Starting phenix.real_space_refine (version: dev) on Fri Dec 16 15:33:14 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6khj_9990/12_2022/6khj_9990_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6khj_9990/12_2022/6khj_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6khj_9990/12_2022/6khj_9990.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6khj_9990/12_2022/6khj_9990.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6khj_9990/12_2022/6khj_9990_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6khj_9990/12_2022/6khj_9990_updated.pdb" } 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 62": "NH1" <-> "NH2" Residue "A GLU 194": "OE1" <-> "OE2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A GLU 239": "OE1" <-> "OE2" Residue "A GLU 240": "OE1" <-> "OE2" Residue "B ARG 41": "NH1" <-> "NH2" Residue "B ARG 100": "NH1" <-> "NH2" Residue "B GLU 103": "OE1" <-> "OE2" Residue "B GLU 111": "OE1" <-> "OE2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "B ARG 155": "NH1" <-> "NH2" Residue "B PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 458": "NH1" <-> "NH2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "C ARG 73": "NH1" <-> "NH2" Residue "C GLU 130": "OE1" <-> "OE2" Residue "D ARG 162": "NH1" <-> "NH2" Residue "D ARG 300": "NH1" <-> "NH2" Residue "D ARG 356": "NH1" <-> "NH2" Residue "D GLU 452": "OE1" <-> "OE2" Residue "D ARG 462": "NH1" <-> "NH2" Residue "D ARG 498": "NH1" <-> "NH2" Residue "D ARG 500": "NH1" <-> "NH2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "F ARG 37": "NH1" <-> "NH2" Residue "F ARG 123": "NH1" <-> "NH2" Residue "F ARG 279": "NH1" <-> "NH2" Residue "F TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 388": "NH1" <-> "NH2" Residue "F ARG 448": "NH1" <-> "NH2" Residue "F ARG 459": "NH1" <-> "NH2" Residue "F ARG 465": "NH1" <-> "NH2" Residue "F ARG 599": "NH1" <-> "NH2" Residue "F GLU 625": "OE1" <-> "OE2" Residue "F ARG 634": "NH1" <-> "NH2" Residue "G GLU 85": "OE1" <-> "OE2" Residue "G ARG 93": "NH1" <-> "NH2" Residue "G ARG 96": "NH1" <-> "NH2" Residue "G ARG 166": "NH1" <-> "NH2" Residue "G ARG 167": "NH1" <-> "NH2" Residue "G GLU 168": "OE1" <-> "OE2" Residue "H ARG 7": "NH1" <-> "NH2" Residue "H ARG 136": "NH1" <-> "NH2" Residue "H GLU 139": "OE1" <-> "OE2" Residue "H ARG 177": "NH1" <-> "NH2" Residue "H GLU 191": "OE1" <-> "OE2" Residue "H ARG 192": "NH1" <-> "NH2" Residue "H ARG 202": "NH1" <-> "NH2" Residue "H ARG 203": "NH1" <-> "NH2" Residue "H GLU 213": "OE1" <-> "OE2" Residue "H GLU 214": "OE1" <-> "OE2" Residue "H ARG 226": "NH1" <-> "NH2" Residue "H GLU 289": "OE1" <-> "OE2" Residue "H ARG 330": "NH1" <-> "NH2" Residue "H ARG 352": "NH1" <-> "NH2" Residue "I ARG 33": "NH1" <-> "NH2" Residue "I GLU 50": "OE1" <-> "OE2" Residue "I ARG 55": "NH1" <-> "NH2" Residue "I TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 133": "OE1" <-> "OE2" Residue "I GLU 185": "OE1" <-> "OE2" Residue "J ARG 17": "NH1" <-> "NH2" Residue "J ARG 31": "NH1" <-> "NH2" Residue "J GLU 37": "OE1" <-> "OE2" Residue "J ARG 90": "NH1" <-> "NH2" Residue "J GLU 133": "OE1" <-> "OE2" Residue "J GLU 145": "OE1" <-> "OE2" Residue "K ARG 75": "NH1" <-> "NH2" Residue "K ARG 100": "NH1" <-> "NH2" Residue "K GLU 103": "OE1" <-> "OE2" Residue "K ARG 133": "NH1" <-> "NH2" Residue "K ARG 151": "NH1" <-> "NH2" Residue "K ARG 182": "NH1" <-> "NH2" Residue "M ARG 72": "NH1" <-> "NH2" Residue "M ARG 82": "NH1" <-> "NH2" Residue "M ARG 97": "NH1" <-> "NH2" Residue "M ARG 99": "NH1" <-> "NH2" Residue "N ARG 32": "NH1" <-> "NH2" Residue "N ARG 36": "NH1" <-> "NH2" Residue "N ARG 38": "NH1" <-> "NH2" Residue "N ARG 136": "NH1" <-> "NH2" Residue "O GLU 14": "OE1" <-> "OE2" Residue "O ARG 44": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/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: 17.08, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.59 Conformation dependent library (CDL) restraints added in 4.7 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... running ksdssp... Secondary structure from input PDB file: 159 helices and 13 sheets defined 56.8% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.56 Creating SS restraints... Processing helix chain 'A' and resid 7 through 16 Processing helix chain 'A' and resid 22 through 59 Proline residue: A 31 - end of helix 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 72 through 85 Proline residue: A 76 - end of helix removed outlier: 4.509A pdb=" N LYS A 82 " --> pdb=" O ASP A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 115 Proline residue: A 103 - end of helix Proline residue: A 109 - end of helix removed outlier: 4.196A pdb=" N TYR A 114 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ILE A 115 " --> pdb=" O PHE A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 151 removed outlier: 3.894A pdb=" N ILE A 141 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ALA A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Proline residue: A 143 - end of helix removed outlier: 4.426A pdb=" N LEU A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 170 Processing helix chain 'A' and resid 173 through 187 removed outlier: 3.616A pdb=" N VAL A 183 " --> pdb=" O ALA A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 208 through 211 No H-bonds generated for 'chain 'A' and resid 208 through 211' Processing helix chain 'A' and resid 213 through 226 removed outlier: 3.835A pdb=" N LEU A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 275 removed outlier: 3.733A pdb=" N TYR A 262 " --> pdb=" O TYR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 293 Processing helix chain 'A' and resid 300 through 331 removed outlier: 3.960A pdb=" N TRP A 330 " --> pdb=" O ILE A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 345 Processing helix chain 'A' and resid 348 through 365 Processing helix chain 'B' and resid 16 through 34 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 43 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 78 through 97 Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 109 through 127 Processing helix chain 'B' and resid 132 through 150 Processing helix chain 'B' and resid 157 through 187 removed outlier: 3.600A pdb=" N ILE B 169 " --> pdb=" O LYS B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 200 Processing helix chain 'B' and resid 208 through 223 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 238 removed outlier: 4.612A pdb=" N ASP B 234 " --> pdb=" O GLN B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 263 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) Processing helix chain 'B' and resid 271 through 292 removed outlier: 3.718A pdb=" N VAL B 292 " --> pdb=" O LEU B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 320 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) Processing helix chain 'B' and resid 323 through 354 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 359 through 362 Processing helix chain 'B' and resid 365 through 368 No H-bonds generated for 'chain 'B' and resid 365 through 368' Processing helix chain 'B' and resid 370 through 384 Processing helix chain 'B' and resid 390 through 403 removed outlier: 4.422A pdb=" N GLY B 402 " --> pdb=" O LEU B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 433 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 437 through 439 No H-bonds generated for 'chain 'B' and resid 437 through 439' Processing helix chain 'B' and resid 442 through 445 No H-bonds generated for 'chain 'B' and resid 442 through 445' Processing helix chain 'B' and resid 457 through 475 removed outlier: 5.370A pdb=" N GLY B 475 " --> pdb=" O THR B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 486 Processing helix chain 'C' and resid 20 through 42 removed outlier: 4.025A pdb=" N GLY C 24 " --> pdb=" O GLU C 20 " (cutoff:3.500A) Proline residue: C 33 - end of helix Processing helix chain 'C' and resid 57 through 59 No H-bonds generated for 'chain 'C' and resid 57 through 59' Processing helix chain 'C' and resid 73 through 96 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 103 through 125 Processing helix chain 'D' and resid 6 through 20 Proline residue: D 14 - end of helix removed outlier: 3.700A pdb=" N ALA D 20 " --> pdb=" O VAL D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 56 Processing helix chain 'D' and resid 86 through 105 Proline residue: D 90 - end of helix Processing helix chain 'D' and resid 113 through 132 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) Processing helix chain 'D' and resid 136 through 155 removed outlier: 4.353A pdb=" N GLU D 146 " --> pdb=" O ALA D 142 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N LEU D 147 " --> pdb=" O TRP D 143 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ILE D 148 " --> pdb=" O GLU D 144 " (cutoff:3.500A) Proline residue: D 149 - end of helix Processing helix chain 'D' and resid 162 through 188 removed outlier: 4.231A pdb=" N PHE D 179 " --> pdb=" O GLY D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 202 Processing helix chain 'D' and resid 210 through 225 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 240 removed outlier: 4.470A pdb=" N ASP D 237 " --> pdb=" O THR D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 251 Processing helix chain 'D' and resid 261 through 264 No H-bonds generated for 'chain 'D' and resid 261 through 264' Processing helix chain 'D' and resid 271 through 298 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 302 through 322 removed outlier: 4.033A pdb=" N ILE D 314 " --> pdb=" O SER D 310 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLY D 315 " --> pdb=" O ILE D 311 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N PHE D 316 " --> pdb=" O SER D 312 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL D 317 " --> pdb=" O HIS D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 357 removed outlier: 4.093A pdb=" N GLY D 340 " --> pdb=" O MET D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 370 No H-bonds generated for 'chain 'D' and resid 368 through 370' Processing helix chain 'D' and resid 373 through 386 Processing helix chain 'D' and resid 393 through 406 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 413 through 422 Processing helix chain 'D' and resid 425 through 441 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 448 through 451 No H-bonds generated for 'chain 'D' and resid 448 through 451' Processing helix chain 'D' and resid 461 through 479 Proline residue: D 473 - end of helix Processing helix chain 'D' and resid 481 through 499 removed outlier: 4.252A pdb=" N THR D 485 " --> pdb=" O LYS D 482 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLN D 486 " --> pdb=" O LEU D 483 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ASP D 489 " --> pdb=" O GLN D 486 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ALA D 490 " --> pdb=" O ILE D 487 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR D 491 " --> pdb=" O TYR D 488 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N THR D 492 " --> pdb=" O ASP D 489 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ILE D 496 " --> pdb=" O GLY D 493 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA D 497 " --> pdb=" O GLN D 494 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 21 removed outlier: 4.425A pdb=" N GLY E 20 " --> pdb=" O ILE E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 51 removed outlier: 3.700A pdb=" N LEU E 31 " --> pdb=" O ALA E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 87 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 93 through 95 No H-bonds generated for 'chain 'E' and resid 93 through 95' Processing helix chain 'F' and resid 3 through 6 No H-bonds generated for 'chain 'F' and resid 3 through 6' Processing helix chain 'F' and resid 8 through 27 Proline residue: F 12 - end of helix Proline residue: F 15 - end of helix removed outlier: 4.219A pdb=" N ILE F 21 " --> pdb=" O GLY F 18 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL F 22 " --> pdb=" O ALA F 19 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLY F 23 " --> pdb=" O LEU F 20 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE F 27 " --> pdb=" O PHE F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 35 removed outlier: 3.786A pdb=" N SER F 34 " --> pdb=" O SER F 30 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LYS F 35 " --> pdb=" O GLU F 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 30 through 35' Processing helix chain 'F' and resid 37 through 63 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 91 through 117 removed outlier: 4.019A pdb=" N GLY F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ALA F 116 " --> pdb=" O ASP F 112 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N HIS F 117 " --> pdb=" O GLY F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 139 Processing helix chain 'F' and resid 146 through 164 removed outlier: 4.705A pdb=" N TRP F 151 " --> pdb=" O VAL F 147 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE F 164 " --> pdb=" O LEU F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 199 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 205 through 217 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) Processing helix chain 'F' and resid 223 through 240 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 252 through 255 Processing helix chain 'F' and resid 258 through 266 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 273 through 286 Proline residue: F 282 - end of helix removed outlier: 4.735A pdb=" N GLN F 286 " --> pdb=" O PRO F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 311 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) Processing helix chain 'F' and resid 315 through 335 removed outlier: 3.623A pdb=" N LEU F 319 " --> pdb=" O ILE F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 348 Processing helix chain 'F' and resid 353 through 368 Processing helix chain 'F' and resid 375 through 378 No H-bonds generated for 'chain 'F' and resid 375 through 378' Processing helix chain 'F' and resid 381 through 383 No H-bonds generated for 'chain 'F' and resid 381 through 383' Processing helix chain 'F' and resid 387 through 390 No H-bonds generated for 'chain 'F' and resid 387 through 390' Processing helix chain 'F' and resid 392 through 406 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 414 through 425 Processing helix chain 'F' and resid 429 through 454 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) Processing helix chain 'F' and resid 484 through 504 Proline residue: F 489 - end of helix removed outlier: 3.724A pdb=" N ILE F 495 " --> pdb=" O VAL F 491 " (cutoff:3.500A) Proline residue: F 496 - end of helix removed outlier: 3.713A pdb=" N ILE F 500 " --> pdb=" O PRO F 496 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLY F 501 " --> pdb=" O SER F 497 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N PHE F 502 " --> pdb=" O THR F 498 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL F 503 " --> pdb=" O LEU F 499 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N GLY F 504 " --> pdb=" O ILE F 500 " (cutoff:3.500A) Processing helix chain 'F' and resid 510 through 514 Processing helix chain 'F' and resid 533 through 555 removed outlier: 3.966A pdb=" N VAL F 541 " --> pdb=" O GLY F 537 " (cutoff:3.500A) Processing helix chain 'F' and resid 564 through 568 Processing helix chain 'F' and resid 570 through 577 Processing helix chain 'F' and resid 579 through 588 removed outlier: 3.562A pdb=" N PHE F 582 " --> pdb=" O LYS F 579 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ASP F 583 " --> pdb=" O TRP F 580 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU F 584 " --> pdb=" O TYR F 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 591 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 628 through 630 No H-bonds generated for 'chain 'F' and resid 628 through 630' Processing helix chain 'F' and resid 635 through 653 Processing helix chain 'G' and resid 4 through 27 Processing helix chain 'G' and resid 32 through 52 removed outlier: 4.174A pdb=" N GLY G 40 " --> pdb=" O ALA G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 65 Processing helix chain 'G' and resid 70 through 80 Processing helix chain 'G' and resid 93 through 117 removed outlier: 3.980A pdb=" N GLY G 99 " --> pdb=" O LEU G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 140 removed outlier: 3.979A pdb=" N PHE G 140 " --> pdb=" O GLY G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 164 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) Processing helix chain 'H' and resid 51 through 57 removed outlier: 3.933A pdb=" N GLU H 56 " --> pdb=" O GLU H 52 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASN H 57 " --> pdb=" O LYS H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 63 No H-bonds generated for 'chain 'H' and resid 60 through 63' Processing helix chain 'H' and resid 75 through 89 removed outlier: 3.572A pdb=" N GLU H 79 " --> pdb=" O GLY H 75 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASN H 84 " --> pdb=" O ALA H 80 " (cutoff:3.500A) Proline residue: H 86 - end of helix removed outlier: 3.642A pdb=" N LEU H 89 " --> pdb=" O ALA H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 125 Proline residue: H 120 - end of helix Processing helix chain 'H' and resid 131 through 148 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 172 through 195 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 198 through 204 Processing helix chain 'H' and resid 212 through 217 Processing helix chain 'H' and resid 222 through 226 removed outlier: 3.813A pdb=" N ARG H 226 " --> pdb=" O PRO H 223 " (cutoff:3.500A) Processing helix chain 'H' and resid 234 through 237 No H-bonds generated for 'chain 'H' and resid 234 through 237' Processing helix chain 'H' and resid 258 through 281 removed outlier: 3.687A pdb=" N LYS H 274 " --> pdb=" O ARG H 270 " (cutoff:3.500A) Processing helix chain 'H' and resid 288 through 297 Processing helix chain 'H' and resid 307 through 309 No H-bonds generated for 'chain 'H' and resid 307 through 309' Processing helix chain 'H' and resid 366 through 369 No H-bonds generated for 'chain 'H' and resid 366 through 369' Processing helix chain 'H' and resid 378 through 384 Processing helix chain 'H' and resid 389 through 393 Processing helix chain 'I' and resid 5 through 29 removed outlier: 3.630A pdb=" N ASN I 9 " --> pdb=" O ASN I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 68 through 71 No H-bonds generated for 'chain 'I' and resid 68 through 71' Processing helix chain 'I' and resid 108 through 111 No H-bonds generated for 'chain 'I' and resid 108 through 111' Processing helix chain 'I' and resid 131 through 134 Processing helix chain 'I' and resid 148 through 150 No H-bonds generated for 'chain 'I' and resid 148 through 150' Processing helix chain 'I' and resid 184 through 190 removed outlier: 4.175A pdb=" N ALA I 188 " --> pdb=" O PRO I 184 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ASN I 189 " --> pdb=" O GLU I 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 19 No H-bonds generated for 'chain 'J' and resid 16 through 19' Processing helix chain 'J' and resid 43 through 54 removed outlier: 5.645A pdb=" N LEU J 47 " --> pdb=" O ASP J 44 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA J 48 " --> pdb=" O ARG J 45 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N CYS J 50 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR J 52 " --> pdb=" O VAL J 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 115 through 128 removed outlier: 3.812A pdb=" N TRP J 119 " --> pdb=" O THR J 116 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLN J 120 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLU J 121 " --> pdb=" O ASP J 118 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR J 125 " --> pdb=" O ARG J 122 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET J 127 " --> pdb=" O SER J 124 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE J 128 " --> pdb=" O TYR J 125 " (cutoff:3.500A) Processing helix chain 'K' and resid 27 through 40 Processing helix chain 'K' and resid 52 through 61 Processing helix chain 'K' and resid 68 through 70 No H-bonds generated for 'chain 'K' and resid 68 through 70' Processing helix chain 'K' and resid 78 through 80 No H-bonds generated for 'chain 'K' and resid 78 through 80' Processing helix chain 'K' and resid 95 through 103 Processing helix chain 'K' and resid 116 through 119 No H-bonds generated for 'chain 'K' and resid 116 through 119' Processing helix chain 'K' and resid 122 through 124 No H-bonds generated for 'chain 'K' and resid 122 through 124' Processing helix chain 'K' and resid 135 through 137 No H-bonds generated for 'chain 'K' and resid 135 through 137' Processing helix chain 'K' and resid 152 through 168 removed outlier: 3.741A pdb=" N VAL K 160 " --> pdb=" O MET K 156 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASN K 168 " --> pdb=" O LYS K 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 21 Processing helix chain 'L' and resid 23 through 32 Processing helix chain 'L' and resid 41 through 53 Processing helix chain 'L' and resid 55 through 64 Proline residue: L 63 - end of helix Processing helix chain 'M' and resid 43 through 59 Processing helix chain 'M' and resid 67 through 87 Processing helix chain 'N' and resid 8 through 16 Processing helix chain 'N' and resid 31 through 39 Processing helix chain 'N' and resid 49 through 51 No H-bonds generated for 'chain 'N' and resid 49 through 51' Processing helix chain 'N' and resid 55 through 58 No H-bonds generated for 'chain 'N' and resid 55 through 58' Processing helix chain 'N' and resid 83 through 89 Processing helix chain 'N' and resid 110 through 122 Processing helix chain 'O' and resid 13 through 16 No H-bonds generated for 'chain 'O' and resid 13 through 16' Processing helix chain 'O' and resid 63 through 65 No H-bonds generated for 'chain 'O' and resid 63 through 65' Processing helix chain 'P' and resid 7 through 27 Proline residue: P 16 - end of helix removed outlier: 4.257A pdb=" N THR P 27 " --> pdb=" O LEU P 23 " (cutoff:3.500A) Processing helix chain 'Q' and resid 18 through 41 Processing helix chain 'S' and resid 92 through 94 No H-bonds generated for 'chain 'S' and resid 92 through 94' Processing sheet with id= A, first strand: chain 'D' and resid 68 through 73 removed outlier: 6.979A pdb=" N LEU D 78 " --> pdb=" O TRP D 72 " (cutoff:3.500A) Processing sheet with id= B, 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= C, first strand: chain 'H' and resid 27 through 30 Processing sheet with id= D, first strand: chain 'H' and resid 327 through 331 Processing sheet with id= E, first strand: chain 'I' and resid 97 through 99 Processing sheet with id= F, first strand: chain 'J' and resid 38 through 41 removed outlier: 6.784A pdb=" N ARG J 95 " --> pdb=" O ILE J 39 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N VAL J 41 " --> pdb=" O ARG J 95 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LYS J 97 " --> pdb=" O VAL J 41 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS J 80 " --> pdb=" O ARG J 62 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'J' and resid 106 through 108 removed outlier: 6.192A pdb=" N VAL J 131 " --> pdb=" O VAL J 107 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'K' and resid 83 through 86 removed outlier: 6.376A pdb=" N TYR K 110 " --> pdb=" O ILE K 84 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N THR K 86 " --> pdb=" O TYR K 110 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE K 112 " --> pdb=" O THR K 86 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL K 143 " --> pdb=" O ALA K 113 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'N' and resid 19 through 22 Processing sheet with id= J, first strand: chain 'N' and resid 42 through 47 removed outlier: 6.676A pdb=" N GLY N 97 " --> pdb=" O THR N 43 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N LEU N 45 " --> pdb=" O GLY N 97 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL N 99 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N MET N 47 " --> pdb=" O VAL N 99 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N TRP N 101 " --> pdb=" O MET N 47 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'O' and resid 9 through 11 Processing sheet with id= L, first strand: chain 'O' and resid 59 through 62 removed outlier: 3.578A pdb=" N ASP O 42 " --> pdb=" O GLN O 49 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LYS O 51 " --> pdb=" O VAL O 40 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N VAL O 40 " --> pdb=" O LYS O 51 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'S' and resid 95 through 97 removed outlier: 3.766A pdb=" N GLU S 96 " --> pdb=" O LYS S 52 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ALA S 76 " --> pdb=" O GLN S 68 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ILE S 70 " --> pdb=" O LYS S 74 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N LYS S 74 " --> pdb=" O ILE S 70 " (cutoff:3.500A) 1440 hydrogen bonds defined for protein. 4143 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: 10.18 Time building geometry restraints manager: 13.48 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: 73.19 - 86.93: 42 86.93 - 100.68: 69 100.68 - 114.43: 19670 114.43 - 128.17: 23138 128.17 - 141.92: 323 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 - 24.77: 17396 24.77 - 49.54: 982 49.54 - 74.30: 121 74.30 - 99.07: 24 99.07 - 123.84: 12 Dihedral angle restraints: 18535 sinusoidal: 7374 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 18532 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 4192 0.077 - 0.155: 654 0.155 - 0.232: 85 0.232 - 0.310: 15 0.310 - 0.387: 7 Chirality restraints: 4953 Sorted by residual: chirality pdb=" C2G DGD A 401 " pdb=" C1G DGD A 401 " pdb=" C3G DGD A 401 " pdb=" O2G DGD A 401 " both_signs ideal model delta sigma weight residual False 2.74 2.36 0.39 2.00e-01 2.50e+01 3.74e+00 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 -2.30 -1.93 -0.36 2.00e-01 2.50e+01 3.30e+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 ... (remaining 4950 not shown) Planarity restraints: 5313 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 5310 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 7538 2.79 - 3.31: 28775 3.31 - 3.84: 56474 3.84 - 4.37: 68236 4.37 - 4.90: 115119 Nonbonded interactions: 276142 Sorted by model distance: nonbonded pdb=" OH TYR C 75 " pdb=" O ALA E 75 " model vdw 2.258 2.440 nonbonded pdb=" OE2 GLU H 107 " pdb=" OH TYR H 243 " model vdw 2.267 2.440 nonbonded pdb=" O ILE A 5 " pdb=" O2D DGD A 402 " model vdw 2.273 2.440 nonbonded pdb=" O ALA D 322 " pdb=" OH TYR D 411 " model vdw 2.281 2.440 nonbonded pdb=" O TYR H 190 " pdb=" OH TYR H 262 " model vdw 2.289 2.440 ... (remaining 276137 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians 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. 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: 5.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 18.460 Check model and map are aligned: 0.430 Convert atoms to be neutral: 0.270 Process input model: 83.720 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.870 ------------------------------------------------------------------------------- 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 31815 Z= 0.599 Angle : 1.298 38.131 43242 Z= 0.593 Chirality : 0.060 0.387 4953 Planarity : 0.012 0.292 5313 Dihedral : 15.799 123.839 11399 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.85 % Favored : 92.13 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 *********************** 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 fitting. rotamer outliers: 13 poor density : 533 time to evaluate : 3.718 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 outliers start: 13 outliers final: 4 residues processed: 544 average time/residue: 1.4550 time to fit residues: 934.3016 Evaluate side-chains 341 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 337 time to evaluate : 3.908 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 1 average time/residue: 0.4218 time to fit residues: 5.6150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 320 optimal weight: 0.6980 chunk 288 optimal weight: 0.9980 chunk 159 optimal weight: 0.2980 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 297 optimal weight: 0.0670 chunk 115 optimal weight: 0.9980 chunk 181 optimal weight: 0.1980 chunk 221 optimal weight: 3.9990 chunk 345 optimal weight: 4.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 199 GLN B 340 ASN D 134 GLN D 266 ASN D 274 HIS ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN D 453 HIS E 39 ASN E 44 ASN F 62 GLN 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 217 ASN H 267 GLN H 361 ASN I 95 HIS I 135 ASN J 120 GLN J 165 GLN K 32 ASN K 179 GLN K 200 GLN K 203 ASN L 70 GLN ** M 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 95 ASN N 90 ASN N 118 GLN O 18 ASN S 55 ASN S 64 GLN S 83 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 31815 Z= 0.178 Angle : 0.649 14.124 43242 Z= 0.319 Chirality : 0.041 0.316 4953 Planarity : 0.005 0.066 5313 Dihedral : 10.549 126.503 4584 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.12 % Favored : 92.86 % Rotamer Outliers : 2.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.13), residues: 3835 helix: -0.59 (0.10), residues: 2274 sheet: -2.57 (0.36), residues: 178 loop : -2.53 (0.15), residues: 1383 *********************** 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 465 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 395 time to evaluate : 3.643 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 outliers start: 70 outliers final: 17 residues processed: 443 average time/residue: 1.3213 time to fit residues: 703.8758 Evaluate side-chains 361 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 344 time to evaluate : 3.766 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 16 residues processed: 3 average time/residue: 0.4336 time to fit residues: 7.0238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 191 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 287 optimal weight: 6.9990 chunk 234 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 345 optimal weight: 4.9990 chunk 373 optimal weight: 1.9990 chunk 307 optimal weight: 3.9990 chunk 342 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 277 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 HIS B 340 ASN D 163 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 453 HIS ** F 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 205 GLN H 267 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 25 ASN K 172 ASN K 200 GLN M 9 HIS N 118 GLN O 18 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.087 31815 Z= 0.378 Angle : 0.717 13.603 43242 Z= 0.354 Chirality : 0.045 0.334 4953 Planarity : 0.005 0.066 5313 Dihedral : 10.121 126.799 4584 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.34 % Favored : 91.63 % Rotamer Outliers : 3.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.13), residues: 3835 helix: 0.02 (0.11), residues: 2282 sheet: -2.51 (0.35), residues: 179 loop : -2.29 (0.16), residues: 1374 *********************** 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 464 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 352 time to evaluate : 3.687 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 outliers start: 112 outliers final: 49 residues processed: 431 average time/residue: 1.3392 time to fit residues: 691.9354 Evaluate side-chains 387 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 338 time to evaluate : 3.583 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 34 residues processed: 16 average time/residue: 0.4502 time to fit residues: 16.0180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 341 optimal weight: 2.9990 chunk 259 optimal weight: 2.9990 chunk 179 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 164 optimal weight: 5.9990 chunk 232 optimal weight: 1.9990 chunk 346 optimal weight: 7.9990 chunk 367 optimal weight: 1.9990 chunk 181 optimal weight: 0.3980 chunk 328 optimal weight: 6.9990 chunk 98 optimal weight: 0.6980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 453 HIS G 117 GLN ** H 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 205 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 135 ASN K 172 ASN K 179 GLN ** K 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 200 GLN M 37 ASN ** M 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 118 GLN O 18 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.084 31815 Z= 0.243 Angle : 0.639 13.384 43242 Z= 0.317 Chirality : 0.042 0.325 4953 Planarity : 0.005 0.065 5313 Dihedral : 9.696 129.663 4584 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.38 % Favored : 92.59 % Rotamer Outliers : 2.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.14), residues: 3835 helix: 0.45 (0.11), residues: 2276 sheet: -2.46 (0.35), residues: 177 loop : -2.09 (0.16), residues: 1382 *********************** 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 457 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 362 time to evaluate : 3.964 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 outliers start: 95 outliers final: 43 residues processed: 433 average time/residue: 1.2843 time to fit residues: 670.3572 Evaluate side-chains 383 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 340 time to evaluate : 3.343 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 36 residues processed: 7 average time/residue: 0.9708 time to fit residues: 13.0158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 305 optimal weight: 0.4980 chunk 208 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 273 optimal weight: 0.9980 chunk 151 optimal weight: 0.0670 chunk 313 optimal weight: 2.9990 chunk 253 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 187 optimal weight: 3.9990 chunk 329 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.5122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 117 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 172 ASN K 200 GLN ** M 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 90 ASN N 118 GLN O 18 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 31815 Z= 0.284 Angle : 0.654 13.758 43242 Z= 0.323 Chirality : 0.043 0.327 4953 Planarity : 0.005 0.065 5313 Dihedral : 9.486 126.938 4584 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.93 % Favored : 92.05 % Rotamer Outliers : 3.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.14), residues: 3835 helix: 0.62 (0.11), residues: 2278 sheet: -2.36 (0.35), residues: 174 loop : -1.99 (0.17), residues: 1383 *********************** 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 455 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 357 time to evaluate : 3.685 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 outliers start: 98 outliers final: 53 residues processed: 428 average time/residue: 1.3207 time to fit residues: 687.2302 Evaluate side-chains 382 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 329 time to evaluate : 3.857 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 42 residues processed: 12 average time/residue: 0.5557 time to fit residues: 15.0030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 123 optimal weight: 0.5980 chunk 330 optimal weight: 0.9980 chunk 72 optimal weight: 0.0030 chunk 215 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 367 optimal weight: 0.8980 chunk 305 optimal weight: 2.9990 chunk 170 optimal weight: 0.2980 chunk 30 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 193 optimal weight: 4.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 453 HIS F 326 GLN F 345 HIS ** H 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 135 ASN K 200 GLN ** M 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 87 GLN O 18 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 31815 Z= 0.175 Angle : 0.602 14.259 43242 Z= 0.297 Chirality : 0.041 0.321 4953 Planarity : 0.004 0.066 5313 Dihedral : 9.106 129.003 4584 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.17 % Favored : 92.80 % Rotamer Outliers : 2.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.14), residues: 3835 helix: 0.91 (0.11), residues: 2282 sheet: -1.91 (0.39), residues: 160 loop : -1.93 (0.17), residues: 1393 *********************** 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 463 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 368 time to evaluate : 3.564 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 outliers start: 95 outliers final: 44 residues processed: 434 average time/residue: 1.2698 time to fit residues: 668.8132 Evaluate side-chains 381 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 337 time to evaluate : 3.862 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 38 residues processed: 6 average time/residue: 1.3789 time to fit residues: 14.6638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 354 optimal weight: 0.0770 chunk 41 optimal weight: 0.9980 chunk 209 optimal weight: 0.6980 chunk 268 optimal weight: 6.9990 chunk 208 optimal weight: 0.7980 chunk 309 optimal weight: 0.0670 chunk 205 optimal weight: 7.9990 chunk 366 optimal weight: 0.4980 chunk 229 optimal weight: 3.9990 chunk 223 optimal weight: 2.9990 chunk 169 optimal weight: 0.6980 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 453 HIS ** E 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN ** H 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 290 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 135 ASN K 172 ASN K 200 GLN ** M 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 87 GLN N 90 ASN N 118 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 31815 Z= 0.167 Angle : 0.594 15.256 43242 Z= 0.293 Chirality : 0.041 0.321 4953 Planarity : 0.004 0.065 5313 Dihedral : 8.817 123.969 4584 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.48 % Favored : 92.49 % Rotamer Outliers : 2.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.14), residues: 3835 helix: 1.09 (0.11), residues: 2272 sheet: -1.73 (0.40), residues: 160 loop : -1.85 (0.17), residues: 1403 *********************** 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 446 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 365 time to evaluate : 3.312 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 outliers start: 81 outliers final: 40 residues processed: 429 average time/residue: 1.2750 time to fit residues: 667.1196 Evaluate side-chains 381 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 341 time to evaluate : 4.031 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 37 residues processed: 4 average time/residue: 0.5994 time to fit residues: 8.2874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 226 optimal weight: 0.6980 chunk 146 optimal weight: 0.9980 chunk 218 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 232 optimal weight: 0.9990 chunk 249 optimal weight: 0.9990 chunk 181 optimal weight: 0.1980 chunk 34 optimal weight: 0.9980 chunk 287 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 453 HIS ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 135 ASN K 25 ASN ** M 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 87 GLN N 90 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 31815 Z= 0.188 Angle : 0.604 15.888 43242 Z= 0.297 Chirality : 0.041 0.323 4953 Planarity : 0.004 0.067 5313 Dihedral : 8.698 125.797 4584 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.56 % Favored : 92.41 % Rotamer Outliers : 2.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.14), residues: 3835 helix: 1.15 (0.11), residues: 2274 sheet: -1.60 (0.41), residues: 160 loop : -1.80 (0.17), residues: 1401 *********************** 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 429 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 353 time to evaluate : 3.696 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 outliers start: 76 outliers final: 43 residues processed: 411 average time/residue: 1.3419 time to fit residues: 667.0420 Evaluate side-chains 379 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 336 time to evaluate : 3.624 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 36 residues processed: 7 average time/residue: 1.2319 time to fit residues: 15.2897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 333 optimal weight: 1.9990 chunk 350 optimal weight: 0.0370 chunk 320 optimal weight: 1.9990 chunk 341 optimal weight: 6.9990 chunk 205 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 268 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 308 optimal weight: 7.9990 chunk 322 optimal weight: 3.9990 chunk 340 optimal weight: 1.9990 overall best weight: 1.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 57 HIS K 25 ASN ** M 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 87 GLN N 90 ASN O 49 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 31815 Z= 0.301 Angle : 0.664 17.216 43242 Z= 0.328 Chirality : 0.044 0.328 4953 Planarity : 0.005 0.066 5313 Dihedral : 8.851 132.130 4584 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.77 % Favored : 92.20 % Rotamer Outliers : 2.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.14), residues: 3835 helix: 1.01 (0.11), residues: 2288 sheet: -1.66 (0.40), residues: 165 loop : -1.84 (0.17), residues: 1382 *********************** 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 410 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 343 time to evaluate : 3.402 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 outliers start: 67 outliers final: 41 residues processed: 399 average time/residue: 1.3579 time to fit residues: 658.4605 Evaluate side-chains 371 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 330 time to evaluate : 3.639 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 38 residues processed: 3 average time/residue: 1.1134 time to fit residues: 8.9238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 224 optimal weight: 0.4980 chunk 360 optimal weight: 0.1980 chunk 220 optimal weight: 0.9990 chunk 171 optimal weight: 0.7980 chunk 250 optimal weight: 4.9990 chunk 378 optimal weight: 6.9990 chunk 348 optimal weight: 2.9990 chunk 301 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 232 optimal weight: 0.9980 chunk 184 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 453 HIS E 97 ASN ** H 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 135 ASN K 25 ASN ** K 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 11 HIS M 87 GLN N 90 ASN O 49 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 31815 Z= 0.188 Angle : 0.618 17.193 43242 Z= 0.304 Chirality : 0.042 0.321 4953 Planarity : 0.004 0.067 5313 Dihedral : 8.614 131.493 4584 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.33 % Favored : 92.65 % Rotamer Outliers : 1.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.14), residues: 3835 helix: 1.18 (0.11), residues: 2278 sheet: -1.57 (0.41), residues: 165 loop : -1.79 (0.17), residues: 1392 ********************** 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 394 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 343 time to evaluate : 3.609 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 outliers start: 51 outliers final: 41 residues processed: 385 average time/residue: 1.3231 time to fit residues: 628.3473 Evaluate side-chains 377 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 336 time to evaluate : 3.784 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 38 residues processed: 5 average time/residue: 0.7057 time to fit residues: 10.1812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 239 optimal weight: 6.9990 chunk 321 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 277 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 301 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 310 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 55 optimal weight: 0.0470 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 ASN G 117 GLN ** H 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 135 ASN ** K 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 203 ASN M 87 GLN O 49 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.099087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.080970 restraints weight = 54804.035| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 1.72 r_work: 0.2946 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 31815 Z= 0.194 Angle : 0.614 17.144 43242 Z= 0.302 Chirality : 0.042 0.323 4953 Planarity : 0.004 0.067 5313 Dihedral : 8.504 131.086 4584 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.64 % Favored : 92.33 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.14), residues: 3835 helix: 1.23 (0.11), residues: 2277 sheet: -1.54 (0.41), residues: 163 loop : -1.75 (0.17), residues: 1395 =============================================================================== Job complete usr+sys time: 10918.90 seconds wall clock time: 195 minutes 11.38 seconds (11711.38 seconds total)