cc_start: 0.8068 (tt0) cc_final: 0.7675 (tt0) REVERT: H 570 ASP cc_start: 0.7534 (m-30) cc_final: 0.6977 (t70) REVERT: H 1031 ASP cc_start: 0.8798 (m-30) cc_final: 0.8484 (p0) REVERT: H 1064 TYR cc_start: 0.7670 (m-80) cc_final: 0.7447 (m-80) REVERT: H 1168 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8039 (tp) REVERT: H 1171 LEU cc_start: 0.8466 (mt) cc_final: 0.8262 (pp) REVERT: H 1246 ARG cc_start: 0.9094 (OUTLIER) cc_final: 0.8782 (mmp80) REVERT: H 1252 MET cc_start: 0.9036 (ttm) cc_final: 0.8723 (mmt) outliers start: 248 outliers final: 48 residues processed: 1114 average time/residue: 0.1886 time to fit residues: 343.8610 Evaluate side-chains 525 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 465 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 262 ASN B 326 HIS B1020 GLN B1296 ASN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 ASN D 326 HIS D 485 GLN D1020 GLN D1135 HIS D1296 ASN F 262 ASN F 326 HIS F1020 GLN F1296 ASN H 262 ASN H 326 HIS H1020 GLN H1296 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.100113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.083142 restraints weight = 110492.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.082629 restraints weight = 101917.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.083195 restraints weight = 92467.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.083882 restraints weight = 65241.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.083961 restraints weight = 58591.814| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 31316 Z= 0.180 Angle : 0.697 7.772 42596 Z= 0.358 Chirality : 0.041 0.176 5196 Planarity : 0.005 0.063 5116 Dihedral : 5.213 62.407 4204 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.14 % Favored : 97.76 % Rotamer: Outliers : 0.12 % Allowed : 4.17 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.13), residues: 3832 helix: 0.76 (0.09), residues: 3172 sheet: None (None), residues: 0 loop : -1.42 (0.27), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D1251 TYR 0.015 0.001 TYR H 512 PHE 0.027 0.002 PHE F 295 TRP 0.015 0.001 TRP D 514 HIS 0.005 0.001 HIS F1316 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.18 (31312) covalent geometry : angle 0.69661 / 0.36 (42588) SS BOND : bond 0.00998 / 0.50 ( 4) SS BOND : angle 1.88683 / 1.46 ( 8) hydrogen bonds : bond 0.06794 / 4.71 ( 2472) hydrogen bonds : angle 4.59370 / 3.33 ( 7392) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 627 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.7866 (tptt) cc_final: 0.7049 (mptt) REVERT: A 54 ARG cc_start: 0.5219 (mtm-85) cc_final: 0.4863 (ptm160) REVERT: A 137 MET cc_start: 0.7893 (mmm) cc_final: 0.7279 (tmm) REVERT: A 154 ILE cc_start: 0.9508 (tp) cc_final: 0.9285 (tp) REVERT: B 51 TRP cc_start: 0.7328 (t60) cc_final: 0.6735 (m-10) REVERT: B 157 PHE cc_start: 0.5390 (t80) cc_final: 0.5163 (t80) REVERT: B 184 LEU cc_start: 0.9239 (mt) cc_final: 0.8688 (tt) REVERT: B 186 GLU cc_start: 0.7318 (mm-30) cc_final: 0.7089 (tp30) REVERT: B 507 LYS cc_start: 0.8374 (tptt) cc_final: 0.8163 (mmtm) REVERT: B 1298 MET cc_start: 0.8340 (ttt) cc_final: 0.8073 (ttt) REVERT: C 54 ARG cc_start: 0.5236 (mtm-85) cc_final: 0.4880 (ptm160) REVERT: C 137 MET cc_start: 0.7925 (mmm) cc_final: 0.7321 (tmm) REVERT: D 51 TRP cc_start: 0.7325 (t60) cc_final: 0.6743 (m-10) REVERT: D 157 PHE cc_start: 0.5370 (t80) cc_final: 0.5158 (t80) REVERT: D 184 LEU cc_start: 0.9232 (mt) cc_final: 0.8681 (tt) REVERT: D 186 GLU cc_start: 0.7299 (mm-30) cc_final: 0.7078 (tp30) REVERT: D 507 LYS cc_start: 0.8361 (tptt) cc_final: 0.8158 (mmtm) REVERT: D 1298 MET cc_start: 0.8327 (ttt) cc_final: 0.8057 (ttt) REVERT: E 54 ARG cc_start: 0.5229 (mtm-85) cc_final: 0.4869 (ptm160) REVERT: E 91 TRP cc_start: 0.8609 (t60) cc_final: 0.8409 (t60) REVERT: E 137 MET cc_start: 0.8029 (mmm) cc_final: 0.7343 (tmm) REVERT: F 51 TRP cc_start: 0.7325 (t60) cc_final: 0.6729 (m-10) REVERT: F 157 PHE cc_start: 0.5384 (t80) cc_final: 0.5155 (t80) REVERT: F 184 LEU cc_start: 0.9236 (mt) cc_final: 0.8687 (tt) REVERT: F 186 GLU cc_start: 0.7322 (mm-30) cc_final: 0.7093 (tp30) REVERT: F 507 LYS cc_start: 0.8363 (tptt) cc_final: 0.8155 (mmtm) REVERT: F 1298 MET cc_start: 0.8320 (ttt) cc_final: 0.8050 (ttt) REVERT: G 54 ARG cc_start: 0.5237 (mtm-85) cc_final: 0.4874 (ptm160) REVERT: G 137 MET cc_start: 0.7991 (mmm) cc_final: 0.7453 (tmm) REVERT: H 51 TRP cc_start: 0.7329 (t60) cc_final: 0.6746 (m-10) REVERT: H 157 PHE cc_start: 0.5401 (t80) cc_final: 0.5176 (t80) REVERT: H 184 LEU cc_start: 0.9231 (mt) cc_final: 0.8683 (tt) REVERT: H 186 GLU cc_start: 0.7300 (mm-30) cc_final: 0.7082 (tp30) REVERT: H 507 LYS cc_start: 0.8357 (tptt) cc_final: 0.8155 (mmtm) REVERT: H 1298 MET cc_start: 0.8336 (ttt) cc_final: 0.8073 (ttt) outliers start: 4 outliers final: 0 residues processed: 631 average time/residue: 0.1852 time to fit residues: 192.5757 Evaluate side-chains 392 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 392 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 157 optimal weight: 2.9990 chunk 187 optimal weight: 5.9990 chunk 124 optimal weight: 0.3980 chunk 43 optimal weight: 0.8980 chunk 345 optimal weight: 8.9990 chunk 348 optimal weight: 4.9990 chunk 366 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 359 optimal weight: 8.9990 chunk 213 optimal weight: 6.9990 chunk 190 optimal weight: 20.0000 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 GLN ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1020 GLN ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1020 GLN E 152 GLN ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1020 GLN G 152 GLN ** H 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H1020 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.096415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.080096 restraints weight = 108923.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.079730 restraints weight = 96433.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.080412 restraints weight = 87432.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.080389 restraints weight = 64364.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.080502 restraints weight = 55395.921| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 31316 Z= 0.182 Angle : 0.670 7.960 42596 Z= 0.343 Chirality : 0.040 0.173 5196 Planarity : 0.005 0.057 5116 Dihedral : 4.943 56.106 4204 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.40 % Favored : 97.49 % Rotamer: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.14), residues: 3832 helix: 1.28 (0.09), residues: 3184 sheet: None (None), residues: 0 loop : -0.98 (0.28), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 306 TYR 0.009 0.001 TYR B 124 PHE 0.034 0.002 PHE C 168 TRP 0.037 0.002 TRP D1088 HIS 0.008 0.001 HIS D 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.18 (31312) covalent geometry : angle 0.66975 / 0.34 (42588) SS BOND : bond 0.00631 / 0.32 ( 4) SS BOND : angle 1.06817 / 0.85 ( 8) hydrogen bonds : bond 0.05992 / 4.12 ( 2472) hydrogen bonds : angle 4.22338 / 3.06 ( 7392) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 506 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.8229 (tptt) cc_final: 0.7396 (mptt) REVERT: A 54 ARG cc_start: 0.5620 (mtm-85) cc_final: 0.5119 (ptm160) REVERT: A 82 SER cc_start: 0.9400 (p) cc_final: 0.9100 (m) REVERT: A 118 SER cc_start: 0.9073 (m) cc_final: 0.8515 (t) REVERT: B 104 LEU cc_start: 0.8709 (mt) cc_final: 0.8304 (mt) REVERT: B 136 LEU cc_start: 0.7336 (mt) cc_final: 0.7055 (pp) REVERT: B 184 LEU cc_start: 0.9185 (mt) cc_final: 0.8714 (tt) REVERT: B 186 GLU cc_start: 0.7227 (mm-30) cc_final: 0.7012 (tp30) REVERT: C 54 ARG cc_start: 0.5626 (mtm-85) cc_final: 0.5139 (ptm160) REVERT: C 82 SER cc_start: 0.9386 (p) cc_final: 0.9082 (m) REVERT: C 168 PHE cc_start: 0.6859 (t80) cc_final: 0.6473 (t80) REVERT: D 104 LEU cc_start: 0.8691 (mt) cc_final: 0.8309 (mt) REVERT: D 136 LEU cc_start: 0.7326 (mt) cc_final: 0.7060 (pp) REVERT: D 184 LEU cc_start: 0.9179 (mt) cc_final: 0.8715 (tt) REVERT: D 186 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6989 (tp30) REVERT: E 54 ARG cc_start: 0.5617 (mtm-85) cc_final: 0.5105 (ptm160) REVERT: E 82 SER cc_start: 0.9406 (p) cc_final: 0.9064 (m) REVERT: E 168 PHE cc_start: 0.6849 (t80) cc_final: 0.6573 (t80) REVERT: F 104 LEU cc_start: 0.8713 (mt) cc_final: 0.8324 (mt) REVERT: F 136 LEU cc_start: 0.7331 (mt) cc_final: 0.7063 (pp) REVERT: F 184 LEU cc_start: 0.9179 (mt) cc_final: 0.8706 (tt) REVERT: F 186 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6994 (tp30) REVERT: G 54 ARG cc_start: 0.5623 (mtm-85) cc_final: 0.5132 (ptm160) REVERT: G 82 SER cc_start: 0.9384 (p) cc_final: 0.9078 (m) REVERT: G 168 PHE cc_start: 0.6978 (t80) cc_final: 0.6687 (t80) REVERT: H 104 LEU cc_start: 0.8681 (mt) cc_final: 0.8304 (mt) REVERT: H 136 LEU cc_start: 0.7337 (mt) cc_final: 0.7056 (pp) REVERT: H 184 LEU cc_start: 0.9178 (mt) cc_final: 0.8701 (tt) REVERT: H 186 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6993 (tp30) outliers start: 0 outliers final: 0 residues processed: 506 average time/residue: 0.1688 time to fit residues: 146.8344 Evaluate side-chains 345 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 345 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 302 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 218 optimal weight: 4.9990 chunk 221 optimal weight: 0.4980 chunk 187 optimal weight: 0.0970 chunk 90 optimal weight: 0.9990 chunk 342 optimal weight: 20.0000 chunk 96 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 242 optimal weight: 0.9980 chunk 161 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 219 GLN B 262 ASN B 485 GLN B1020 GLN ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 GLN D 262 ASN D1020 GLN F 219 GLN F 262 ASN F 485 GLN F1020 GLN H 219 GLN H 262 ASN H 485 GLN H1020 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.097376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.081592 restraints weight = 110853.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.080523 restraints weight = 116395.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.081250 restraints weight = 96177.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.081777 restraints weight = 65786.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.082175 restraints weight = 58372.350| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31316 Z= 0.147 Angle : 0.625 7.829 42596 Z= 0.315 Chirality : 0.038 0.168 5196 Planarity : 0.005 0.080 5116 Dihedral : 4.824 52.469 4204 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.27 % Favored : 97.63 % Rotamer: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.14), residues: 3832 helix: 1.60 (0.09), residues: 3192 sheet: None (None), residues: 0 loop : -0.78 (0.29), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 136 TYR 0.019 0.001 TYR D 123 PHE 0.033 0.002 PHE C 168 TRP 0.012 0.001 TRP D1088 HIS 0.007 0.001 HIS F 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.15 (31312) covalent geometry : angle 0.62434 / 0.32 (42588) SS BOND : bond 0.00624 / 0.31 ( 4) SS BOND : angle 1.57562 / 1.22 ( 8) hydrogen bonds : bond 0.05487 / 3.78 ( 2472) hydrogen bonds : angle 4.08450 / 2.95 ( 7392) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 484 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.8281 (tptt) cc_final: 0.7461 (mptt) REVERT: A 54 ARG cc_start: 0.5627 (mtm-85) cc_final: 0.5154 (ptm160) REVERT: A 82 SER cc_start: 0.9388 (p) cc_final: 0.9053 (m) REVERT: A 137 MET cc_start: 0.7634 (mmm) cc_final: 0.7365 (mmm) REVERT: B 184 LEU cc_start: 0.9196 (mt) cc_final: 0.8679 (tt) REVERT: B 186 GLU cc_start: 0.7286 (mm-30) cc_final: 0.7047 (tp30) REVERT: B 583 PHE cc_start: 0.9079 (m-10) cc_final: 0.8822 (m-10) REVERT: C 54 ARG cc_start: 0.5615 (mtm-85) cc_final: 0.5152 (ptm160) REVERT: C 82 SER cc_start: 0.9364 (p) cc_final: 0.9046 (m) REVERT: C 168 PHE cc_start: 0.6593 (t80) cc_final: 0.5352 (t80) REVERT: D 184 LEU cc_start: 0.9187 (mt) cc_final: 0.8676 (tt) REVERT: D 186 GLU cc_start: 0.7265 (mm-30) cc_final: 0.7032 (tp30) REVERT: D 583 PHE cc_start: 0.9076 (m-10) cc_final: 0.8820 (m-10) REVERT: E 54 ARG cc_start: 0.5611 (mtm-85) cc_final: 0.5116 (ptm160) REVERT: E 82 SER cc_start: 0.9377 (p) cc_final: 0.9034 (m) REVERT: E 168 PHE cc_start: 0.6827 (t80) cc_final: 0.6513 (t80) REVERT: F 184 LEU cc_start: 0.9177 (mt) cc_final: 0.8663 (tt) REVERT: F 186 GLU cc_start: 0.7255 (mm-30) cc_final: 0.7018 (tp30) REVERT: F 583 PHE cc_start: 0.9086 (m-10) cc_final: 0.8828 (m-10) REVERT: G 54 ARG cc_start: 0.5645 (mtm-85) cc_final: 0.5127 (ptm160) REVERT: G 82 SER cc_start: 0.9388 (p) cc_final: 0.9055 (m) REVERT: G 168 PHE cc_start: 0.7001 (t80) cc_final: 0.6771 (t80) REVERT: H 184 LEU cc_start: 0.9180 (mt) cc_final: 0.8668 (tt) REVERT: H 186 GLU cc_start: 0.7264 (mm-30) cc_final: 0.7038 (tp30) REVERT: H 583 PHE cc_start: 0.9077 (m-10) cc_final: 0.8822 (m-10) outliers start: 0 outliers final: 0 residues processed: 484 average time/residue: 0.1678 time to fit residues: 139.5386 Evaluate side-chains 337 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 337 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 192 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 248 optimal weight: 9.9990 chunk 127 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 325 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 287 optimal weight: 8.9990 chunk 213 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 374 GLN B1203 HIS ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 GLN D1203 HIS F 374 GLN F1203 HIS H 374 GLN H1203 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.090403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.074257 restraints weight = 112901.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.073780 restraints weight = 96366.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.074118 restraints weight = 97249.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.074119 restraints weight = 68518.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.074367 restraints weight = 59296.326| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.5524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 31316 Z= 0.333 Angle : 0.841 8.692 42596 Z= 0.436 Chirality : 0.045 0.185 5196 Planarity : 0.006 0.065 5116 Dihedral : 5.408 51.759 4204 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.44 % Favored : 96.45 % Rotamer: Outliers : 0.12 % Allowed : 3.83 % Favored : 96.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.14), residues: 3832 helix: 1.17 (0.09), residues: 3196 sheet: None (None), residues: 0 loop : -0.87 (0.30), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 136 TYR 0.025 0.002 TYR H 124 PHE 0.045 0.003 PHE E 168 TRP 0.031 0.002 TRP C 90 HIS 0.010 0.002 HIS B 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00745 / 0.33 (31312) covalent geometry : angle 0.84115 / 0.44 (42588) SS BOND : bond 0.01039 / 0.52 ( 4) SS BOND : angle 1.71715 / 1.38 ( 8) hydrogen bonds : bond 0.06202 / 4.26 ( 2472) hydrogen bonds : angle 4.58476 / 3.33 ( 7392) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 393 time to evaluate : 1.201 Fit side-chains REVERT: A 47 LYS cc_start: 0.8426 (tptt) cc_final: 0.7620 (mptt) REVERT: A 81 CYS cc_start: 0.8093 (t) cc_final: 0.7794 (t) REVERT: A 159 ILE cc_start: 0.9262 (tp) cc_final: 0.9022 (tp) REVERT: B 41 PHE cc_start: 0.7721 (m-10) cc_final: 0.7245 (m-80) REVERT: B 184 LEU cc_start: 0.9279 (mt) cc_final: 0.8737 (tt) REVERT: B 507 LYS cc_start: 0.8753 (mmtm) cc_final: 0.8012 (mttp) REVERT: B 1298 MET cc_start: 0.8623 (ttt) cc_final: 0.8413 (ttt) REVERT: C 81 CYS cc_start: 0.8123 (t) cc_final: 0.7784 (t) REVERT: C 118 SER cc_start: 0.9231 (m) cc_final: 0.8800 (t) REVERT: D 41 PHE cc_start: 0.7756 (m-10) cc_final: 0.7271 (m-80) REVERT: D 184 LEU cc_start: 0.9266 (mt) cc_final: 0.8731 (tt) REVERT: D 507 LYS cc_start: 0.8742 (mmtm) cc_final: 0.7995 (mttp) REVERT: D 1298 MET cc_start: 0.8635 (ttt) cc_final: 0.8425 (ttt) REVERT: E 81 CYS cc_start: 0.8151 (t) cc_final: 0.7832 (t) REVERT: E 159 ILE cc_start: 0.9280 (tp) cc_final: 0.9062 (tp) REVERT: F 41 PHE cc_start: 0.7742 (m-10) cc_final: 0.7242 (m-80) REVERT: F 184 LEU cc_start: 0.9279 (mt) cc_final: 0.8734 (tt) REVERT: F 507 LYS cc_start: 0.8739 (mmtm) cc_final: 0.8000 (mttp) REVERT: F 1298 MET cc_start: 0.8622 (ttt) cc_final: 0.8411 (ttt) REVERT: G 81 CYS cc_start: 0.8102 (t) cc_final: 0.7814 (t) REVERT: H 41 PHE cc_start: 0.7712 (m-10) cc_final: 0.7223 (m-80) REVERT: H 184 LEU cc_start: 0.9270 (mt) cc_final: 0.8730 (tt) REVERT: H 507 LYS cc_start: 0.8756 (mmtm) cc_final: 0.8017 (mttp) outliers start: 4 outliers final: 0 residues processed: 397 average time/residue: 0.1631 time to fit residues: 113.1409 Evaluate side-chains 284 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 239 optimal weight: 6.9990 chunk 136 optimal weight: 2.9990 chunk 240 optimal weight: 4.9990 chunk 228 optimal weight: 1.9990 chunk 231 optimal weight: 5.9990 chunk 314 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 237 optimal weight: 0.8980 chunk 104 optimal weight: 0.7980 chunk 322 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 GLN B1020 GLN B1098 HIS ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 GLN D1020 GLN D1098 HIS F 219 GLN F1020 GLN F1098 HIS H 219 GLN H1020 GLN H1098 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.094323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.077858 restraints weight = 109647.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.077800 restraints weight = 103029.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.078273 restraints weight = 93535.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.078328 restraints weight = 63466.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.078785 restraints weight = 56417.602| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.5732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31316 Z= 0.159 Angle : 0.665 7.711 42596 Z= 0.341 Chirality : 0.040 0.173 5196 Planarity : 0.005 0.077 5116 Dihedral : 5.012 50.504 4204 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.53 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.14), residues: 3832 helix: 1.48 (0.09), residues: 3188 sheet: None (None), residues: 0 loop : -1.03 (0.28), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 168 TYR 0.032 0.001 TYR D 123 PHE 0.050 0.002 PHE D 157 TRP 0.010 0.001 TRP E 91 HIS 0.008 0.001 HIS H 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.16 (31312) covalent geometry : angle 0.66480 / 0.34 (42588) SS BOND : bond 0.00163 / 0.08 ( 4) SS BOND : angle 1.20192 / 0.91 ( 8) hydrogen bonds : bond 0.05442 / 3.74 ( 2472) hydrogen bonds : angle 4.18276 / 3.03 ( 7392) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 460 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.8317 (tptt) cc_final: 0.7650 (mptt) REVERT: A 54 ARG cc_start: 0.6241 (mtm-85) cc_final: 0.5351 (ptm160) REVERT: A 110 CYS cc_start: 0.6876 (m) cc_final: 0.6667 (m) REVERT: B 184 LEU cc_start: 0.9294 (mt) cc_final: 0.8787 (tt) REVERT: B 507 LYS cc_start: 0.8648 (mmtm) cc_final: 0.7944 (mttt) REVERT: B 583 PHE cc_start: 0.9168 (m-80) cc_final: 0.8813 (m-80) REVERT: B 1206 GLU cc_start: 0.6155 (tp30) cc_final: 0.5945 (tp30) REVERT: C 54 ARG cc_start: 0.6322 (mtm-85) cc_final: 0.5443 (ptm160) REVERT: C 81 CYS cc_start: 0.8052 (t) cc_final: 0.7850 (t) REVERT: C 110 CYS cc_start: 0.6787 (m) cc_final: 0.6565 (m) REVERT: D 184 LEU cc_start: 0.9272 (mt) cc_final: 0.8776 (tt) REVERT: D 507 LYS cc_start: 0.8630 (mmtm) cc_final: 0.7924 (mttt) REVERT: D 583 PHE cc_start: 0.9178 (m-80) cc_final: 0.8823 (m-80) REVERT: D 1206 GLU cc_start: 0.6142 (tp30) cc_final: 0.5938 (tp30) REVERT: E 54 ARG cc_start: 0.6276 (mtm-85) cc_final: 0.5366 (ptm160) REVERT: E 110 CYS cc_start: 0.6834 (m) cc_final: 0.6631 (m) REVERT: F 184 LEU cc_start: 0.9278 (mt) cc_final: 0.8762 (tt) REVERT: F 507 LYS cc_start: 0.8657 (mmtm) cc_final: 0.7950 (mttt) REVERT: F 583 PHE cc_start: 0.9173 (m-80) cc_final: 0.8822 (m-80) REVERT: F 1206 GLU cc_start: 0.6142 (tp30) cc_final: 0.5934 (tp30) REVERT: G 54 ARG cc_start: 0.6270 (mtm-85) cc_final: 0.5374 (ptm160) REVERT: G 110 CYS cc_start: 0.6853 (m) cc_final: 0.6599 (m) REVERT: H 184 LEU cc_start: 0.9276 (mt) cc_final: 0.8774 (tt) REVERT: H 507 LYS cc_start: 0.8645 (mmtm) cc_final: 0.7942 (mttt) REVERT: H 583 PHE cc_start: 0.9170 (m-80) cc_final: 0.8814 (m-80) REVERT: H 1206 GLU cc_start: 0.6145 (tp30) cc_final: 0.5939 (tp30) outliers start: 0 outliers final: 0 residues processed: 460 average time/residue: 0.1690 time to fit residues: 134.2171 Evaluate side-chains 300 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 91 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 180 optimal weight: 6.9990 chunk 341 optimal weight: 9.9990 chunk 365 optimal weight: 10.0000 chunk 254 optimal weight: 0.9990 chunk 292 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 139 optimal weight: 0.8980 chunk 7 optimal weight: 0.0370 overall best weight: 1.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1135 HIS ** B1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 GLN ** D1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1135 HIS ** F1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1135 HIS ** H1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.094758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.078245 restraints weight = 109398.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.077544 restraints weight = 100857.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.077960 restraints weight = 93048.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.078540 restraints weight = 65073.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.079110 restraints weight = 57071.323| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.5957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31316 Z= 0.154 Angle : 0.643 7.345 42596 Z= 0.330 Chirality : 0.039 0.194 5196 Planarity : 0.005 0.068 5116 Dihedral : 4.880 51.659 4204 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.53 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.14), residues: 3832 helix: 1.63 (0.09), residues: 3188 sheet: None (None), residues: 0 loop : -0.93 (0.29), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H1251 TYR 0.034 0.001 TYR B 123 PHE 0.039 0.002 PHE G 75 TRP 0.030 0.001 TRP D1037 HIS 0.008 0.001 HIS H 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (31312) covalent geometry : angle 0.64284 / 0.33 (42588) SS BOND : bond 0.00352 / 0.18 ( 4) SS BOND : angle 1.19270 / 0.96 ( 8) hydrogen bonds : bond 0.05140 / 3.52 ( 2472) hydrogen bonds : angle 4.05960 / 2.93 ( 7392) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 429 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.8338 (tptt) cc_final: 0.7681 (mptt) REVERT: A 54 ARG cc_start: 0.6167 (mtm-85) cc_final: 0.5115 (ptm160) REVERT: B 184 LEU cc_start: 0.9294 (mt) cc_final: 0.8743 (tt) REVERT: B 507 LYS cc_start: 0.8647 (mmtm) cc_final: 0.7945 (mttt) REVERT: B 583 PHE cc_start: 0.9211 (m-80) cc_final: 0.8831 (m-80) REVERT: C 54 ARG cc_start: 0.6318 (mtm-85) cc_final: 0.5395 (ptm160) REVERT: C 110 CYS cc_start: 0.6348 (m) cc_final: 0.6135 (m) REVERT: D 184 LEU cc_start: 0.9291 (mt) cc_final: 0.8739 (tt) REVERT: D 507 LYS cc_start: 0.8644 (mmtm) cc_final: 0.7933 (mttt) REVERT: D 583 PHE cc_start: 0.9211 (m-80) cc_final: 0.8832 (m-80) REVERT: E 54 ARG cc_start: 0.6207 (mtm-85) cc_final: 0.5302 (ptm160) REVERT: E 110 CYS cc_start: 0.6428 (m) cc_final: 0.6204 (m) REVERT: F 104 LEU cc_start: 0.8611 (mp) cc_final: 0.8395 (mt) REVERT: F 184 LEU cc_start: 0.9274 (mt) cc_final: 0.8730 (tt) REVERT: F 507 LYS cc_start: 0.8646 (mmtm) cc_final: 0.7940 (mttt) REVERT: F 583 PHE cc_start: 0.9211 (m-80) cc_final: 0.8830 (m-80) REVERT: G 54 ARG cc_start: 0.6226 (mtm-85) cc_final: 0.5300 (ptm160) REVERT: H 184 LEU cc_start: 0.9280 (mt) cc_final: 0.8728 (tt) REVERT: H 507 LYS cc_start: 0.8650 (mmtm) cc_final: 0.7946 (mttt) REVERT: H 583 PHE cc_start: 0.9222 (m-80) cc_final: 0.8835 (m-80) outliers start: 0 outliers final: 0 residues processed: 429 average time/residue: 0.1706 time to fit residues: 124.9900 Evaluate side-chains 286 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 136 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 363 optimal weight: 9.9990 chunk 375 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 143 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 281 optimal weight: 8.9990 chunk 311 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 352 optimal weight: 6.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1197 GLN ** D1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1197 GLN ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1197 GLN ** H1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1197 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.091316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.074970 restraints weight = 112079.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.074407 restraints weight = 85404.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.074462 restraints weight = 73064.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.074791 restraints weight = 52637.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.074981 restraints weight = 47307.674| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.6243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 31316 Z= 0.279 Angle : 0.785 9.202 42596 Z= 0.404 Chirality : 0.044 0.234 5196 Planarity : 0.006 0.079 5116 Dihedral : 5.147 54.984 4204 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.39 % Favored : 96.50 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.14), residues: 3832 helix: 1.34 (0.09), residues: 3212 sheet: None (None), residues: 0 loop : -1.01 (0.29), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 526 TYR 0.042 0.002 TYR F 123 PHE 0.058 0.003 PHE G 75 TRP 0.014 0.002 TRP D 232 HIS 0.014 0.002 HIS F 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00626 / 0.28 (31312) covalent geometry : angle 0.78447 / 0.40 (42588) SS BOND : bond 0.00600 / 0.31 ( 4) SS BOND : angle 1.58486 / 1.19 ( 8) hydrogen bonds : bond 0.05601 / 3.83 ( 2472) hydrogen bonds : angle 4.39358 / 3.18 ( 7392) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 383 time to evaluate : 1.259 Fit side-chains REVERT: A 47 LYS cc_start: 0.8317 (tptt) cc_final: 0.7736 (mptt) REVERT: B 184 LEU cc_start: 0.9427 (mt) cc_final: 0.8859 (tt) REVERT: B 507 LYS cc_start: 0.8801 (mmtm) cc_final: 0.8411 (tppt) REVERT: B 583 PHE cc_start: 0.9341 (m-80) cc_final: 0.8994 (m-80) REVERT: D 108 MET cc_start: 0.7842 (mmm) cc_final: 0.7631 (mpp) REVERT: D 184 LEU cc_start: 0.9415 (mt) cc_final: 0.8856 (tt) REVERT: D 507 LYS cc_start: 0.8803 (mmtm) cc_final: 0.8416 (tppt) REVERT: D 583 PHE cc_start: 0.9355 (m-80) cc_final: 0.9007 (m-80) REVERT: F 184 LEU cc_start: 0.9418 (mt) cc_final: 0.8844 (tt) REVERT: F 507 LYS cc_start: 0.8802 (mmtm) cc_final: 0.8411 (tppt) REVERT: F 583 PHE cc_start: 0.9357 (m-80) cc_final: 0.9006 (m-80) REVERT: H 184 LEU cc_start: 0.9417 (mt) cc_final: 0.8850 (tt) REVERT: H 507 LYS cc_start: 0.8811 (mmtm) cc_final: 0.8424 (tppt) REVERT: H 583 PHE cc_start: 0.9345 (m-80) cc_final: 0.9001 (m-80) outliers start: 0 outliers final: 0 residues processed: 383 average time/residue: 0.1644 time to fit residues: 109.4964 Evaluate side-chains 265 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 287 optimal weight: 5.9990 chunk 350 optimal weight: 1.9990 chunk 324 optimal weight: 6.9990 chunk 82 optimal weight: 0.5980 chunk 302 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 46 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 221 optimal weight: 3.9990 chunk 263 optimal weight: 8.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1020 GLN ** B1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1020 GLN ** D1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1020 GLN ** F1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1020 GLN ** H1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.094029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.077891 restraints weight = 109543.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.079000 restraints weight = 105861.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.078892 restraints weight = 90527.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.079265 restraints weight = 58090.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.079836 restraints weight = 50135.283| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.6363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31316 Z= 0.158 Angle : 0.678 13.283 42596 Z= 0.343 Chirality : 0.040 0.202 5196 Planarity : 0.005 0.067 5116 Dihedral : 4.885 54.009 4204 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.51 % Favored : 97.39 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.14), residues: 3832 helix: 1.53 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : -0.98 (0.30), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 176 TYR 0.040 0.002 TYR B 123 PHE 0.044 0.002 PHE C 75 TRP 0.011 0.001 TRP H1037 HIS 0.009 0.001 HIS F 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 (31312) covalent geometry : angle 0.67727 / 0.34 (42588) SS BOND : bond 0.00515 / 0.26 ( 4) SS BOND : angle 1.50026 / 1.09 ( 8) hydrogen bonds : bond 0.05183 / 3.53 ( 2472) hydrogen bonds : angle 4.10381 / 2.96 ( 7392) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 410 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.8312 (tptt) cc_final: 0.7748 (mptt) REVERT: B 184 LEU cc_start: 0.9287 (mt) cc_final: 0.8790 (tt) REVERT: B 507 LYS cc_start: 0.8517 (mmtm) cc_final: 0.8089 (tppt) REVERT: B 583 PHE cc_start: 0.9148 (m-80) cc_final: 0.8804 (m-80) REVERT: C 54 ARG cc_start: 0.6260 (mtm-85) cc_final: 0.4808 (ttm170) REVERT: C 60 PHE cc_start: 0.7600 (m-80) cc_final: 0.7329 (m-80) REVERT: C 81 CYS cc_start: 0.8173 (t) cc_final: 0.7966 (t) REVERT: C 110 CYS cc_start: 0.6569 (m) cc_final: 0.6206 (m) REVERT: D 184 LEU cc_start: 0.9269 (mt) cc_final: 0.8778 (tt) REVERT: D 507 LYS cc_start: 0.8486 (mmtm) cc_final: 0.8064 (tppt) REVERT: D 583 PHE cc_start: 0.9159 (m-80) cc_final: 0.8814 (m-80) REVERT: E 60 PHE cc_start: 0.7697 (m-80) cc_final: 0.7485 (m-80) REVERT: E 110 CYS cc_start: 0.6499 (m) cc_final: 0.6113 (m) REVERT: F 184 LEU cc_start: 0.9273 (mt) cc_final: 0.8782 (tt) REVERT: F 507 LYS cc_start: 0.8517 (mmtm) cc_final: 0.8089 (tppt) REVERT: F 583 PHE cc_start: 0.9164 (m-80) cc_final: 0.8820 (m-80) REVERT: H 184 LEU cc_start: 0.9269 (mt) cc_final: 0.8781 (tt) REVERT: H 507 LYS cc_start: 0.8511 (mmtm) cc_final: 0.8086 (tppt) REVERT: H 583 PHE cc_start: 0.9162 (m-80) cc_final: 0.8812 (m-80) outliers start: 0 outliers final: 0 residues processed: 410 average time/residue: 0.1632 time to fit residues: 116.7820 Evaluate side-chains 262 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 349 optimal weight: 20.0000 chunk 313 optimal weight: 0.2980 chunk 48 optimal weight: 0.9990 chunk 189 optimal weight: 7.9990 chunk 277 optimal weight: 1.9990 chunk 208 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 188 optimal weight: 0.9980 chunk 164 optimal weight: 0.9980 chunk 257 optimal weight: 0.8980 chunk 258 optimal weight: 0.0370 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.095782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.078906 restraints weight = 109773.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.077277 restraints weight = 82941.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.077918 restraints weight = 73238.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.078404 restraints weight = 56525.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.078426 restraints weight = 53010.864| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.6541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 31316 Z= 0.148 Angle : 0.669 11.164 42596 Z= 0.336 Chirality : 0.039 0.187 5196 Planarity : 0.005 0.067 5116 Dihedral : 4.784 53.239 4204 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.48 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.14), residues: 3832 helix: 1.61 (0.09), residues: 3232 sheet: None (None), residues: 0 loop : -0.95 (0.29), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 504 TYR 0.036 0.001 TYR F 123 PHE 0.033 0.002 PHE C 75 TRP 0.010 0.001 TRP H 288 HIS 0.009 0.001 HIS D 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (31312) covalent geometry : angle 0.66908 / 0.34 (42588) SS BOND : bond 0.00399 / 0.20 ( 4) SS BOND : angle 1.48963 / 1.07 ( 8) hydrogen bonds : bond 0.04874 / 3.32 ( 2472) hydrogen bonds : angle 3.97476 / 2.88 ( 7392) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 422 time to evaluate : 1.239 Fit side-chains REVERT: A 47 LYS cc_start: 0.8175 (tptt) cc_final: 0.7803 (mptt) REVERT: A 54 ARG cc_start: 0.6022 (mtm-85) cc_final: 0.4554 (ttm170) REVERT: B 184 LEU cc_start: 0.9322 (mt) cc_final: 0.8805 (tt) REVERT: B 507 LYS cc_start: 0.8462 (mmtm) cc_final: 0.7765 (mttt) REVERT: B 530 MET cc_start: 0.8518 (mpp) cc_final: 0.8194 (mpp) REVERT: B 583 PHE cc_start: 0.9227 (m-80) cc_final: 0.8830 (m-80) REVERT: B 1298 MET cc_start: 0.8496 (ttt) cc_final: 0.8291 (ttt) REVERT: C 54 ARG cc_start: 0.6091 (mtm-85) cc_final: 0.4574 (ttm170) REVERT: D 184 LEU cc_start: 0.9307 (mt) cc_final: 0.8802 (tt) REVERT: D 507 LYS cc_start: 0.8463 (mmtm) cc_final: 0.7738 (mttt) REVERT: D 530 MET cc_start: 0.8552 (mpp) cc_final: 0.8216 (mpp) REVERT: D 583 PHE cc_start: 0.9226 (m-80) cc_final: 0.8837 (m-80) REVERT: E 54 ARG cc_start: 0.6056 (mtm-85) cc_final: 0.4533 (ttm170) REVERT: F 184 LEU cc_start: 0.9308 (mt) cc_final: 0.8794 (tt) REVERT: F 507 LYS cc_start: 0.8488 (mmtm) cc_final: 0.7789 (mttt) REVERT: F 530 MET cc_start: 0.8550 (mpp) cc_final: 0.8220 (mpp) REVERT: F 583 PHE cc_start: 0.9229 (m-80) cc_final: 0.8837 (m-80) REVERT: F 1298 MET cc_start: 0.8500 (ttt) cc_final: 0.8293 (ttt) REVERT: H 184 LEU cc_start: 0.9314 (mt) cc_final: 0.8809 (tt) REVERT: H 507 LYS cc_start: 0.8478 (mmtm) cc_final: 0.7780 (mttt) REVERT: H 530 MET cc_start: 0.8532 (mpp) cc_final: 0.8204 (mpp) REVERT: H 583 PHE cc_start: 0.9231 (m-80) cc_final: 0.8835 (m-80) REVERT: H 1298 MET cc_start: 0.8497 (ttt) cc_final: 0.8289 (ttt) outliers start: 0 outliers final: 0 residues processed: 422 average time/residue: 0.1678 time to fit residues: 122.4510 Evaluate side-chains 272 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 37 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 335 optimal weight: 6.9990 chunk 10 optimal weight: 0.5980 chunk 341 optimal weight: 0.0870 chunk 176 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 352 optimal weight: 0.9980 chunk 150 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 overall best weight: 1.5362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1020 GLN ** B1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1020 GLN ** D1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1020 GLN ** F1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1020 GLN ** H1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.095011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.078323 restraints weight = 110515.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.076863 restraints weight = 79461.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.077331 restraints weight = 73412.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.077609 restraints weight = 60538.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.077683 restraints weight = 55124.692| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.6678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31316 Z= 0.157 Angle : 0.665 9.692 42596 Z= 0.340 Chirality : 0.040 0.277 5196 Planarity : 0.005 0.066 5116 Dihedral : 4.695 53.609 4204 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.79 % Favored : 97.10 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.14), residues: 3832 helix: 1.66 (0.09), residues: 3224 sheet: None (None), residues: 0 loop : -0.89 (0.29), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 176 TYR 0.040 0.002 TYR D 123 PHE 0.037 0.002 PHE H 432 TRP 0.022 0.001 TRP E 83 HIS 0.009 0.001 HIS F 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (31312) covalent geometry : angle 0.66455 / 0.34 (42588) SS BOND : bond 0.00443 / 0.22 ( 4) SS BOND : angle 1.11347 / 0.92 ( 8) hydrogen bonds : bond 0.04834 / 3.30 ( 2472) hydrogen bonds : angle 4.03473 / 2.92 ( 7392) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4678.34 seconds wall clock time: 82 minutes 22.77 seconds (4942.77 seconds total)