Starting phenix.real_space_refine on Mon Sep 14 15:56:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6khj_9990/09_2026/6khj_9990.cif Found real_map, /net/cci-nas-00/data/ceres_data/6khj_9990/09_2026/6khj_9990.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6khj_9990/09_2026/6khj_9990.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6khj_9990/09_2026/6khj_9990.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6khj_9990/09_2026/6khj_9990.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6khj_9990/09_2026/6khj_9990.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6khj_9990/09_2026/6khj_9990.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6khj_9990/09_2026/6khj_9990.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 12 7.16 5 P 6 5.49 5 S 174 5.16 5 C 20516 2.51 5 N 4894 2.21 5 O 5425 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.03s 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: 31027 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 2843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2843 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 19, 'TRANS': 349} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3697 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 18, 'TRANS': 469} Chain: "C" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 971 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "D" Number of atoms: 3896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3896 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 26, 'TRANS': 477} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 783 Classifications: {'peptide': 101} Link IDs: {'TRANS': 100} Chain: "F" Number of atoms: 4933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 4933 Classifications: {'peptide': 639} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 32, 'TRANS': 606} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 1286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1286 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 7, 'TRANS': 162} Chain: "H" Number of atoms: 3177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3177 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 22, 'TRANS': 370} Chain: "I" Number of atoms: 1516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1516 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 12, 'TRANS': 176} Chain: "J" Number of atoms: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1292 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 11, 'TRANS': 146} Chain: "K" Number of atoms: 1584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1584 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 19, 'TRANS': 184} Chain: "L" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 590 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 5, 'TRANS': 67} Chain: "M" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 885 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 3, 'TRANS': 107} Chain: "N" Number of atoms: 1148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1148 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 11, 'TRANS': 133} Chain: "O" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 538 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 5, 'TRANS': 62} Chain: "P" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 321 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "Q" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 333 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "S" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 469 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "A" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 136 Unusual residues: {'DGD': 2, 'PL9': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 43 Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'SQD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 83 Unusual residues: {'LHG': 1, 'SQD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "D" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 121 Unusual residues: {'BCR': 1, 'LHG': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "F" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 265 Unusual residues: {'BCR': 1, 'LHG': 3, 'LMG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 32 Chain: "I" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Unusual residues: {'LHG': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "K" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'SQD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 22424 SG CYS I 103 40.526 137.501 128.019 1.00 29.44 S ATOM 22468 SG CYS I 109 35.531 141.450 127.723 1.00 40.95 S ATOM 22173 SG CYS I 73 35.291 135.943 124.372 1.00 33.98 S ATOM 22449 SG CYS I 106 39.153 140.401 122.481 1.00 35.43 S ATOM 22120 SG CYS I 66 24.237 142.538 129.021 1.00 48.85 S ATOM 22142 SG CYS I 69 29.759 139.438 129.349 1.00 41.90 S ATOM 22101 SG CYS I 63 27.029 141.668 134.691 1.00 56.23 S ATOM 22502 SG CYS I 113 29.587 145.790 130.398 1.00 52.64 S ATOM 25486 SG CYS K 148 46.614 136.301 121.360 1.00 32.31 S ATOM 24762 SG CYS K 53 52.413 134.051 122.487 1.00 29.10 S ATOM 24756 SG CYS K 52 50.710 134.767 116.487 1.00 30.16 S ATOM 25260 SG CYS K 117 47.630 130.322 120.168 1.00 23.69 S Time building chain proxies: 5.49, per 1000 atoms: 0.18 Number of scatterers: 31027 At special positions: 0 Unit cell: (164.32, 189.28, 174.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 12 26.01 S 174 16.00 P 6 15.00 O 5425 8.00 N 4894 7.00 C 20516 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.74 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 I 202 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 73 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 106 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 109 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 103 " pdb=" SF4 I 203 " pdb="FE3 SF4 I 203 " - pdb=" SG CYS I 63 " pdb="FE1 SF4 I 203 " - pdb=" SG CYS I 66 " pdb="FE4 SF4 I 203 " - pdb=" SG CYS I 113 " pdb="FE2 SF4 I 203 " - pdb=" SG CYS I 69 " pdb=" SF4 K 301 " pdb="FE1 SF4 K 301 " - pdb=" SG CYS K 148 " pdb="FE2 SF4 K 301 " - pdb=" SG CYS K 53 " pdb="FE4 SF4 K 301 " - pdb=" SG CYS K 117 " pdb="FE3 SF4 K 301 " - pdb=" SG CYS K 52 " Number of angles added : 36 7670 Ramachandran restraints generated. 3835 Oldfield, 0 Emsley, 3835 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7136 Finding SS restraints... Secondary structure from input PDB file: 167 helices and 18 sheets defined 63.2% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 6 through 17 Processing helix chain 'A' and resid 21 through 30 Processing helix chain 'A' and resid 30 through 60 removed outlier: 4.148A pdb=" N MET A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 74 through 86 removed outlier: 3.957A pdb=" N LEU A 83 " --> pdb=" O ASP A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 113 Proline residue: A 103 - end of helix Proline residue: A 109 - end of helix Processing helix chain 'A' and resid 114 through 116 No H-bonds generated for 'chain 'A' and resid 114 through 116' Processing helix chain 'A' and resid 131 through 140 Processing helix chain 'A' and resid 141 through 152 removed outlier: 3.724A pdb=" N GLY A 145 " --> pdb=" O ILE A 141 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LEU A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 170 Processing helix chain 'A' and resid 172 through 188 removed outlier: 3.511A pdb=" N LEU A 176 " --> pdb=" O TYR A 172 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL A 183 " --> pdb=" O ALA A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 198 Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.064A pdb=" N ARG A 211 " --> pdb=" O TRP A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 224 removed outlier: 3.835A pdb=" N LEU A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 276 removed outlier: 3.733A pdb=" N TYR A 262 " --> pdb=" O TYR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.537A pdb=" N ILE A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 332 removed outlier: 3.960A pdb=" N TRP A 330 " --> pdb=" O ILE A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 346 Processing helix chain 'A' and resid 347 through 366 Processing helix chain 'B' and resid 15 through 35 Processing helix chain 'B' and resid 36 through 41 removed outlier: 3.773A pdb=" N ARG B 41 " --> pdb=" O GLN B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 63 removed outlier: 3.580A pdb=" N ILE B 59 " --> pdb=" O ILE B 55 " (cutoff:3.500A) Proline residue: B 60 - end of helix removed outlier: 4.110A pdb=" N THR B 63 " --> pdb=" O ILE B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 98 Processing helix chain 'B' and resid 99 through 105 removed outlier: 3.597A pdb=" N GLU B 103 " --> pdb=" O ILE B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 128 removed outlier: 3.888A pdb=" N PHE B 112 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY B 128 " --> pdb=" O MET B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 151 Processing helix chain 'B' and resid 156 through 188 removed outlier: 3.600A pdb=" N ILE B 169 " --> pdb=" O LYS B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 201 Processing helix chain 'B' and resid 207 through 224 removed outlier: 4.139A pdb=" N LYS B 222 " --> pdb=" O GLY B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 239 removed outlier: 4.612A pdb=" N ASP B 234 " --> pdb=" O GLN B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 264 removed outlier: 4.034A pdb=" N SER B 251 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N LYS B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR B 264 " --> pdb=" O ILE B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 293 removed outlier: 3.718A pdb=" N VAL B 292 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA B 293 " --> pdb=" O GLY B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 321 removed outlier: 3.834A pdb=" N GLY B 317 " --> pdb=" O PHE B 313 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 320 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLY B 321 " --> pdb=" O GLY B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 355 removed outlier: 3.745A pdb=" N PHE B 338 " --> pdb=" O LEU B 334 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG B 353 " --> pdb=" O LEU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 363 removed outlier: 3.557A pdb=" N ALA B 363 " --> pdb=" O SER B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 385 Processing helix chain 'B' and resid 389 through 404 removed outlier: 3.958A pdb=" N PHE B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLY B 402 " --> pdb=" O LEU B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 434 removed outlier: 3.857A pdb=" N TYR B 423 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N TYR B 424 " --> pdb=" O ILE B 420 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL B 428 " --> pdb=" O TYR B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 440 removed outlier: 3.636A pdb=" N MET B 440 " --> pdb=" O PRO B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 446 Processing helix chain 'B' and resid 456 through 474 Processing helix chain 'B' and resid 478 through 487 removed outlier: 3.536A pdb=" N THR B 487 " --> pdb=" O ASN B 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 43 removed outlier: 4.025A pdb=" N GLY C 24 " --> pdb=" O GLU C 20 " (cutoff:3.500A) Proline residue: C 33 - end of helix removed outlier: 3.699A pdb=" N LEU C 43 " --> pdb=" O ALA C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 72 through 97 removed outlier: 3.644A pdb=" N ALA C 78 " --> pdb=" O TYR C 74 " (cutoff:3.500A) Proline residue: C 93 - end of helix Processing helix chain 'C' and resid 102 through 126 Processing helix chain 'D' and resid 5 through 19 removed outlier: 3.562A pdb=" N THR D 9 " --> pdb=" O PRO D 5 " (cutoff:3.500A) Proline residue: D 14 - end of helix Processing helix chain 'D' and resid 31 through 57 Processing helix chain 'D' and resid 88 through 106 Processing helix chain 'D' and resid 112 through 133 removed outlier: 4.407A pdb=" N GLY D 126 " --> pdb=" O ALA D 122 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE D 128 " --> pdb=" O TYR D 124 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ALA D 129 " --> pdb=" O GLY D 125 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL D 130 " --> pdb=" O GLY D 126 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE D 131 " --> pdb=" O GLN D 127 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL D 133 " --> pdb=" O ALA D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 145 Processing helix chain 'D' and resid 146 through 156 removed outlier: 3.657A pdb=" N VAL D 150 " --> pdb=" O GLU D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 189 removed outlier: 4.231A pdb=" N PHE D 179 " --> pdb=" O GLY D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 203 Processing helix chain 'D' and resid 209 through 226 removed outlier: 3.522A pdb=" N LEU D 213 " --> pdb=" O GLY D 209 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 241 removed outlier: 4.470A pdb=" N ASP D 237 " --> pdb=" O THR D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 252 Processing helix chain 'D' and resid 260 through 265 Processing helix chain 'D' and resid 270 through 299 removed outlier: 3.839A pdb=" N LYS D 276 " --> pdb=" O ALA D 272 " (cutoff:3.500A) Proline residue: D 279 - end of helix Processing helix chain 'D' and resid 301 through 313 Processing helix chain 'D' and resid 314 through 323 Processing helix chain 'D' and resid 325 through 358 removed outlier: 4.093A pdb=" N GLY D 340 " --> pdb=" O MET D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 371 removed outlier: 3.566A pdb=" N GLN D 370 " --> pdb=" O GLY D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 387 Processing helix chain 'D' and resid 392 through 407 removed outlier: 4.188A pdb=" N VAL D 396 " --> pdb=" O MET D 392 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA D 397 " --> pdb=" O SER D 393 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU D 398 " --> pdb=" O GLY D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 423 Processing helix chain 'D' and resid 424 through 442 removed outlier: 3.832A pdb=" N ILE D 428 " --> pdb=" O ALA D 424 " (cutoff:3.500A) Proline residue: D 431 - end of helix removed outlier: 3.984A pdb=" N LEU D 438 " --> pdb=" O LEU D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 452 Processing helix chain 'D' and resid 460 through 480 Proline residue: D 473 - end of helix Processing helix chain 'D' and resid 481 through 500 removed outlier: 3.650A pdb=" N GLN D 486 " --> pdb=" O LYS D 482 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ILE D 487 " --> pdb=" O LEU D 483 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TYR D 488 " --> pdb=" O LEU D 484 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ALA D 490 " --> pdb=" O GLN D 486 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N THR D 491 " --> pdb=" O ILE D 487 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA D 497 " --> pdb=" O GLY D 493 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 22 removed outlier: 4.425A pdb=" N GLY E 20 " --> pdb=" O ILE E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 52 removed outlier: 3.503A pdb=" N VAL E 30 " --> pdb=" O ASN E 26 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU E 31 " --> pdb=" O ALA E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 88 removed outlier: 3.545A pdb=" N VAL E 61 " --> pdb=" O ILE E 57 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA E 72 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 96 Processing helix chain 'F' and resid 3 through 7 Processing helix chain 'F' and resid 9 through 28 Proline residue: F 15 - end of helix removed outlier: 3.578A pdb=" N VAL F 22 " --> pdb=" O GLY F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 34 removed outlier: 3.786A pdb=" N SER F 34 " --> pdb=" O SER F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 64 removed outlier: 4.273A pdb=" N GLY F 53 " --> pdb=" O ALA F 49 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N LEU F 56 " --> pdb=" O MET F 52 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR F 57 " --> pdb=" O GLY F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 115 removed outlier: 4.019A pdb=" N GLY F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 118 No H-bonds generated for 'chain 'F' and resid 116 through 118' Processing helix chain 'F' and resid 121 through 140 removed outlier: 3.747A pdb=" N VAL F 140 " --> pdb=" O LEU F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 163 removed outlier: 4.705A pdb=" N TRP F 151 " --> pdb=" O VAL F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 200 removed outlier: 3.710A pdb=" N ALA F 172 " --> pdb=" O ARG F 168 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY F 185 " --> pdb=" O THR F 181 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N GLY F 188 " --> pdb=" O VAL F 184 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LEU F 191 " --> pdb=" O PHE F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 218 removed outlier: 3.591A pdb=" N ASP F 210 " --> pdb=" O ALA F 206 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU F 212 " --> pdb=" O MET F 208 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR F 213 " --> pdb=" O GLY F 209 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR F 218 " --> pdb=" O GLU F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 241 removed outlier: 3.992A pdb=" N GLY F 236 " --> pdb=" O LEU F 232 " (cutoff:3.500A) Proline residue: F 237 - end of helix Processing helix chain 'F' and resid 251 through 256 removed outlier: 3.657A pdb=" N GLY F 256 " --> pdb=" O ALA F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 267 removed outlier: 4.118A pdb=" N HIS F 265 " --> pdb=" O SER F 261 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA F 266 " --> pdb=" O ALA F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 280 Processing helix chain 'F' and resid 280 through 285 Processing helix chain 'F' and resid 287 through 312 removed outlier: 4.000A pdb=" N ILE F 310 " --> pdb=" O ALA F 306 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N THR F 311 " --> pdb=" O THR F 307 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN F 312 " --> pdb=" O ILE F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 336 removed outlier: 3.623A pdb=" N LEU F 319 " --> pdb=" O ILE F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 349 Processing helix chain 'F' and resid 352 through 369 removed outlier: 3.597A pdb=" N GLY F 369 " --> pdb=" O HIS F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 379 Processing helix chain 'F' and resid 380 through 384 Processing helix chain 'F' and resid 386 through 391 removed outlier: 4.277A pdb=" N TYR F 390 " --> pdb=" O GLY F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 391 through 407 removed outlier: 5.008A pdb=" N GLY F 401 " --> pdb=" O THR F 397 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ALA F 404 " --> pdb=" O VAL F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 413 through 426 removed outlier: 3.684A pdb=" N LYS F 417 " --> pdb=" O GLY F 413 " (cutoff:3.500A) Processing helix chain 'F' and resid 428 through 455 removed outlier: 3.789A pdb=" N LEU F 433 " --> pdb=" O PRO F 429 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU F 434 " --> pdb=" O ALA F 430 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU F 455 " --> pdb=" O PHE F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 483 through 495 Proline residue: F 489 - end of helix removed outlier: 3.724A pdb=" N ILE F 495 " --> pdb=" O VAL F 491 " (cutoff:3.500A) Processing helix chain 'F' and resid 499 through 505 removed outlier: 3.636A pdb=" N VAL F 503 " --> pdb=" O ILE F 500 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY F 504 " --> pdb=" O GLY F 501 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR F 505 " --> pdb=" O PHE F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 509 through 515 removed outlier: 3.613A pdb=" N VAL F 513 " --> pdb=" O ASN F 509 " (cutoff:3.500A) Processing helix chain 'F' and resid 532 through 556 removed outlier: 3.966A pdb=" N VAL F 541 " --> pdb=" O GLY F 537 " (cutoff:3.500A) Processing helix chain 'F' and resid 563 through 569 Processing helix chain 'F' and resid 569 through 578 Processing helix chain 'F' and resid 581 through 589 Processing helix chain 'F' and resid 590 through 619 removed outlier: 3.907A pdb=" N VAL F 609 " --> pdb=" O ASP F 605 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASP F 610 " --> pdb=" O TYR F 606 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 631 removed outlier: 3.529A pdb=" N LEU F 630 " --> pdb=" O LEU F 627 " (cutoff:3.500A) Processing helix chain 'F' and resid 634 through 654 Processing helix chain 'G' and resid 3 through 28 Processing helix chain 'G' and resid 31 through 53 removed outlier: 4.174A pdb=" N GLY G 40 " --> pdb=" O ALA G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 66 Processing helix chain 'G' and resid 69 through 81 Processing helix chain 'G' and resid 92 through 118 removed outlier: 3.709A pdb=" N ARG G 96 " --> pdb=" O GLY G 92 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLY G 99 " --> pdb=" O LEU G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 139 removed outlier: 3.873A pdb=" N THR G 134 " --> pdb=" O ASP G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 165 removed outlier: 3.921A pdb=" N SER G 151 " --> pdb=" O PHE G 147 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL G 152 " --> pdb=" O GLU G 148 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA G 165 " --> pdb=" O ALA G 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 56 removed outlier: 3.933A pdb=" N GLU H 56 " --> pdb=" O GLU H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 64 Processing helix chain 'H' and resid 74 through 83 removed outlier: 4.324A pdb=" N ASN H 78 " --> pdb=" O ALA H 74 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU H 79 " --> pdb=" O GLY H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 91 removed outlier: 3.642A pdb=" N LEU H 89 " --> pdb=" O ALA H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 125 Proline residue: H 120 - end of helix Processing helix chain 'H' and resid 130 through 149 removed outlier: 3.884A pdb=" N PHE H 135 " --> pdb=" O PHE H 131 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG H 136 " --> pdb=" O PHE H 132 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU H 137 " --> pdb=" O TYR H 133 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA H 147 " --> pdb=" O ASP H 143 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA H 148 " --> pdb=" O LEU H 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 196 Proline residue: H 185 - end of helix removed outlier: 4.069A pdb=" N ASP H 188 " --> pdb=" O LEU H 184 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE H 194 " --> pdb=" O TYR H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 205 Processing helix chain 'H' and resid 211 through 218 Processing helix chain 'H' and resid 222 through 227 Processing helix chain 'H' and resid 233 through 238 Processing helix chain 'H' and resid 257 through 282 removed outlier: 3.687A pdb=" N LYS H 274 " --> pdb=" O ARG H 270 " (cutoff:3.500A) Processing helix chain 'H' and resid 287 through 298 Processing helix chain 'H' and resid 306 through 310 removed outlier: 3.577A pdb=" N TYR H 309 " --> pdb=" O GLY H 306 " (cutoff:3.500A) Processing helix chain 'H' and resid 365 through 370 Processing helix chain 'H' and resid 377 through 386 removed outlier: 4.210A pdb=" N ASP H 386 " --> pdb=" O LEU H 382 " (cutoff:3.500A) Processing helix chain 'H' and resid 388 through 394 Processing helix chain 'I' and resid 4 through 28 removed outlier: 3.630A pdb=" N ASN I 9 " --> pdb=" O ASN I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 72 Processing helix chain 'I' and resid 107 through 112 Processing helix chain 'I' and resid 130 through 133 Processing helix chain 'I' and resid 147 through 151 removed outlier: 3.770A pdb=" N ASP I 151 " --> pdb=" O VAL I 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 186 through 191 Processing helix chain 'J' and resid 15 through 20 Processing helix chain 'J' and resid 42 through 44 No H-bonds generated for 'chain 'J' and resid 42 through 44' Processing helix chain 'J' and resid 45 through 55 removed outlier: 3.672A pdb=" N GLN J 51 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 116 through 129 removed outlier: 3.896A pdb=" N GLN J 120 " --> pdb=" O THR J 116 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG J 122 " --> pdb=" O ASP J 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 41 Processing helix chain 'K' and resid 52 through 62 removed outlier: 4.020A pdb=" N GLU K 56 " --> pdb=" O CYS K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 71 removed outlier: 3.646A pdb=" N PHE K 70 " --> pdb=" O PHE K 67 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 104 Processing helix chain 'K' and resid 115 through 120 Processing helix chain 'K' and resid 121 through 125 removed outlier: 3.766A pdb=" N SER K 125 " --> pdb=" O GLY K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 134 through 138 Processing helix chain 'K' and resid 151 through 167 removed outlier: 3.741A pdb=" N VAL K 160 " --> pdb=" O MET K 156 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 22 Processing helix chain 'L' and resid 22 through 33 Processing helix chain 'L' and resid 40 through 54 Processing helix chain 'L' and resid 54 through 62 Processing helix chain 'L' and resid 63 through 65 No H-bonds generated for 'chain 'L' and resid 63 through 65' Processing helix chain 'M' and resid 42 through 60 Processing helix chain 'M' and resid 66 through 87 Processing helix chain 'N' and resid 7 through 17 removed outlier: 3.718A pdb=" N LYS N 11 " --> pdb=" O TYR N 7 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 40 Processing helix chain 'N' and resid 48 through 52 removed outlier: 3.509A pdb=" N GLY N 51 " --> pdb=" O SER N 48 " (cutoff:3.500A) Processing helix chain 'N' and resid 54 through 59 Processing helix chain 'N' and resid 82 through 90 Processing helix chain 'N' and resid 109 through 123 removed outlier: 3.514A pdb=" N LEU N 123 " --> pdb=" O LEU N 119 " (cutoff:3.500A) Processing helix chain 'O' and resid 12 through 17 Processing helix chain 'P' and resid 6 through 26 removed outlier: 4.383A pdb=" N ILE P 10 " --> pdb=" O SER P 6 " (cutoff:3.500A) Proline residue: P 16 - end of helix Processing helix chain 'Q' and resid 17 through 42 Processing sheet with id=AA1, first strand: chain 'C' and resid 67 through 69 removed outlier: 6.053A pdb=" N ILE C 68 " --> pdb=" O ARG H 7 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'D' and resid 65 through 73 removed outlier: 4.562A pdb=" N TRP D 67 " --> pdb=" O VAL D 82 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL D 82 " --> pdb=" O TRP D 67 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER D 69 " --> pdb=" O TRP D 80 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N TRP D 80 " --> pdb=" O SER D 69 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ASP D 71 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N LEU D 78 " --> pdb=" O ASP D 71 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 69 through 76 removed outlier: 6.892A pdb=" N ILE F 83 " --> pdb=" O TRP F 75 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 27 through 30 Processing sheet with id=AA5, first strand: chain 'H' and resid 159 through 160 Processing sheet with id=AA6, first strand: chain 'H' and resid 327 through 331 Processing sheet with id=AA7, first strand: chain 'I' and resid 56 through 57 removed outlier: 6.224A pdb=" N VAL I 120 " --> pdb=" O LEU S 87 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N THR S 89 " --> pdb=" O VAL I 120 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N LYS S 74 " --> pdb=" O ILE S 70 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ILE S 70 " --> pdb=" O LYS S 74 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ALA S 76 " --> pdb=" O GLN S 68 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU S 96 " --> pdb=" O LYS S 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 79 through 82 removed outlier: 6.825A pdb=" N VAL I 79 " --> pdb=" O TYR I 96 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR I 96 " --> pdb=" O VAL I 79 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ASP I 81 " --> pdb=" O LYS I 94 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 30 through 31 removed outlier: 4.137A pdb=" N GLY J 30 " --> pdb=" O MET J 38 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLU J 37 " --> pdb=" O ARG J 95 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LYS J 97 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE J 39 " --> pdb=" O LYS J 97 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N PHE J 99 " --> pdb=" O ILE J 39 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS J 80 " --> pdb=" O ARG J 62 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 30 through 31 removed outlier: 4.137A pdb=" N GLY J 30 " --> pdb=" O MET J 38 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLU J 37 " --> pdb=" O ARG J 95 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LYS J 97 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE J 39 " --> pdb=" O LYS J 97 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N PHE J 99 " --> pdb=" O ILE J 39 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 106 through 108 removed outlier: 6.820A pdb=" N VAL J 107 " --> pdb=" O GLU J 133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'K' and resid 83 through 86 removed outlier: 6.708A pdb=" N VAL K 111 " --> pdb=" O VAL K 143 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N LEU K 145 " --> pdb=" O VAL K 111 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ALA K 113 " --> pdb=" O LEU K 145 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 186 through 187 Processing sheet with id=AB5, first strand: chain 'M' and resid 16 through 17 Processing sheet with id=AB6, first strand: chain 'N' and resid 19 through 22 Processing sheet with id=AB7, first strand: chain 'N' and resid 43 through 47 Processing sheet with id=AB8, first strand: chain 'N' and resid 63 through 64 Processing sheet with id=AB9, first strand: chain 'O' and resid 59 through 62 removed outlier: 7.149A pdb=" N TYR O 47 " --> pdb=" O ILE O 43 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ILE O 43 " --> pdb=" O TYR O 47 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLN O 49 " --> pdb=" O VAL O 41 " (cutoff:3.500A) 1700 hydrogen bonds defined for protein. 4977 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.80 Time building geometry restraints manager: 3.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 12787 1.40 - 1.62: 18686 1.62 - 1.84: 306 1.84 - 2.07: 0 2.07 - 2.29: 36 Bond restraints: 31815 Sorted by residual: bond pdb=" C6 SQD N 201 " pdb=" S SQD N 201 " ideal model delta sigma weight residual 1.840 1.615 0.225 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C6 SQD B 601 " pdb=" S SQD B 601 " ideal model delta sigma weight residual 1.840 1.619 0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C6 SQD C 201 " pdb=" S SQD C 201 " ideal model delta sigma weight residual 1.840 1.624 0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C25 BCR F 701 " pdb=" C26 BCR F 701 " ideal model delta sigma weight residual 1.347 1.556 -0.209 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C25 BCR D 602 " pdb=" C26 BCR D 602 " ideal model delta sigma weight residual 1.347 1.555 -0.208 2.00e-02 2.50e+03 1.08e+02 ... (remaining 31810 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.63: 43083 7.63 - 15.25: 135 15.25 - 22.88: 12 22.88 - 30.51: 8 30.51 - 38.13: 4 Bond angle restraints: 43242 Sorted by residual: angle pdb=" C6 SQD B 601 " pdb=" S SQD B 601 " pdb=" O7 SQD B 601 " ideal model delta sigma weight residual 111.32 73.19 38.13 3.00e+00 1.11e-01 1.62e+02 angle pdb=" C6 SQD N 201 " pdb=" S SQD N 201 " pdb=" O7 SQD N 201 " ideal model delta sigma weight residual 111.32 74.36 36.96 3.00e+00 1.11e-01 1.52e+02 angle pdb=" C6 SQD C 201 " pdb=" S SQD C 201 " pdb=" O7 SQD C 201 " ideal model delta sigma weight residual 111.32 76.77 34.55 3.00e+00 1.11e-01 1.33e+02 angle pdb=" C6 SQD B 601 " pdb=" S SQD B 601 " pdb=" O9 SQD B 601 " ideal model delta sigma weight residual 111.28 141.92 -30.64 3.00e+00 1.11e-01 1.04e+02 angle pdb=" C6 SQD C 201 " pdb=" S SQD C 201 " pdb=" O9 SQD C 201 " ideal model delta sigma weight residual 111.28 141.77 -30.49 3.00e+00 1.11e-01 1.03e+02 ... (remaining 43237 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.27: 17342 24.27 - 48.53: 1023 48.53 - 72.80: 127 72.80 - 97.06: 25 97.06 - 121.33: 10 Dihedral angle restraints: 18527 sinusoidal: 7366 harmonic: 11161 Sorted by residual: dihedral pdb=" CA LYS F 457 " pdb=" C LYS F 457 " pdb=" N PHE F 458 " pdb=" CA PHE F 458 " ideal model delta harmonic sigma weight residual -180.00 -150.14 -29.86 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA ILE B 68 " pdb=" C ILE B 68 " pdb=" N SER B 69 " pdb=" CA SER B 69 " ideal model delta harmonic sigma weight residual -180.00 -150.78 -29.22 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA GLY F 558 " pdb=" C GLY F 558 " pdb=" N THR F 559 " pdb=" CA THR F 559 " ideal model delta harmonic sigma weight residual 180.00 -151.30 -28.70 0 5.00e+00 4.00e-02 3.29e+01 ... (remaining 18524 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 4688 0.115 - 0.229: 250 0.229 - 0.344: 13 0.344 - 0.459: 1 0.459 - 0.573: 1 Chirality restraints: 4953 Sorted by residual: chirality pdb=" C5' LMT D 603 " pdb=" C4' LMT D 603 " pdb=" C6' LMT D 603 " pdb=" O5' LMT D 603 " both_signs ideal model delta sigma weight residual False -2.51 -1.93 -0.57 2.00e-01 2.50e+01 8.22e+00 chirality pdb=" C1 LMG F 704 " pdb=" C2 LMG F 704 " pdb=" O1 LMG F 704 " pdb=" O6 LMG F 704 " both_signs ideal model delta sigma weight residual False 2.29 2.64 -0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" C3 LMG F 704 " pdb=" C2 LMG F 704 " pdb=" C4 LMG F 704 " pdb=" O3 LMG F 704 " both_signs ideal model delta sigma weight residual False 2.40 2.70 -0.30 2.00e-01 2.50e+01 2.27e+00 ... (remaining 4950 not shown) Planarity restraints: 5317 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 BCR D 602 " 0.502 2.00e-02 2.50e+03 2.92e-01 1.07e+03 pdb=" C11 BCR D 602 " -0.247 2.00e-02 2.50e+03 pdb=" C34 BCR D 602 " 0.109 2.00e-02 2.50e+03 pdb=" C8 BCR D 602 " -0.045 2.00e-02 2.50e+03 pdb=" C9 BCR D 602 " -0.318 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C16 BCR D 602 " 0.239 2.00e-02 2.50e+03 2.90e-01 1.05e+03 pdb=" C17 BCR D 602 " -0.492 2.00e-02 2.50e+03 pdb=" C18 BCR D 602 " 0.326 2.00e-02 2.50e+03 pdb=" C19 BCR D 602 " 0.040 2.00e-02 2.50e+03 pdb=" C36 BCR D 602 " -0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 BCR F 701 " -0.357 2.00e-02 2.50e+03 2.41e-01 7.26e+02 pdb=" C11 BCR F 701 " 0.176 2.00e-02 2.50e+03 pdb=" C34 BCR F 701 " -0.160 2.00e-02 2.50e+03 pdb=" C8 BCR F 701 " 0.016 2.00e-02 2.50e+03 pdb=" C9 BCR F 701 " 0.326 2.00e-02 2.50e+03 ... (remaining 5314 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 7502 2.79 - 3.31: 28618 3.31 - 3.84: 56241 3.84 - 4.37: 67732 4.37 - 4.90: 115037 Nonbonded interactions: 275130 Sorted by model distance: nonbonded pdb=" OH TYR C 75 " pdb=" O ALA E 75 " model vdw 2.258 3.040 nonbonded pdb=" OE2 GLU H 107 " pdb=" OH TYR H 243 " model vdw 2.267 3.040 nonbonded pdb=" O ILE A 5 " pdb=" O2D DGD A 402 " model vdw 2.273 3.040 nonbonded pdb=" O ALA D 322 " pdb=" OH TYR D 411 " model vdw 2.281 3.040 nonbonded pdb=" O TYR H 190 " pdb=" OH TYR H 262 " model vdw 2.289 3.040 ... (remaining 275125 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 29.370 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.060 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:5.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 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 : 0.009 0.225 31827 Z= 0.426 Angle : 1.301 38.131 43278 Z= 0.591 Chirality : 0.058 0.573 4953 Planarity : 0.012 0.292 5317 Dihedral : 15.666 121.327 11391 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.85 % Favored : 92.13 % Rotamer: Outliers : 0.41 % Allowed : 6.71 % Favored : 92.88 % 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: -4.07 (0.10), residues: 3835 helix: -2.38 (0.08), residues: 2263 sheet: -3.15 (0.34), residues: 175 loop : -2.94 (0.14), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 62 TYR 0.049 0.003 TYR B 166 PHE 0.038 0.002 PHE K 67 TRP 0.031 0.002 TRP B 274 HIS 0.014 0.002 HIS D 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00916 / 0.43 (31815) covalent geometry : angle 1.29985 / 0.59 (43242) hydrogen bonds : bond 0.15174 / 10.14 ( 1693) hydrogen bonds : angle 7.09257 / 5.06 ( 4977) metal coordination : bond 0.01901 / 1.24 ( 12) metal coordination : angle 2.29674 / 1.43 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7670 Ramachandran restraints generated. 3835 Oldfield, 0 Emsley, 3835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7670 Ramachandran restraints generated. 3835 Oldfield, 0 Emsley, 3835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 533 time to evaluate : 1.197 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 232 PHE cc_start: 0.7033 (OUTLIER) cc_final: 0.5228 (m-80) REVERT: A 338 ASP cc_start: 0.7542 (p0) cc_final: 0.7087 (p0) REVERT: B 237 GLU cc_start: 0.8145 (tt0) cc_final: 0.7872 (tt0) REVERT: B 361 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8080 (mm-30) REVERT: D 89 MET cc_start: 0.8239 (tpt) cc_final: 0.7950 (tpt) REVERT: F 530 LEU cc_start: 0.6719 (tp) cc_final: 0.6490 (tp) REVERT: G 53 MET cc_start: 0.8941 (ptp) cc_final: 0.8685 (ptm) REVERT: G 113 LYS cc_start: 0.8353 (tttm) cc_final: 0.8141 (ttmm) REVERT: I 13 GLU cc_start: 0.7429 (tp30) cc_final: 0.7224 (tp30) REVERT: I 130 ASP cc_start: 0.8760 (t0) cc_final: 0.8530 (t70) REVERT: J 22 GLN cc_start: 0.7870 (pt0) cc_final: 0.7669 (pt0) REVERT: J 143 MET cc_start: 0.8881 (mmm) cc_final: 0.8634 (mmm) REVERT: K 172 ASN cc_start: 0.7184 (m-40) cc_final: 0.6860 (t0) REVERT: L 12 VAL cc_start: 0.8560 (p) cc_final: 0.8305 (t) REVERT: M 87 GLN cc_start: 0.8289 (mt0) cc_final: 0.7900 (mt0) REVERT: O 15 LYS cc_start: 0.8376 (tptp) cc_final: 0.8164 (mmmt) REVERT: Q 10 MET cc_start: 0.7970 (mmt) cc_final: 0.7691 (mpt) REVERT: S 43 MET cc_start: 0.2683 (ttt) cc_final: 0.2293 (ttp) outliers start: 13 outliers final: 4 residues processed: 544 average time/residue: 0.6930 time to fit residues: 443.2732 Evaluate side-chains 343 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 338 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain P residue 29 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.0570 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.9980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 199 GLN D 163 GLN ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN D 274 HIS D 288 ASN D 335 GLN D 453 HIS E 39 ASN E 44 ASN F 182 ASN F 217 ASN F 374 ASN G 71 ASN G 138 HIS H 18 HIS H 48 HIS ** H 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 156 ASN H 157 ASN H 217 ASN H 267 GLN H 290 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 95 HIS I 135 ASN J 165 GLN K 32 ASN K 179 GLN K 200 GLN K 203 ASN L 70 GLN M 95 ASN N 90 ASN N 118 GLN O 18 ASN P 36 GLN S 55 ASN S 64 GLN S 83 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.100665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.082800 restraints weight = 54176.791| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.70 r_work: 0.2985 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 31827 Z= 0.142 Angle : 0.711 17.323 43278 Z= 0.339 Chirality : 0.042 0.270 4953 Planarity : 0.006 0.068 5317 Dihedral : 10.075 89.353 4584 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.09 % Favored : 92.88 % Rotamer: Outliers : 2.13 % Allowed : 13.46 % Favored : 84.41 % 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: -1.92 (0.13), residues: 3835 helix: -0.43 (0.10), residues: 2276 sheet: -2.54 (0.37), residues: 170 loop : -2.44 (0.16), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 107 TYR 0.024 0.001 TYR F 445 PHE 0.021 0.001 PHE H 131 TRP 0.023 0.001 TRP B 274 HIS 0.007 0.001 HIS N 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (31815) covalent geometry : angle 0.68051 / 0.34 (43242) hydrogen bonds : bond 0.04184 / 2.74 ( 1693) hydrogen bonds : angle 4.84505 / 3.43 ( 4977) metal coordination : bond 0.00880 / 0.56 ( 12) metal coordination : angle 7.12498 / 4.61 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7670 Ramachandran restraints generated. 3835 Oldfield, 0 Emsley, 3835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7670 Ramachandran restraints generated. 3835 Oldfield, 0 Emsley, 3835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 404 time to evaluate : 1.142 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 173 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8231 (mt-10) REVERT: A 232 PHE cc_start: 0.7173 (OUTLIER) cc_final: 0.5326 (m-80) REVERT: A 338 ASP cc_start: 0.8184 (p0) cc_final: 0.7813 (p0) REVERT: B 131 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7949 (tp30) REVERT: B 436 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.8059 (mt-10) REVERT: C 20 GLU cc_start: 0.8470 (pm20) cc_final: 0.8202 (pm20) REVERT: D 89 MET cc_start: 0.8782 (tpt) cc_final: 0.8461 (tpt) REVERT: D 392 MET cc_start: 0.9014 (mtp) cc_final: 0.8792 (mtt) REVERT: F 457 LYS cc_start: 0.7774 (ptpp) cc_final: 0.7113 (pttm) REVERT: G 83 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7760 (mmtt) REVERT: G 113 LYS cc_start: 0.8895 (tttm) cc_final: 0.8525 (ttmm) REVERT: G 123 SER cc_start: 0.8561 (m) cc_final: 0.8231 (p) REVERT: I 67 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7534 (mp0) REVERT: I 130 ASP cc_start: 0.8996 (t0) cc_final: 0.8792 (t70) REVERT: I 141 MET cc_start: 0.9179 (ptm) cc_final: 0.8975 (ptm) REVERT: J 22 GLN cc_start: 0.7844 (pt0) cc_final: 0.7591 (pt0) REVERT: K 24 GLU cc_start: 0.6153 (tp30) cc_final: 0.5462 (mp0) REVERT: K 172 ASN cc_start: 0.7464 (m-40) cc_final: 0.7015 (t0) REVERT: M 87 GLN cc_start: 0.8675 (mt0) cc_final: 0.8307 (mt0) REVERT: N 104 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7851 (m-30) REVERT: Q 10 MET cc_start: 0.8195 (mmt) cc_final: 0.7266 (mmt) REVERT: S 43 MET cc_start: 0.2350 (ttt) cc_final: 0.1997 (ttp) outliers start: 68 outliers final: 16 residues processed: 450 average time/residue: 0.6355 time to fit residues: 340.3484 Evaluate side-chains 361 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 338 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain F residue 382 ARG Chi-restraints excluded: chain G residue 83 LYS Chi-restraints excluded: chain H residue 36 ASP Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 67 GLU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 157 ILE Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain N residue 104 ASP Chi-restraints excluded: chain P residue 14 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 142 optimal weight: 0.7980 chunk 254 optimal weight: 0.8980 chunk 208 optimal weight: 7.9990 chunk 327 optimal weight: 0.5980 chunk 124 optimal weight: 0.9990 chunk 206 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 275 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 453 HIS ** H 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 205 GLN H 267 GLN K 25 ASN K 200 GLN ** M 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 23 HIS N 118 GLN O 18 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.098876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.080865 restraints weight = 55079.402| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.72 r_work: 0.2940 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 31827 Z= 0.139 Angle : 0.684 18.337 43278 Z= 0.322 Chirality : 0.042 0.232 4953 Planarity : 0.005 0.068 5317 Dihedral : 9.294 85.648 4580 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.67 % Favored : 92.31 % Rotamer: Outliers : 2.98 % Allowed : 14.27 % Favored : 82.75 % 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: -1.00 (0.13), residues: 3835 helix: 0.36 (0.11), residues: 2296 sheet: -2.37 (0.36), residues: 172 loop : -2.18 (0.16), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 498 TYR 0.022 0.001 TYR F 445 PHE 0.015 0.001 PHE A 321 TRP 0.021 0.001 TRP B 274 HIS 0.005 0.001 HIS D 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (31815) covalent geometry : angle 0.64530 / 0.32 (43242) hydrogen bonds : bond 0.03970 / 2.58 ( 1693) hydrogen bonds : angle 4.51636 / 3.21 ( 4977) metal coordination : bond 0.00924 / 0.64 ( 12) metal coordination : angle 7.86012 / 4.96 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7670 Ramachandran restraints generated. 3835 Oldfield, 0 Emsley, 3835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7670 Ramachandran restraints generated. 3835 Oldfield, 0 Emsley, 3835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 378 time to evaluate : 1.239 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8084 (mt) REVERT: A 232 PHE cc_start: 0.7011 (OUTLIER) cc_final: 0.5056 (m-80) REVERT: B 131 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8102 (tp30) REVERT: B 436 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.8069 (mt-10) REVERT: C 20 GLU cc_start: 0.8615 (pm20) cc_final: 0.8324 (pm20) REVERT: C 60 MET cc_start: 0.7532 (ptp) cc_final: 0.7332 (ptp) REVERT: D 89 MET cc_start: 0.8800 (tpt) cc_final: 0.8460 (tpt) REVERT: F 457 LYS cc_start: 0.7860 (ptpp) cc_final: 0.7152 (pttm) REVERT: F 458 PHE cc_start: 0.8152 (t80) cc_final: 0.7489 (t80) REVERT: F 610 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.8188 (m-30) REVERT: G 53 MET cc_start: 0.8856 (mtm) cc_final: 0.8582 (mtm) REVERT: G 113 LYS cc_start: 0.8878 (tttm) cc_final: 0.8507 (ttmm) REVERT: G 123 SER cc_start: 0.8606 (m) cc_final: 0.8332 (p) REVERT: I 67 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7355 (mp0) REVERT: I 141 MET cc_start: 0.9205 (ptm) cc_final: 0.8983 (ptm) REVERT: I 150 GLN cc_start: 0.7981 (mm-40) cc_final: 0.7663 (mt0) REVERT: J 22 GLN cc_start: 0.7761 (pt0) cc_final: 0.7511 (pt0) REVERT: K 172 ASN cc_start: 0.7359 (m-40) cc_final: 0.6938 (t0) REVERT: L 27 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8421 (mp) REVERT: L 66 ASN cc_start: 0.9222 (t0) cc_final: 0.8895 (t0) REVERT: L 72 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.6198 (ttt-90) REVERT: M 87 GLN cc_start: 0.8652 (mt0) cc_final: 0.8343 (mt0) REVERT: N 104 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7911 (m-30) REVERT: N 141 GLU cc_start: 0.7406 (mt-10) cc_final: 0.7200 (mm-30) REVERT: O 14 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7951 (pm20) REVERT: O 15 LYS cc_start: 0.9100 (mmmt) cc_final: 0.8853 (mmmt) REVERT: Q 10 MET cc_start: 0.8229 (mmt) cc_final: 0.7402 (mmt) REVERT: S 43 MET cc_start: 0.2246 (ttt) cc_final: 0.1937 (ttp) outliers start: 95 outliers final: 27 residues processed: 442 average time/residue: 0.6186 time to fit residues: 326.7544 Evaluate side-chains 380 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 343 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 304 MET Chi-restraints excluded: chain F residue 382 ARG Chi-restraints excluded: chain F residue 610 ASP Chi-restraints excluded: chain H residue 36 ASP Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 67 GLU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain J residue 62 ARG Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 72 ARG Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 97 ARG Chi-restraints excluded: chain N residue 61 GLN Chi-restraints excluded: chain N residue 104 ASP Chi-restraints excluded: chain O residue 14 GLU Chi-restraints excluded: chain Q residue 3 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 122 optimal weight: 3.9990 chunk 208 optimal weight: 0.9980 chunk 1 optimal weight: 7.9990 chunk 136 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 279 optimal weight: 2.9990 chunk 273 optimal weight: 2.9990 chunk 219 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 HIS B 340 ASN ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 453 HIS F 62 GLN ** F 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 239 HIS ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 25 ASN K 181 HIS K 200 GLN N 90 ASN N 118 GLN O 18 ASN P 36 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.096344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.078193 restraints weight = 54903.302| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.70 r_work: 0.2892 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 31827 Z= 0.196 Angle : 0.712 21.623 43278 Z= 0.336 Chirality : 0.044 0.272 4953 Planarity : 0.005 0.067 5317 Dihedral : 9.052 88.962 4580 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.64 % Favored : 92.33 % Rotamer: Outliers : 3.32 % Allowed : 15.46 % Favored : 81.21 % 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: -0.61 (0.14), residues: 3835 helix: 0.68 (0.11), residues: 2283 sheet: -2.19 (0.37), residues: 174 loop : -2.00 (0.17), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 167 TYR 0.018 0.002 TYR K 35 PHE 0.019 0.001 PHE F 131 TRP 0.024 0.001 TRP B 274 HIS 0.007 0.001 HIS M 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.20 (31815) covalent geometry : angle 0.67340 / 0.34 (43242) hydrogen bonds : bond 0.04149 / 2.70 ( 1693) hydrogen bonds : angle 4.47868 / 3.19 ( 4977) metal coordination : bond 0.01304 / 0.85 ( 12) metal coordination : angle 8.04001 / 5.03 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7670 Ramachandran restraints generated. 3835 Oldfield, 0 Emsley, 3835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7670 Ramachandran restraints generated. 3835 Oldfield, 0 Emsley, 3835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 365 time to evaluate : 1.081 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8299 (tp30) REVERT: A 293 LEU cc_start: 0.8583 (mt) cc_final: 0.8362 (mt) REVERT: A 346 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8687 (mmtp) REVERT: A 358 LEU cc_start: 0.8947 (tm) cc_final: 0.8742 (tp) REVERT: A 364 LEU cc_start: 0.9037 (tp) cc_final: 0.8828 (tp) REVERT: B 131 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8056 (tp30) REVERT: C 20 GLU cc_start: 0.8655 (pm20) cc_final: 0.8380 (pm20) REVERT: C 60 MET cc_start: 0.7649 (ptp) cc_final: 0.7419 (ptp) REVERT: D 448 LYS cc_start: 0.7834 (pmtt) cc_final: 0.7230 (mptt) REVERT: E 89 ASP cc_start: 0.8243 (t0) cc_final: 0.7942 (t0) REVERT: F 108 MET cc_start: 0.9195 (mtp) cc_final: 0.8927 (mtt) REVERT: F 255 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7874 (mp0) REVERT: F 458 PHE cc_start: 0.8128 (t80) cc_final: 0.7489 (t80) REVERT: F 559 THR cc_start: 0.7133 (OUTLIER) cc_final: 0.6723 (m) REVERT: F 610 ASP cc_start: 0.8461 (OUTLIER) cc_final: 0.8249 (m-30) REVERT: G 53 MET cc_start: 0.9014 (mtm) cc_final: 0.8738 (mtm) REVERT: G 113 LYS cc_start: 0.8915 (tttm) cc_final: 0.8490 (ttmm) REVERT: G 123 SER cc_start: 0.8631 (m) cc_final: 0.8329 (p) REVERT: H 387 VAL cc_start: 0.9245 (OUTLIER) cc_final: 0.9009 (t) REVERT: I 67 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7777 (mp0) REVERT: I 141 MET cc_start: 0.9247 (ptm) cc_final: 0.9023 (ptm) REVERT: I 150 GLN cc_start: 0.7997 (mm-40) cc_final: 0.7650 (mt0) REVERT: J 22 GLN cc_start: 0.7773 (pt0) cc_final: 0.7563 (pt0) REVERT: K 172 ASN cc_start: 0.7426 (m-40) cc_final: 0.7035 (t0) REVERT: L 27 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8440 (mp) REVERT: L 66 ASN cc_start: 0.9261 (t0) cc_final: 0.8918 (t0) REVERT: L 72 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.6172 (ttt-90) REVERT: M 87 GLN cc_start: 0.8664 (mt0) cc_final: 0.8336 (mt0) REVERT: N 104 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.7898 (m-30) REVERT: N 135 ASP cc_start: 0.8533 (t0) cc_final: 0.8201 (t0) REVERT: N 141 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7260 (mm-30) REVERT: O 14 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7882 (pm20) REVERT: Q 10 MET cc_start: 0.8217 (mmt) cc_final: 0.7383 (mmt) REVERT: S 43 MET cc_start: 0.2326 (ttt) cc_final: 0.1947 (ttp) outliers start: 106 outliers final: 44 residues processed: 440 average time/residue: 0.6277 time to fit residues: 330.0908 Evaluate side-chains 403 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 347 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 304 MET Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 382 ARG Chi-restraints excluded: chain F residue 559 THR Chi-restraints excluded: chain F residue 610 ASP Chi-restraints excluded: chain H residue 36 ASP Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 238 ASP Chi-restraints excluded: chain H residue 387 VAL Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 67 GLU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain J residue 62 ARG Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 157 ILE Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain K residue 181 HIS Chi-restraints excluded: chain K residue 196 ILE Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 72 ARG Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain M residue 86 MET Chi-restraints excluded: chain M residue 97 ARG Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 61 GLN Chi-restraints excluded: chain N residue 104 ASP Chi-restraints excluded: chain N residue 131 GLU Chi-restraints excluded: chain O residue 14 GLU Chi-restraints excluded: chain P residue 14 MET Chi-restraints excluded: chain Q residue 3 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 136 optimal weight: 0.6980 chunk 178 optimal weight: 0.8980 chunk 280 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 331 optimal weight: 10.0000 chunk 119 optimal weight: 0.9990 chunk 246 optimal weight: 1.9990 chunk 290 optimal weight: 0.9990 chunk 345 optimal weight: 0.9990 chunk 187 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 453 HIS G 117 GLN ** H 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 25 ASN K 181 HIS K 200 GLN ** M 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 118 GLN O 18 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.098061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.080061 restraints weight = 54880.205| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.71 r_work: 0.2920 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 31827 Z= 0.140 Angle : 0.674 21.950 43278 Z= 0.316 Chirality : 0.042 0.215 4953 Planarity : 0.005 0.067 5317 Dihedral : 8.832 89.898 4578 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.72 % Favored : 92.26 % Rotamer: Outliers : 2.89 % Allowed : 16.66 % Favored : 80.46 % 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: -0.31 (0.14), residues: 3835 helix: 0.93 (0.11), residues: 2293 sheet: -2.11 (0.37), residues: 174 loop : -1.90 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 167 TYR 0.020 0.001 TYR F 445 PHE 0.015 0.001 PHE A 321 TRP 0.022 0.001 TRP B 274 HIS 0.012 0.001 HIS K 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (31815) covalent geometry : angle 0.63425 / 0.32 (43242) hydrogen bonds : bond 0.03873 / 2.51 ( 1693) hydrogen bonds : angle 4.36367 / 3.11 ( 4977) metal coordination : bond 0.01111 / 0.78 ( 12) metal coordination : angle 7.96675 / 4.95 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7670 Ramachandran restraints generated. 3835 Oldfield, 0 Emsley, 3835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7670 Ramachandran restraints generated. 3835 Oldfield, 0 Emsley, 3835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 373 time to evaluate : 1.028 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8123 (tp30) REVERT: A 293 LEU cc_start: 0.8596 (mt) cc_final: 0.8355 (mt) REVERT: A 358 LEU cc_start: 0.8935 (tm) cc_final: 0.8718 (tp) REVERT: A 364 LEU cc_start: 0.9013 (tp) cc_final: 0.8789 (tp) REVERT: B 131 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.8077 (tp30) REVERT: B 315 MET cc_start: 0.9185 (mtm) cc_final: 0.8947 (mtp) REVERT: C 20 GLU cc_start: 0.8636 (pm20) cc_final: 0.8311 (pm20) REVERT: C 50 MET cc_start: 0.4027 (ttt) cc_final: 0.3299 (ptm) REVERT: C 60 MET cc_start: 0.7522 (ptp) cc_final: 0.7286 (ptp) REVERT: D 448 LYS cc_start: 0.7927 (pmtt) cc_final: 0.7483 (mptt) REVERT: E 89 ASP cc_start: 0.8212 (t0) cc_final: 0.7897 (t0) REVERT: F 108 MET cc_start: 0.9111 (mtp) cc_final: 0.8910 (mtp) REVERT: F 169 LYS cc_start: 0.8676 (ttmt) cc_final: 0.8368 (ttmp) REVERT: F 458 PHE cc_start: 0.8129 (t80) cc_final: 0.7503 (t80) REVERT: F 559 THR cc_start: 0.7158 (OUTLIER) cc_final: 0.6737 (m) REVERT: G 53 MET cc_start: 0.8957 (mtm) cc_final: 0.8731 (mtm) REVERT: G 113 LYS cc_start: 0.8928 (tttm) cc_final: 0.8536 (ttmm) REVERT: G 123 SER cc_start: 0.8620 (m) cc_final: 0.8318 (p) REVERT: H 202 ARG cc_start: 0.8001 (ttp-110) cc_final: 0.7736 (mtp180) REVERT: H 238 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7812 (m-30) REVERT: I 67 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7386 (mp0) REVERT: I 86 LYS cc_start: 0.7887 (mppt) cc_final: 0.7500 (mptm) REVERT: I 141 MET cc_start: 0.9178 (ptm) cc_final: 0.8970 (ptm) REVERT: K 24 GLU cc_start: 0.6364 (tp30) cc_final: 0.5207 (mp0) REVERT: K 169 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8166 (mt-10) REVERT: K 172 ASN cc_start: 0.7340 (m-40) cc_final: 0.7005 (t0) REVERT: L 27 ILE cc_start: 0.8884 (OUTLIER) cc_final: 0.8372 (mp) REVERT: L 66 ASN cc_start: 0.9227 (t0) cc_final: 0.8918 (t0) REVERT: L 72 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.6192 (ttt-90) REVERT: M 87 GLN cc_start: 0.8642 (mt0) cc_final: 0.8328 (mt0) REVERT: N 104 ASP cc_start: 0.8233 (OUTLIER) cc_final: 0.7926 (m-30) REVERT: N 135 ASP cc_start: 0.8527 (t0) cc_final: 0.8166 (t0) REVERT: N 141 GLU cc_start: 0.7480 (mt-10) cc_final: 0.7249 (mm-30) REVERT: O 14 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7884 (pm20) REVERT: O 15 LYS cc_start: 0.9125 (mmmt) cc_final: 0.8798 (mmmt) REVERT: Q 10 MET cc_start: 0.8185 (mmt) cc_final: 0.7348 (mmt) REVERT: S 43 MET cc_start: 0.2198 (ttt) cc_final: 0.1852 (ttp) outliers start: 92 outliers final: 40 residues processed: 437 average time/residue: 0.6294 time to fit residues: 328.0290 Evaluate side-chains 391 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 342 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 304 MET Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 382 ARG Chi-restraints excluded: chain F residue 559 THR Chi-restraints excluded: chain H residue 36 ASP Chi-restraints excluded: chain H residue 135 PHE Chi-restraints excluded: chain H residue 238 ASP Chi-restraints excluded: chain H residue 387 VAL Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 67 GLU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 62 ARG Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain K residue 196 ILE Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 72 ARG Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 86 MET Chi-restraints excluded: chain M residue 97 ARG Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 61 GLN Chi-restraints excluded: chain N residue 104 ASP Chi-restraints excluded: chain N residue 131 GLU Chi-restraints excluded: chain O residue 14 GLU Chi-restraints excluded: chain P residue 14 MET Chi-restraints excluded: chain Q residue 3 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 61 optimal weight: 0.3980 chunk 324 optimal weight: 5.9990 chunk 306 optimal weight: 0.7980 chunk 295 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 242 optimal weight: 0.9980 chunk 184 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 453 HIS E 55 GLN G 117 GLN ** H 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 25 ASN K 181 HIS K 200 GLN ** M 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 90 ASN O 18 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.097766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.079685 restraints weight = 54932.363| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.71 r_work: 0.2918 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 31827 Z= 0.153 Angle : 0.679 22.129 43278 Z= 0.318 Chirality : 0.043 0.252 4953 Planarity : 0.005 0.066 5317 Dihedral : 8.684 88.542 4578 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.61 % Favored : 92.36 % Rotamer: Outliers : 3.32 % Allowed : 16.97 % Favored : 79.71 % 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: -0.16 (0.14), residues: 3835 helix: 1.04 (0.11), residues: 2283 sheet: -2.10 (0.37), residues: 174 loop : -1.81 (0.17), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 53 TYR 0.019 0.001 TYR F 445 PHE 0.016 0.001 PHE A 321 TRP 0.023 0.001 TRP B 274 HIS 0.006 0.001 HIS M 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (31815) covalent geometry : angle 0.63891 / 0.32 (43242) hydrogen bonds : bond 0.03875 / 2.51 ( 1693) hydrogen bonds : angle 4.31680 / 3.07 ( 4977) metal coordination : bond 0.01015 / 0.67 ( 12) metal coordination : angle 7.95147 / 4.94 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7670 Ramachandran restraints generated. 3835 Oldfield, 0 Emsley, 3835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7670 Ramachandran restraints generated. 3835 Oldfield, 0 Emsley, 3835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 362 time to evaluate : 1.224 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8069 (tp30) REVERT: A 293 LEU cc_start: 0.8589 (mt) cc_final: 0.8358 (mt) REVERT: A 358 LEU cc_start: 0.8979 (tm) cc_final: 0.8723 (tp) REVERT: B 131 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.8057 (tp30) REVERT: B 315 MET cc_start: 0.9189 (mtm) cc_final: 0.8961 (mtp) REVERT: C 20 GLU cc_start: 0.8663 (pm20) cc_final: 0.8345 (pm20) REVERT: C 50 MET cc_start: 0.4024 (ttt) cc_final: 0.3384 (ptm) REVERT: C 60 MET cc_start: 0.7481 (ptp) cc_final: 0.7208 (ptp) REVERT: D 448 LYS cc_start: 0.7904 (pmtt) cc_final: 0.7419 (tppt) REVERT: F 458 PHE cc_start: 0.8163 (t80) cc_final: 0.7500 (t80) REVERT: F 534 LEU cc_start: 0.8700 (mm) cc_final: 0.8420 (tp) REVERT: F 559 THR cc_start: 0.7167 (OUTLIER) cc_final: 0.6742 (m) REVERT: G 113 LYS cc_start: 0.8944 (tttm) cc_final: 0.8531 (ttmm) REVERT: G 123 SER cc_start: 0.8610 (m) cc_final: 0.8339 (p) REVERT: H 202 ARG cc_start: 0.7944 (ttp-110) cc_final: 0.7714 (mtp180) REVERT: H 238 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7845 (m-30) REVERT: I 16 GLN cc_start: 0.7922 (pp30) cc_final: 0.7553 (pp30) REVERT: I 67 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7469 (mp0) REVERT: I 86 LYS cc_start: 0.7896 (mppt) cc_final: 0.7549 (mptm) REVERT: I 141 MET cc_start: 0.9203 (ptm) cc_final: 0.8977 (ptm) REVERT: I 150 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.7612 (mt0) REVERT: K 169 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8095 (mt-10) REVERT: K 172 ASN cc_start: 0.7236 (m-40) cc_final: 0.6965 (t0) REVERT: L 27 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8359 (mp) REVERT: L 66 ASN cc_start: 0.9222 (t0) cc_final: 0.8923 (t0) REVERT: L 72 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.6178 (ttt-90) REVERT: M 87 GLN cc_start: 0.8606 (mt0) cc_final: 0.8295 (mt0) REVERT: N 15 SER cc_start: 0.8824 (OUTLIER) cc_final: 0.8489 (p) REVERT: N 135 ASP cc_start: 0.8520 (t0) cc_final: 0.8157 (t0) REVERT: N 141 GLU cc_start: 0.7430 (mt-10) cc_final: 0.7196 (mm-30) REVERT: O 14 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7855 (pm20) REVERT: O 15 LYS cc_start: 0.9131 (mmmt) cc_final: 0.8785 (mmmt) REVERT: Q 10 MET cc_start: 0.8176 (mmt) cc_final: 0.7326 (mmt) REVERT: S 43 MET cc_start: 0.2405 (ttt) cc_final: 0.2012 (ttp) outliers start: 106 outliers final: 50 residues processed: 431 average time/residue: 0.6124 time to fit residues: 316.6099 Evaluate side-chains 407 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 347 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain F residue 203 PHE Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 304 MET Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 382 ARG Chi-restraints excluded: chain F residue 559 THR Chi-restraints excluded: chain H residue 36 ASP Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 135 PHE Chi-restraints excluded: chain H residue 238 ASP Chi-restraints excluded: chain H residue 387 VAL Chi-restraints excluded: chain I residue 67 GLU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 150 GLN Chi-restraints excluded: chain J residue 62 ARG Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 157 ILE Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain K residue 181 HIS Chi-restraints excluded: chain K residue 196 ILE Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain L residue 72 ARG Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain M residue 86 MET Chi-restraints excluded: chain M residue 97 ARG Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 61 GLN Chi-restraints excluded: chain N residue 131 GLU Chi-restraints excluded: chain O residue 14 GLU Chi-restraints excluded: chain P residue 14 MET Chi-restraints excluded: chain Q residue 3 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 343 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 228 optimal weight: 10.0000 chunk 44 optimal weight: 0.8980 chunk 87 optimal weight: 0.3980 chunk 248 optimal weight: 6.9990 chunk 119 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 453 HIS G 117 GLN ** H 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 25 ASN K 181 HIS K 200 GLN ** M 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 90 ASN P 36 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.098679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.080567 restraints weight = 55051.557| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.73 r_work: 0.2937 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31827 Z= 0.134 Angle : 0.668 22.162 43278 Z= 0.313 Chirality : 0.042 0.212 4953 Planarity : 0.005 0.067 5317 Dihedral : 8.528 88.966 4578 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.48 % Favored : 92.49 % Rotamer: Outliers : 3.42 % Allowed : 17.10 % Favored : 79.49 % 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: -0.01 (0.14), residues: 3835 helix: 1.17 (0.11), residues: 2288 sheet: -2.17 (0.37), residues: 169 loop : -1.76 (0.17), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 53 TYR 0.020 0.001 TYR F 445 PHE 0.015 0.001 PHE A 321 TRP 0.022 0.001 TRP B 274 HIS 0.019 0.001 HIS K 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (31815) covalent geometry : angle 0.62843 / 0.31 (43242) hydrogen bonds : bond 0.03755 / 2.43 ( 1693) hydrogen bonds : angle 4.25872 / 3.03 ( 4977) metal coordination : bond 0.00937 / 0.65 ( 12) metal coordination : angle 7.86376 / 4.87 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7670 Ramachandran restraints generated. 3835 Oldfield, 0 Emsley, 3835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7670 Ramachandran restraints generated. 3835 Oldfield, 0 Emsley, 3835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 364 time to evaluate : 1.207 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8057 (tp30) REVERT: A 68 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8684 (mt) REVERT: A 293 LEU cc_start: 0.8590 (mt) cc_final: 0.8363 (mt) REVERT: A 358 LEU cc_start: 0.8950 (tm) cc_final: 0.8682 (tp) REVERT: B 131 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.8005 (tp30) REVERT: B 315 MET cc_start: 0.9191 (mtm) cc_final: 0.8977 (mtp) REVERT: C 20 GLU cc_start: 0.8666 (pm20) cc_final: 0.8331 (pm20) REVERT: C 50 MET cc_start: 0.3920 (ttt) cc_final: 0.3499 (ptm) REVERT: C 60 MET cc_start: 0.7381 (ptp) cc_final: 0.7121 (ptp) REVERT: D 448 LYS cc_start: 0.7903 (pmtt) cc_final: 0.7464 (tppt) REVERT: F 458 PHE cc_start: 0.8178 (t80) cc_final: 0.7468 (t80) REVERT: F 534 LEU cc_start: 0.8692 (mm) cc_final: 0.8414 (tp) REVERT: F 559 THR cc_start: 0.7153 (OUTLIER) cc_final: 0.6724 (m) REVERT: G 113 LYS cc_start: 0.8947 (tttm) cc_final: 0.8543 (ttmt) REVERT: G 123 SER cc_start: 0.8637 (m) cc_final: 0.8360 (p) REVERT: H 36 ASP cc_start: 0.8400 (OUTLIER) cc_final: 0.7411 (p0) REVERT: H 202 ARG cc_start: 0.7945 (ttp-110) cc_final: 0.7742 (mtp180) REVERT: H 238 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.7870 (m-30) REVERT: I 67 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7193 (mp0) REVERT: I 86 LYS cc_start: 0.7890 (mppt) cc_final: 0.7545 (mptm) REVERT: I 141 MET cc_start: 0.9164 (ptm) cc_final: 0.8947 (ptm) REVERT: J 37 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7187 (pp20) REVERT: J 115 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8650 (mttm) REVERT: K 24 GLU cc_start: 0.6591 (tp30) cc_final: 0.5185 (mp0) REVERT: K 169 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8212 (mt-10) REVERT: K 172 ASN cc_start: 0.7313 (m-40) cc_final: 0.6995 (t0) REVERT: L 27 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8361 (mp) REVERT: L 66 ASN cc_start: 0.9196 (t0) cc_final: 0.8927 (t0) REVERT: M 87 GLN cc_start: 0.8608 (mt0) cc_final: 0.8278 (mt0) REVERT: N 15 SER cc_start: 0.8769 (OUTLIER) cc_final: 0.8419 (p) REVERT: N 104 ASP cc_start: 0.8197 (OUTLIER) cc_final: 0.7861 (m-30) REVERT: N 135 ASP cc_start: 0.8504 (t0) cc_final: 0.8162 (t0) REVERT: N 141 GLU cc_start: 0.7432 (mt-10) cc_final: 0.7172 (mm-30) REVERT: O 14 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7865 (pm20) REVERT: O 15 LYS cc_start: 0.9135 (mmmt) cc_final: 0.8784 (mmmt) REVERT: Q 10 MET cc_start: 0.8165 (mmt) cc_final: 0.7317 (mmt) REVERT: S 43 MET cc_start: 0.2264 (ttt) cc_final: 0.1977 (ttp) outliers start: 109 outliers final: 49 residues processed: 437 average time/residue: 0.5904 time to fit residues: 309.9495 Evaluate side-chains 408 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 346 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain D residue 453 HIS Chi-restraints excluded: chain F residue 203 PHE Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 304 MET Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 382 ARG Chi-restraints excluded: chain F residue 559 THR Chi-restraints excluded: chain H residue 36 ASP Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 135 PHE Chi-restraints excluded: chain H residue 238 ASP Chi-restraints excluded: chain H residue 387 VAL Chi-restraints excluded: chain I residue 67 GLU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 62 ARG Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 115 LYS Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain K residue 181 HIS Chi-restraints excluded: chain K residue 196 ILE Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 86 MET Chi-restraints excluded: chain M residue 97 ARG Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 61 GLN Chi-restraints excluded: chain N residue 104 ASP Chi-restraints excluded: chain N residue 131 GLU Chi-restraints excluded: chain O residue 14 GLU Chi-restraints excluded: chain P residue 14 MET Chi-restraints excluded: chain Q residue 3 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 231 optimal weight: 0.0370 chunk 11 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 317 optimal weight: 0.1980 chunk 234 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 331 optimal weight: 0.3980 chunk 211 optimal weight: 0.6980 chunk 378 optimal weight: 0.9990 chunk 168 optimal weight: 0.9980 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 117 GLN ** H 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 25 ASN K 181 HIS K 203 ASN ** M 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 16 HIS ** M 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 90 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.100234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.082257 restraints weight = 54859.763| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.72 r_work: 0.2963 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31827 Z= 0.122 Angle : 0.656 21.164 43278 Z= 0.308 Chirality : 0.042 0.222 4953 Planarity : 0.004 0.067 5317 Dihedral : 8.336 89.688 4578 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.38 % Favored : 92.59 % Rotamer: Outliers : 2.38 % Allowed : 18.13 % Favored : 79.49 % 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: 0.17 (0.14), residues: 3835 helix: 1.33 (0.11), residues: 2282 sheet: -1.84 (0.40), residues: 155 loop : -1.75 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 182 TYR 0.021 0.001 TYR F 445 PHE 0.021 0.001 PHE H 131 TRP 0.021 0.001 TRP B 274 HIS 0.016 0.001 HIS D 453 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (31815) covalent geometry : angle 0.61840 / 0.31 (43242) hydrogen bonds : bond 0.03606 / 2.34 ( 1693) hydrogen bonds : angle 4.18085 / 2.98 ( 4977) metal coordination : bond 0.00694 / 0.48 ( 12) metal coordination : angle 7.57584 / 4.72 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7670 Ramachandran restraints generated. 3835 Oldfield, 0 Emsley, 3835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7670 Ramachandran restraints generated. 3835 Oldfield, 0 Emsley, 3835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 372 time to evaluate : 1.195 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 35 LEU cc_start: 0.8530 (tt) cc_final: 0.8211 (mt) REVERT: A 36 MET cc_start: 0.8942 (tpp) cc_final: 0.8592 (tpt) REVERT: A 293 LEU cc_start: 0.8571 (mt) cc_final: 0.8339 (mt) REVERT: A 358 LEU cc_start: 0.8933 (tm) cc_final: 0.8668 (tp) REVERT: B 131 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7992 (tp30) REVERT: C 20 GLU cc_start: 0.8647 (pm20) cc_final: 0.8365 (pm20) REVERT: C 50 MET cc_start: 0.3983 (ttt) cc_final: 0.3585 (ptm) REVERT: C 60 MET cc_start: 0.7247 (ptp) cc_final: 0.7004 (ptp) REVERT: D 295 THR cc_start: 0.8655 (p) cc_final: 0.8439 (p) REVERT: D 448 LYS cc_start: 0.7866 (pmtt) cc_final: 0.7357 (tppt) REVERT: D 449 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7816 (tm-30) REVERT: F 135 MET cc_start: 0.8540 (tpt) cc_final: 0.7955 (tpt) REVERT: F 391 MET cc_start: 0.8499 (mtt) cc_final: 0.8142 (mpt) REVERT: F 458 PHE cc_start: 0.8192 (t80) cc_final: 0.7478 (t80) REVERT: F 534 LEU cc_start: 0.8690 (mm) cc_final: 0.8422 (tp) REVERT: F 559 THR cc_start: 0.7114 (OUTLIER) cc_final: 0.6672 (m) REVERT: G 113 LYS cc_start: 0.8910 (tttm) cc_final: 0.8508 (ttmt) REVERT: G 123 SER cc_start: 0.8616 (m) cc_final: 0.8355 (p) REVERT: H 36 ASP cc_start: 0.8420 (OUTLIER) cc_final: 0.7617 (p0) REVERT: H 202 ARG cc_start: 0.7965 (ttp-110) cc_final: 0.7732 (mtp180) REVERT: I 67 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7106 (mt-10) REVERT: I 86 LYS cc_start: 0.7932 (mppt) cc_final: 0.7595 (mptm) REVERT: I 141 MET cc_start: 0.9128 (ptm) cc_final: 0.8915 (ptm) REVERT: J 62 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.6470 (ptp-170) REVERT: J 115 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8639 (mttm) REVERT: K 66 ASP cc_start: 0.7622 (t0) cc_final: 0.7421 (t0) REVERT: K 172 ASN cc_start: 0.7301 (m-40) cc_final: 0.7021 (t0) REVERT: L 27 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8384 (mp) REVERT: L 66 ASN cc_start: 0.9136 (t0) cc_final: 0.8891 (t0) REVERT: M 87 GLN cc_start: 0.8587 (mt0) cc_final: 0.8271 (mt0) REVERT: N 15 SER cc_start: 0.8734 (OUTLIER) cc_final: 0.8413 (p) REVERT: N 104 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7845 (m-30) REVERT: N 135 ASP cc_start: 0.8487 (t0) cc_final: 0.8121 (t0) REVERT: N 141 GLU cc_start: 0.7337 (mt-10) cc_final: 0.7088 (mm-30) REVERT: O 14 GLU cc_start: 0.8118 (mp0) cc_final: 0.7891 (pm20) REVERT: O 15 LYS cc_start: 0.9116 (mmmt) cc_final: 0.8752 (mmmt) REVERT: Q 10 MET cc_start: 0.8124 (mmt) cc_final: 0.7253 (mmt) REVERT: S 43 MET cc_start: 0.2245 (ttt) cc_final: 0.1958 (ttp) outliers start: 76 outliers final: 41 residues processed: 424 average time/residue: 0.6148 time to fit residues: 312.1079 Evaluate side-chains 398 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 348 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain F residue 203 PHE Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 304 MET Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 355 MET Chi-restraints excluded: chain F residue 382 ARG Chi-restraints excluded: chain F residue 559 THR Chi-restraints excluded: chain H residue 36 ASP Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 135 PHE Chi-restraints excluded: chain H residue 387 VAL Chi-restraints excluded: chain I residue 67 GLU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 94 LYS Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 62 ARG Chi-restraints excluded: chain J residue 115 LYS Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain K residue 181 HIS Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 97 ARG Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 61 GLN Chi-restraints excluded: chain N residue 104 ASP Chi-restraints excluded: chain N residue 131 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 285 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 288 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 197 optimal weight: 6.9990 chunk 160 optimal weight: 0.6980 chunk 188 optimal weight: 2.9990 chunk 161 optimal weight: 0.5980 chunk 134 optimal weight: 0.8980 chunk 240 optimal weight: 0.6980 chunk 260 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 453 HIS ** H 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 25 ASN K 181 HIS ** M 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 90 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.099555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.081479 restraints weight = 54794.708| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.72 r_work: 0.2956 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31827 Z= 0.137 Angle : 0.668 21.320 43278 Z= 0.313 Chirality : 0.042 0.245 4953 Planarity : 0.005 0.067 5317 Dihedral : 8.272 87.878 4578 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.56 % Favored : 92.41 % Rotamer: Outliers : 2.16 % Allowed : 18.85 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.14), residues: 3835 helix: 1.34 (0.11), residues: 2288 sheet: -1.76 (0.40), residues: 153 loop : -1.70 (0.17), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 182 TYR 0.019 0.001 TYR F 445 PHE 0.020 0.001 PHE H 131 TRP 0.021 0.001 TRP B 274 HIS 0.011 0.001 HIS K 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (31815) covalent geometry : angle 0.63134 / 0.31 (43242) hydrogen bonds : bond 0.03673 / 2.38 ( 1693) hydrogen bonds : angle 4.18828 / 2.99 ( 4977) metal coordination : bond 0.00798 / 0.53 ( 12) metal coordination : angle 7.56059 / 4.72 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7670 Ramachandran restraints generated. 3835 Oldfield, 0 Emsley, 3835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7670 Ramachandran restraints generated. 3835 Oldfield, 0 Emsley, 3835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 354 time to evaluate : 1.152 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LEU cc_start: 0.8554 (tt) cc_final: 0.8197 (mt) REVERT: A 36 MET cc_start: 0.8985 (tpp) cc_final: 0.8624 (tpt) REVERT: A 293 LEU cc_start: 0.8601 (mt) cc_final: 0.8371 (mt) REVERT: A 358 LEU cc_start: 0.8941 (tm) cc_final: 0.8678 (tp) REVERT: B 113 MET cc_start: 0.8767 (ttm) cc_final: 0.8562 (mtp) REVERT: B 131 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.8024 (tp30) REVERT: C 20 GLU cc_start: 0.8633 (pm20) cc_final: 0.8351 (pm20) REVERT: C 50 MET cc_start: 0.3877 (ttt) cc_final: 0.3584 (ptm) REVERT: C 60 MET cc_start: 0.7274 (ptp) cc_final: 0.7041 (ptp) REVERT: D 295 THR cc_start: 0.8642 (p) cc_final: 0.8422 (p) REVERT: D 448 LYS cc_start: 0.7905 (pmtt) cc_final: 0.7451 (tppt) REVERT: D 449 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7738 (tm-30) REVERT: F 135 MET cc_start: 0.8587 (tpt) cc_final: 0.7921 (tpt) REVERT: F 458 PHE cc_start: 0.8229 (t80) cc_final: 0.7531 (t80) REVERT: F 534 LEU cc_start: 0.8699 (mm) cc_final: 0.8422 (tp) REVERT: F 559 THR cc_start: 0.7094 (OUTLIER) cc_final: 0.6649 (m) REVERT: G 113 LYS cc_start: 0.8887 (tttm) cc_final: 0.8593 (ttmt) REVERT: G 123 SER cc_start: 0.8626 (m) cc_final: 0.8355 (p) REVERT: H 36 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.7609 (p0) REVERT: H 202 ARG cc_start: 0.7962 (ttp-110) cc_final: 0.7744 (mtp180) REVERT: H 297 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7462 (pp) REVERT: I 67 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7217 (mt-10) REVERT: I 86 LYS cc_start: 0.7965 (mppt) cc_final: 0.7634 (mptm) REVERT: I 141 MET cc_start: 0.9158 (ptm) cc_final: 0.8954 (ptm) REVERT: K 66 ASP cc_start: 0.7621 (t0) cc_final: 0.7413 (t0) REVERT: K 172 ASN cc_start: 0.7297 (m-40) cc_final: 0.7040 (t0) REVERT: L 23 VAL cc_start: 0.9064 (t) cc_final: 0.8784 (t) REVERT: L 27 ILE cc_start: 0.8886 (OUTLIER) cc_final: 0.8366 (mp) REVERT: M 27 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7306 (pp20) REVERT: M 87 GLN cc_start: 0.8588 (mt0) cc_final: 0.8263 (mt0) REVERT: N 15 SER cc_start: 0.8681 (OUTLIER) cc_final: 0.8355 (p) REVERT: N 104 ASP cc_start: 0.8181 (OUTLIER) cc_final: 0.7839 (m-30) REVERT: N 135 ASP cc_start: 0.8488 (t0) cc_final: 0.8132 (t0) REVERT: N 141 GLU cc_start: 0.7332 (mt-10) cc_final: 0.7094 (mm-30) REVERT: O 14 GLU cc_start: 0.8098 (mp0) cc_final: 0.7860 (pm20) REVERT: O 15 LYS cc_start: 0.9122 (mmmt) cc_final: 0.8761 (mmmt) REVERT: Q 10 MET cc_start: 0.8113 (mmt) cc_final: 0.7245 (mmt) REVERT: S 43 MET cc_start: 0.2219 (ttt) cc_final: 0.1935 (ttp) outliers start: 69 outliers final: 48 residues processed: 401 average time/residue: 0.6169 time to fit residues: 295.8727 Evaluate side-chains 403 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 346 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain D residue 453 HIS Chi-restraints excluded: chain F residue 203 PHE Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 304 MET Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 355 MET Chi-restraints excluded: chain F residue 382 ARG Chi-restraints excluded: chain F residue 559 THR Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 36 ASP Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 135 PHE Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 387 VAL Chi-restraints excluded: chain I residue 67 GLU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 62 ARG Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain K residue 52 CYS Chi-restraints excluded: chain K residue 181 HIS Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 27 GLU Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 97 ARG Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 61 GLN Chi-restraints excluded: chain N residue 90 ASN Chi-restraints excluded: chain N residue 104 ASP Chi-restraints excluded: chain N residue 131 GLU Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 14 MET Chi-restraints excluded: chain Q residue 27 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 131 optimal weight: 2.9990 chunk 293 optimal weight: 2.9990 chunk 379 optimal weight: 0.0020 chunk 58 optimal weight: 0.9980 chunk 143 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 306 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 180 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 25 ASN ** M 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.099493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.081410 restraints weight = 54694.281| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.72 r_work: 0.2950 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 31827 Z= 0.186 Angle : 0.788 59.200 43278 Z= 0.417 Chirality : 0.043 0.410 4953 Planarity : 0.006 0.193 5317 Dihedral : 8.273 87.859 4578 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.48 % Favored : 92.49 % Rotamer: Outliers : 2.10 % Allowed : 18.91 % Favored : 78.98 % Cbeta Deviations : 0.08 % 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: 0.23 (0.14), residues: 3835 helix: 1.35 (0.11), residues: 2288 sheet: -1.76 (0.40), residues: 153 loop : -1.69 (0.17), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 7 TYR 0.019 0.001 TYR F 445 PHE 0.017 0.001 PHE F 411 TRP 0.022 0.001 TRP B 274 HIS 0.298 0.005 HIS D 453 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.19 (31815) covalent geometry : angle 0.75758 / 0.42 (43242) hydrogen bonds : bond 0.03670 / 2.38 ( 1693) hydrogen bonds : angle 4.19210 / 2.99 ( 4977) metal coordination : bond 0.00770 / 0.51 ( 12) metal coordination : angle 7.56490 / 4.72 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7670 Ramachandran restraints generated. 3835 Oldfield, 0 Emsley, 3835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7670 Ramachandran restraints generated. 3835 Oldfield, 0 Emsley, 3835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 348 time to evaluate : 1.089 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LEU cc_start: 0.8565 (tt) cc_final: 0.8214 (mt) REVERT: A 36 MET cc_start: 0.8993 (tpp) cc_final: 0.8634 (tpt) REVERT: A 293 LEU cc_start: 0.8604 (mt) cc_final: 0.8377 (mt) REVERT: A 358 LEU cc_start: 0.8939 (tm) cc_final: 0.8674 (tp) REVERT: B 131 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.8013 (tp30) REVERT: C 20 GLU cc_start: 0.8632 (pm20) cc_final: 0.8361 (pm20) REVERT: C 50 MET cc_start: 0.3873 (ttt) cc_final: 0.3606 (ptm) REVERT: C 60 MET cc_start: 0.7293 (ptp) cc_final: 0.7060 (ptp) REVERT: D 172 TYR cc_start: 0.8760 (OUTLIER) cc_final: 0.7914 (m-80) REVERT: D 295 THR cc_start: 0.8646 (p) cc_final: 0.8428 (p) REVERT: D 392 MET cc_start: 0.9266 (OUTLIER) cc_final: 0.8795 (mtt) REVERT: D 448 LYS cc_start: 0.7901 (pmtt) cc_final: 0.7454 (tppt) REVERT: D 449 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7677 (tm-30) REVERT: F 135 MET cc_start: 0.8592 (tpt) cc_final: 0.7929 (tpt) REVERT: F 458 PHE cc_start: 0.8232 (t80) cc_final: 0.7535 (t80) REVERT: F 534 LEU cc_start: 0.8696 (mm) cc_final: 0.8418 (tp) REVERT: F 559 THR cc_start: 0.7087 (OUTLIER) cc_final: 0.6637 (m) REVERT: G 113 LYS cc_start: 0.8900 (tttm) cc_final: 0.8617 (ttmt) REVERT: G 123 SER cc_start: 0.8631 (m) cc_final: 0.8368 (p) REVERT: H 36 ASP cc_start: 0.8406 (OUTLIER) cc_final: 0.7629 (p0) REVERT: H 202 ARG cc_start: 0.7964 (ttp-110) cc_final: 0.7757 (mtp180) REVERT: H 297 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7468 (pp) REVERT: I 67 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7221 (mt-10) REVERT: I 86 LYS cc_start: 0.7968 (mppt) cc_final: 0.7634 (mptm) REVERT: K 66 ASP cc_start: 0.7608 (t0) cc_final: 0.7392 (t0) REVERT: K 172 ASN cc_start: 0.7306 (m-40) cc_final: 0.7066 (t0) REVERT: L 23 VAL cc_start: 0.9075 (t) cc_final: 0.8798 (t) REVERT: L 27 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8386 (mp) REVERT: M 27 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7335 (pp20) REVERT: M 87 GLN cc_start: 0.8576 (mt0) cc_final: 0.8256 (mt0) REVERT: N 15 SER cc_start: 0.8685 (OUTLIER) cc_final: 0.8358 (p) REVERT: N 90 ASN cc_start: 0.8337 (t0) cc_final: 0.7134 (p0) REVERT: N 104 ASP cc_start: 0.8167 (OUTLIER) cc_final: 0.7829 (m-30) REVERT: N 135 ASP cc_start: 0.8478 (t0) cc_final: 0.8135 (t0) REVERT: N 141 GLU cc_start: 0.7337 (mt-10) cc_final: 0.7115 (mm-30) REVERT: O 14 GLU cc_start: 0.8096 (mp0) cc_final: 0.7860 (pm20) REVERT: O 15 LYS cc_start: 0.9117 (mmmt) cc_final: 0.8766 (mmmt) REVERT: Q 10 MET cc_start: 0.8119 (mmt) cc_final: 0.7261 (mmt) REVERT: S 43 MET cc_start: 0.2222 (ttt) cc_final: 0.1941 (ttp) outliers start: 67 outliers final: 48 residues processed: 397 average time/residue: 0.6195 time to fit residues: 294.4982 Evaluate side-chains 402 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 343 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain D residue 172 TYR Chi-restraints excluded: chain D residue 392 MET Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain F residue 203 PHE Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 304 MET Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 355 MET Chi-restraints excluded: chain F residue 382 ARG Chi-restraints excluded: chain F residue 559 THR Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 36 ASP Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 135 PHE Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 387 VAL Chi-restraints excluded: chain I residue 67 GLU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 62 ARG Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain K residue 52 CYS Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 27 GLU Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 97 ARG Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 61 GLN Chi-restraints excluded: chain N residue 104 ASP Chi-restraints excluded: chain N residue 131 GLU Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 14 MET Chi-restraints excluded: chain Q residue 27 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 221 optimal weight: 4.9990 chunk 247 optimal weight: 0.9980 chunk 212 optimal weight: 0.0980 chunk 197 optimal weight: 6.9990 chunk 193 optimal weight: 0.0670 chunk 333 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 189 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 133 optimal weight: 0.7980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 453 HIS ** H 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 25 ASN ** K 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.099433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.081418 restraints weight = 55012.564| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.71 r_work: 0.2952 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 31827 Z= 0.186 Angle : 0.788 59.200 43278 Z= 0.417 Chirality : 0.043 0.410 4953 Planarity : 0.006 0.193 5317 Dihedral : 8.273 87.859 4578 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.48 % Favored : 92.49 % Rotamer: Outliers : 1.91 % Allowed : 19.17 % Favored : 78.92 % Cbeta Deviations : 0.08 % 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: 0.23 (0.14), residues: 3835 helix: 1.35 (0.11), residues: 2288 sheet: -1.76 (0.40), residues: 153 loop : -1.69 (0.17), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 7 TYR 0.019 0.001 TYR F 445 PHE 0.017 0.001 PHE F 411 TRP 0.022 0.001 TRP B 274 HIS 0.298 0.005 HIS D 453 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.19 (31815) covalent geometry : angle 0.75758 / 0.42 (43242) hydrogen bonds : bond 0.03670 / 2.38 ( 1693) hydrogen bonds : angle 4.19210 / 2.99 ( 4977) metal coordination : bond 0.00770 / 0.51 ( 12) metal coordination : angle 7.56490 / 4.72 ( 36) =============================================================================== Job complete usr+sys time: 10580.72 seconds wall clock time: 180 minutes 54.73 seconds (10854.73 seconds total)