Starting phenix.real_space_refine on Thu Mar 21 19:50:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6khj_9990/03_2024/6khj_9990_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6khj_9990/03_2024/6khj_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_9990/03_2024/6khj_9990.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6khj_9990/03_2024/6khj_9990.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6khj_9990/03_2024/6khj_9990_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6khj_9990/03_2024/6khj_9990_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 12 7.16 5 P 6 5.49 5 S 174 5.16 5 C 20516 2.51 5 N 4894 2.21 5 O 5425 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 16.27, per 1000 atoms: 0.52 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: 11.44 Conformation dependent library (CDL) restraints added in 5.6 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: 5.59 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: 10.28 Time building geometry restraints manager: 12.42 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 - 24.94: 17554 24.94 - 49.87: 1046 49.87 - 74.81: 145 74.81 - 99.74: 46 99.74 - 124.68: 42 Dihedral angle restraints: 18833 sinusoidal: 7672 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 18830 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 4688 0.115 - 0.229: 250 0.229 - 0.344: 13 0.344 - 0.459: 1 0.459 - 0.573: 1 Chirality restraints: 4953 Sorted by residual: chirality pdb=" C5' LMT D 603 " pdb=" C4' LMT D 603 " pdb=" C6' LMT D 603 " pdb=" O5' LMT D 603 " both_signs ideal model delta sigma weight residual False -2.51 -1.93 -0.57 2.00e-01 2.50e+01 8.22e+00 chirality pdb=" C1 LMG F 704 " pdb=" C2 LMG F 704 " pdb=" O1 LMG F 704 " pdb=" O6 LMG F 704 " both_signs ideal model delta sigma weight residual False 2.29 2.64 -0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" C3 LMG F 704 " pdb=" C2 LMG F 704 " pdb=" C4 LMG F 704 " pdb=" O3 LMG F 704 " both_signs ideal model delta sigma weight residual False 2.40 2.70 -0.30 2.00e-01 2.50e+01 2.27e+00 ... (remaining 4950 not shown) Planarity restraints: 5317 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 BCR D 602 " 0.502 2.00e-02 2.50e+03 2.92e-01 1.07e+03 pdb=" C11 BCR D 602 " -0.247 2.00e-02 2.50e+03 pdb=" C34 BCR D 602 " 0.109 2.00e-02 2.50e+03 pdb=" C8 BCR D 602 " -0.045 2.00e-02 2.50e+03 pdb=" C9 BCR D 602 " -0.318 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C16 BCR D 602 " 0.239 2.00e-02 2.50e+03 2.90e-01 1.05e+03 pdb=" C17 BCR D 602 " -0.492 2.00e-02 2.50e+03 pdb=" C18 BCR D 602 " 0.326 2.00e-02 2.50e+03 pdb=" C19 BCR D 602 " 0.040 2.00e-02 2.50e+03 pdb=" C36 BCR D 602 " -0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 BCR F 701 " -0.357 2.00e-02 2.50e+03 2.41e-01 7.26e+02 pdb=" C11 BCR F 701 " 0.176 2.00e-02 2.50e+03 pdb=" C34 BCR F 701 " -0.160 2.00e-02 2.50e+03 pdb=" C8 BCR F 701 " 0.016 2.00e-02 2.50e+03 pdb=" C9 BCR F 701 " 0.326 2.00e-02 2.50e+03 ... (remaining 5314 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 15.610 Check model and map are aligned: 0.420 Set scattering table: 0.280 Process input model: 84.710 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 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= 0.593 Angle : 1.300 38.131 43242 Z= 0.592 Chirality : 0.058 0.573 4953 Planarity : 0.012 0.292 5317 Dihedral : 17.683 124.676 11697 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.85 % Favored : 92.13 % Rotamer: Outliers : 0.41 % Allowed : 6.71 % Favored : 92.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 274 HIS 0.014 0.002 HIS D 339 PHE 0.038 0.002 PHE K 67 TYR 0.049 0.003 TYR B 166 ARG 0.009 0.001 ARG J 62 *********************** 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 : 3.631 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 232 PHE cc_start: 0.7033 (OUTLIER) cc_final: 0.5228 (m-80) REVERT: A 338 ASP cc_start: 0.7542 (p0) cc_final: 0.7087 (p0) REVERT: B 237 GLU cc_start: 0.8145 (tt0) cc_final: 0.7872 (tt0) REVERT: B 361 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8080 (mm-30) REVERT: D 89 MET cc_start: 0.8239 (tpt) cc_final: 0.7950 (tpt) REVERT: F 530 LEU cc_start: 0.6719 (tp) cc_final: 0.6490 (tp) REVERT: G 53 MET cc_start: 0.8941 (ptp) cc_final: 0.8686 (ptm) REVERT: G 113 LYS cc_start: 0.8353 (tttm) cc_final: 0.8141 (ttmm) REVERT: I 13 GLU cc_start: 0.7429 (tp30) cc_final: 0.7224 (tp30) REVERT: I 130 ASP cc_start: 0.8760 (t0) cc_final: 0.8532 (t70) REVERT: J 22 GLN cc_start: 0.7870 (pt0) cc_final: 0.7669 (pt0) REVERT: J 143 MET cc_start: 0.8881 (mmm) cc_final: 0.8634 (mmm) REVERT: K 172 ASN cc_start: 0.7184 (m-40) cc_final: 0.6860 (t0) REVERT: L 12 VAL cc_start: 0.8560 (p) cc_final: 0.8305 (t) REVERT: M 87 GLN cc_start: 0.8289 (mt0) cc_final: 0.7857 (mt0) REVERT: O 15 LYS cc_start: 0.8376 (tptp) cc_final: 0.8164 (mmmt) REVERT: Q 10 MET cc_start: 0.7970 (mmt) cc_final: 0.7693 (mpt) REVERT: S 43 MET cc_start: 0.2683 (ttt) cc_final: 0.2293 (ttp) outliers start: 13 outliers final: 4 residues processed: 544 average time/residue: 1.4710 time to fit residues: 937.7059 Evaluate side-chains 343 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 338 time to evaluate : 3.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain P residue 29 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 320 optimal weight: 0.5980 chunk 288 optimal weight: 0.5980 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: 1.9990 chunk 115 optimal weight: 0.9980 chunk 181 optimal weight: 0.1980 chunk 221 optimal weight: 3.9990 chunk 345 optimal weight: 5.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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: 0.8352 moved from start: 0.1298 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= 0.182 Angle : 0.665 14.086 43242 Z= 0.323 Chirality : 0.042 0.267 4953 Planarity : 0.005 0.066 5317 Dihedral : 13.289 98.753 4890 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.09 % Favored : 92.88 % Rotamer: Outliers : 2.07 % Allowed : 13.68 % Favored : 84.25 % 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: -2.14 (0.13), residues: 3835 helix: -0.61 (0.10), residues: 2273 sheet: -2.58 (0.35), residues: 178 loop : -2.53 (0.15), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 151 HIS 0.005 0.001 HIS N 63 PHE 0.019 0.001 PHE H 131 TYR 0.024 0.001 TYR F 445 ARG 0.005 0.000 ARG N 36 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7670 Ramachandran restraints generated. 3835 Oldfield, 0 Emsley, 3835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7670 Ramachandran restraints generated. 3835 Oldfield, 0 Emsley, 3835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 392 time to evaluate : 3.497 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 173 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7907 (mt-10) REVERT: A 229 ARG cc_start: 0.7407 (mmm160) cc_final: 0.7039 (mtp-110) REVERT: A 232 PHE cc_start: 0.7065 (OUTLIER) cc_final: 0.5435 (m-80) REVERT: A 276 TYR cc_start: 0.8827 (m-80) cc_final: 0.8494 (m-80) REVERT: B 436 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7830 (mt-10) REVERT: D 89 MET cc_start: 0.8390 (tpt) cc_final: 0.8091 (tpt) REVERT: E 89 ASP cc_start: 0.7329 (t0) cc_final: 0.7086 (t0) REVERT: F 255 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7651 (mp0) REVERT: F 457 LYS cc_start: 0.7305 (ptpp) cc_final: 0.6888 (pttm) REVERT: I 67 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7227 (mp0) REVERT: I 141 MET cc_start: 0.9153 (ptm) cc_final: 0.8939 (ptm) REVERT: K 64 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7247 (tmm-80) REVERT: M 87 GLN cc_start: 0.8335 (mt0) cc_final: 0.8013 (mt0) REVERT: N 104 ASP cc_start: 0.7547 (OUTLIER) cc_final: 0.7322 (m-30) REVERT: N 135 ASP cc_start: 0.8138 (t0) cc_final: 0.7883 (t0) REVERT: Q 10 MET cc_start: 0.7855 (mmt) cc_final: 0.7002 (mmt) REVERT: S 43 MET cc_start: 0.2559 (ttt) cc_final: 0.2200 (ttp) outliers start: 66 outliers final: 16 residues processed: 441 average time/residue: 1.3658 time to fit residues: 715.4548 Evaluate side-chains 361 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 338 time to evaluate : 3.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 382 ARG Chi-restraints excluded: chain G residue 83 LYS Chi-restraints excluded: chain H residue 36 ASP Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 67 GLU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain J residue 157 ILE Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain K residue 52 CYS Chi-restraints excluded: chain K residue 64 ARG Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 64 ASP Chi-restraints excluded: chain N residue 104 ASP Chi-restraints excluded: chain P residue 14 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 191 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 287 optimal weight: 6.9990 chunk 234 optimal weight: 0.6980 chunk 95 optimal weight: 0.6980 chunk 345 optimal weight: 0.0370 chunk 373 optimal weight: 2.9990 chunk 307 optimal weight: 4.9990 chunk 342 optimal weight: 0.8980 chunk 117 optimal weight: 0.7980 chunk 277 optimal weight: 2.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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 453 HIS ** H 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 267 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 95 HIS I 135 ASN K 25 ASN K 200 GLN M 23 HIS N 118 GLN O 18 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31815 Z= 0.183 Angle : 0.626 13.594 43242 Z= 0.305 Chirality : 0.041 0.297 4953 Planarity : 0.005 0.066 5317 Dihedral : 10.873 108.908 4886 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.48 % Favored : 92.49 % Rotamer: Outliers : 2.92 % Allowed : 14.52 % Favored : 82.56 % 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: -1.22 (0.13), residues: 3835 helix: 0.22 (0.11), residues: 2267 sheet: -2.43 (0.35), residues: 179 loop : -2.28 (0.16), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 151 HIS 0.005 0.001 HIS D 339 PHE 0.015 0.001 PHE A 321 TYR 0.023 0.001 TYR F 445 ARG 0.008 0.000 ARG D 498 *********************** 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 462 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 369 time to evaluate : 3.566 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7808 (tp30) REVERT: A 232 PHE cc_start: 0.6940 (OUTLIER) cc_final: 0.5237 (m-80) REVERT: A 276 TYR cc_start: 0.8856 (m-80) cc_final: 0.8555 (m-80) REVERT: A 338 ASP cc_start: 0.7504 (OUTLIER) cc_final: 0.7182 (p0) REVERT: E 89 ASP cc_start: 0.7414 (t0) cc_final: 0.7039 (t0) REVERT: F 457 LYS cc_start: 0.7369 (ptpp) cc_final: 0.6997 (pttm) REVERT: F 610 ASP cc_start: 0.7845 (OUTLIER) cc_final: 0.7627 (m-30) REVERT: I 67 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7030 (mp0) REVERT: I 141 MET cc_start: 0.9049 (ptm) cc_final: 0.8846 (ptm) REVERT: L 27 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8448 (mp) REVERT: L 43 GLU cc_start: 0.8101 (tt0) cc_final: 0.7837 (tt0) REVERT: L 66 ASN cc_start: 0.9025 (t0) cc_final: 0.8634 (t0) REVERT: L 72 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.6239 (ttt-90) REVERT: M 87 GLN cc_start: 0.8259 (mt0) cc_final: 0.8000 (mt0) REVERT: N 104 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7442 (m-30) REVERT: N 135 ASP cc_start: 0.8243 (t0) cc_final: 0.7838 (t0) REVERT: O 15 LYS cc_start: 0.8871 (mmmt) cc_final: 0.8651 (mmmt) REVERT: Q 10 MET cc_start: 0.7796 (mmt) cc_final: 0.7034 (mmt) REVERT: S 43 MET cc_start: 0.2512 (ttt) cc_final: 0.2170 (ttp) outliers start: 93 outliers final: 31 residues processed: 437 average time/residue: 1.4106 time to fit residues: 733.4696 Evaluate side-chains 387 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 348 time to evaluate : 3.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 446 ASN Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 304 MET Chi-restraints excluded: chain F residue 382 ARG Chi-restraints excluded: chain F residue 610 ASP Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 83 LYS Chi-restraints excluded: chain H residue 36 ASP Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 67 GLU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 62 ARG Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain K residue 52 CYS Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 72 ARG Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 64 ASP Chi-restraints excluded: chain N residue 61 GLN Chi-restraints excluded: chain N residue 80 GLN Chi-restraints excluded: chain N residue 104 ASP Chi-restraints excluded: chain N residue 125 LYS Chi-restraints excluded: chain P residue 14 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 341 optimal weight: 0.9980 chunk 259 optimal weight: 1.9990 chunk 179 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 164 optimal weight: 0.9980 chunk 232 optimal weight: 2.9990 chunk 346 optimal weight: 1.9990 chunk 367 optimal weight: 4.9990 chunk 181 optimal weight: 0.7980 chunk 328 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 453 HIS ** 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 172 ASN K 181 HIS K 200 GLN M 9 HIS N 90 ASN N 118 GLN O 18 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 31815 Z= 0.260 Angle : 0.640 13.290 43242 Z= 0.315 Chirality : 0.043 0.269 4953 Planarity : 0.005 0.065 5317 Dihedral : 10.246 111.384 4886 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.80 % Favored : 92.18 % Rotamer: Outliers : 3.26 % Allowed : 15.84 % Favored : 80.90 % 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: -0.83 (0.14), residues: 3835 helix: 0.51 (0.11), residues: 2282 sheet: -2.35 (0.35), residues: 179 loop : -2.10 (0.16), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 107 HIS 0.006 0.001 HIS M 9 PHE 0.018 0.001 PHE A 321 TYR 0.019 0.001 TYR F 445 ARG 0.007 0.000 ARG B 445 *********************** 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 469 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 365 time to evaluate : 3.359 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7815 (tp30) REVERT: A 173 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.8040 (mt-10) REVERT: A 338 ASP cc_start: 0.7480 (OUTLIER) cc_final: 0.7203 (p0) REVERT: A 358 LEU cc_start: 0.8739 (tm) cc_final: 0.8478 (tp) REVERT: D 89 MET cc_start: 0.8416 (tpt) cc_final: 0.8069 (tpt) REVERT: E 89 ASP cc_start: 0.7493 (t0) cc_final: 0.7062 (t0) REVERT: E 93 MET cc_start: 0.8965 (mmm) cc_final: 0.8751 (mmm) REVERT: F 6 GLN cc_start: 0.7908 (mt0) cc_final: 0.7707 (mt0) REVERT: F 108 MET cc_start: 0.8843 (mtp) cc_final: 0.8568 (mtt) REVERT: F 367 MET cc_start: 0.8507 (tpt) cc_final: 0.8278 (mmm) REVERT: F 457 LYS cc_start: 0.7504 (ptpp) cc_final: 0.7139 (pttm) REVERT: F 458 PHE cc_start: 0.7844 (t80) cc_final: 0.7321 (t80) REVERT: F 559 THR cc_start: 0.6814 (OUTLIER) cc_final: 0.6357 (m) REVERT: F 610 ASP cc_start: 0.7925 (OUTLIER) cc_final: 0.7699 (m-30) REVERT: F 631 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.7434 (tm-30) REVERT: I 67 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7325 (mp0) REVERT: I 141 MET cc_start: 0.9076 (ptm) cc_final: 0.8865 (ptm) REVERT: J 145 GLU cc_start: 0.7812 (mp0) cc_final: 0.7433 (pm20) REVERT: L 27 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8439 (mp) REVERT: L 66 ASN cc_start: 0.9054 (t0) cc_final: 0.8682 (t0) REVERT: L 72 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.6208 (ttt-90) REVERT: M 67 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7556 (mt-10) REVERT: M 87 GLN cc_start: 0.8289 (mt0) cc_final: 0.7992 (mt0) REVERT: N 14 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7184 (mp0) REVERT: N 19 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8812 (pp) REVERT: N 135 ASP cc_start: 0.8254 (t0) cc_final: 0.7817 (t0) REVERT: O 15 LYS cc_start: 0.8900 (mmmt) cc_final: 0.8689 (mmmt) REVERT: Q 10 MET cc_start: 0.7855 (mmt) cc_final: 0.7130 (mmt) REVERT: S 43 MET cc_start: 0.2425 (ttt) cc_final: 0.2106 (ttp) outliers start: 104 outliers final: 47 residues processed: 438 average time/residue: 1.3239 time to fit residues: 690.3377 Evaluate side-chains 401 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 342 time to evaluate : 3.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 304 MET Chi-restraints excluded: chain F residue 382 ARG Chi-restraints excluded: chain F residue 530 LEU Chi-restraints excluded: chain F residue 559 THR Chi-restraints excluded: chain F residue 610 ASP Chi-restraints excluded: chain F residue 631 GLN Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 83 LYS Chi-restraints excluded: chain H residue 36 ASP Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 67 GLU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 62 ARG Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 157 ILE Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain K residue 52 CYS Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 72 ARG Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 64 ASP Chi-restraints excluded: chain M residue 67 GLU Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain M residue 86 MET Chi-restraints excluded: chain M residue 97 ARG Chi-restraints excluded: chain N residue 14 GLU Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 61 GLN Chi-restraints excluded: chain N residue 80 GLN Chi-restraints excluded: chain N residue 125 LYS Chi-restraints excluded: chain P residue 14 MET Chi-restraints excluded: chain Q residue 3 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 305 optimal weight: 0.8980 chunk 208 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 273 optimal weight: 0.5980 chunk 151 optimal weight: 0.5980 chunk 313 optimal weight: 0.4980 chunk 253 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 187 optimal weight: 4.9990 chunk 329 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 130 GLN B 340 ASN D 453 HIS G 117 GLN ** H 109 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 K 172 ASN K 181 HIS K 200 GLN ** M 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 ASN O 18 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31815 Z= 0.186 Angle : 0.604 13.383 43242 Z= 0.297 Chirality : 0.041 0.227 4953 Planarity : 0.004 0.065 5317 Dihedral : 9.884 109.565 4884 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.46 % Favored : 92.52 % Rotamer: Outliers : 3.11 % Allowed : 16.84 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.48 (0.14), residues: 3835 helix: 0.78 (0.11), residues: 2281 sheet: -2.20 (0.36), residues: 174 loop : -1.94 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 107 HIS 0.005 0.001 HIS K 181 PHE 0.014 0.001 PHE A 321 TYR 0.022 0.001 TYR F 445 ARG 0.007 0.000 ARG H 192 *********************** 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 467 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 368 time to evaluate : 3.573 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 MET cc_start: 0.8019 (tpp) cc_final: 0.7813 (tpt) REVERT: A 173 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.8019 (mt-10) REVERT: A 276 TYR cc_start: 0.8847 (m-80) cc_final: 0.8569 (m-80) REVERT: A 338 ASP cc_start: 0.7452 (OUTLIER) cc_final: 0.7197 (p0) REVERT: A 358 LEU cc_start: 0.8725 (tm) cc_final: 0.8454 (tp) REVERT: E 89 ASP cc_start: 0.7465 (t0) cc_final: 0.7009 (t0) REVERT: E 93 MET cc_start: 0.8959 (mmm) cc_final: 0.8724 (mmm) REVERT: F 382 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7751 (mtt180) REVERT: F 458 PHE cc_start: 0.7822 (t80) cc_final: 0.7292 (t80) REVERT: F 559 THR cc_start: 0.6838 (OUTLIER) cc_final: 0.6355 (m) REVERT: G 53 MET cc_start: 0.8529 (mtm) cc_final: 0.8120 (mtm) REVERT: H 238 ASP cc_start: 0.7772 (OUTLIER) cc_final: 0.7557 (m-30) REVERT: I 67 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7032 (mp0) REVERT: I 141 MET cc_start: 0.8970 (ptm) cc_final: 0.8757 (ptm) REVERT: L 23 VAL cc_start: 0.9077 (t) cc_final: 0.8845 (t) REVERT: L 27 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8398 (mp) REVERT: L 66 ASN cc_start: 0.8951 (t0) cc_final: 0.8622 (t0) REVERT: L 72 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.6173 (ttt-90) REVERT: M 67 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7580 (mt-10) REVERT: M 87 GLN cc_start: 0.8258 (mt0) cc_final: 0.8012 (mt0) REVERT: N 19 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8784 (pp) REVERT: N 104 ASP cc_start: 0.7689 (OUTLIER) cc_final: 0.7410 (m-30) REVERT: Q 10 MET cc_start: 0.7803 (mmt) cc_final: 0.7107 (mmt) REVERT: S 43 MET cc_start: 0.2440 (ttt) cc_final: 0.2137 (ttp) outliers start: 99 outliers final: 48 residues processed: 438 average time/residue: 1.3625 time to fit residues: 712.0325 Evaluate side-chains 397 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 338 time to evaluate : 2.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain B residue 446 ASN Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain D residue 453 HIS Chi-restraints excluded: chain F residue 203 PHE Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 304 MET Chi-restraints excluded: chain F residue 382 ARG Chi-restraints excluded: chain F residue 530 LEU Chi-restraints excluded: chain F residue 559 THR Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 79 MET Chi-restraints excluded: chain G residue 83 LYS Chi-restraints excluded: chain H residue 36 ASP Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 238 ASP Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 67 GLU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 62 ARG Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain K residue 52 CYS Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 72 ARG Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 64 ASP Chi-restraints excluded: chain M residue 67 GLU Chi-restraints excluded: chain M residue 97 ARG Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 61 GLN Chi-restraints excluded: chain N residue 104 ASP Chi-restraints excluded: chain N residue 131 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 123 optimal weight: 1.9990 chunk 330 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 367 optimal weight: 0.8980 chunk 305 optimal weight: 5.9990 chunk 170 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 193 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 453 HIS ** H 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 135 ASN K 25 ASN K 172 ASN K 181 HIS ** M 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 90 ASN N 118 GLN O 18 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 31815 Z= 0.230 Angle : 0.616 13.792 43242 Z= 0.303 Chirality : 0.042 0.226 4953 Planarity : 0.004 0.065 5317 Dihedral : 9.798 110.070 4884 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.69 % Favored : 92.28 % Rotamer: Outliers : 3.42 % Allowed : 17.35 % Favored : 79.23 % 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: -0.38 (0.14), residues: 3835 helix: 0.87 (0.11), residues: 2279 sheet: -2.08 (0.37), residues: 174 loop : -1.92 (0.17), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 107 HIS 0.012 0.001 HIS D 453 PHE 0.016 0.001 PHE A 321 TYR 0.019 0.001 TYR F 445 ARG 0.012 0.000 ARG D 498 *********************** 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 452 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 343 time to evaluate : 3.515 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7543 (tp30) REVERT: A 358 LEU cc_start: 0.8736 (tm) cc_final: 0.8446 (tp) REVERT: B 113 MET cc_start: 0.8168 (ttm) cc_final: 0.7954 (mtp) REVERT: E 89 ASP cc_start: 0.7482 (t0) cc_final: 0.7018 (t0) REVERT: E 93 MET cc_start: 0.8964 (mmm) cc_final: 0.8749 (mmm) REVERT: F 382 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7780 (mtt180) REVERT: F 441 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8758 (mp) REVERT: F 458 PHE cc_start: 0.7896 (t80) cc_final: 0.7341 (t80) REVERT: F 559 THR cc_start: 0.6853 (OUTLIER) cc_final: 0.6368 (m) REVERT: F 631 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.7285 (tm-30) REVERT: G 53 MET cc_start: 0.8704 (mtm) cc_final: 0.8314 (mtm) REVERT: H 238 ASP cc_start: 0.7757 (OUTLIER) cc_final: 0.7537 (m-30) REVERT: I 67 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7227 (mp0) REVERT: I 141 MET cc_start: 0.9022 (ptm) cc_final: 0.8787 (ptm) REVERT: J 115 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8517 (mttm) REVERT: L 23 VAL cc_start: 0.9088 (t) cc_final: 0.8853 (t) REVERT: L 27 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8409 (mp) REVERT: L 66 ASN cc_start: 0.9012 (t0) cc_final: 0.8652 (t0) REVERT: L 72 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.6174 (ttt-90) REVERT: M 67 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7565 (mt-10) REVERT: M 87 GLN cc_start: 0.8260 (mt0) cc_final: 0.8015 (mt0) REVERT: N 19 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8792 (pp) REVERT: N 104 ASP cc_start: 0.7753 (OUTLIER) cc_final: 0.7455 (m-30) REVERT: Q 10 MET cc_start: 0.7846 (mmt) cc_final: 0.7156 (mmt) REVERT: S 43 MET cc_start: 0.2423 (ttt) cc_final: 0.2111 (ttp) outliers start: 109 outliers final: 56 residues processed: 416 average time/residue: 1.3362 time to fit residues: 662.0227 Evaluate side-chains 405 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 336 time to evaluate : 3.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 446 ASN Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 304 MET Chi-restraints excluded: chain F residue 382 ARG Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 530 LEU Chi-restraints excluded: chain F residue 559 THR Chi-restraints excluded: chain F residue 631 GLN Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 79 MET Chi-restraints excluded: chain G residue 83 LYS Chi-restraints excluded: chain H residue 36 ASP Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 238 ASP Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain H residue 387 VAL Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 67 GLU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 62 ARG Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 115 LYS Chi-restraints excluded: chain J residue 157 ILE Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain K residue 52 CYS Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 72 ARG Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 64 ASP Chi-restraints excluded: chain M residue 67 GLU Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain M residue 86 MET Chi-restraints excluded: chain M residue 97 ARG Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 61 GLN Chi-restraints excluded: chain N residue 104 ASP Chi-restraints excluded: chain N residue 131 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 354 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 209 optimal weight: 0.8980 chunk 268 optimal weight: 0.9990 chunk 208 optimal weight: 2.9990 chunk 309 optimal weight: 0.0980 chunk 205 optimal weight: 1.9990 chunk 366 optimal weight: 0.7980 chunk 229 optimal weight: 0.8980 chunk 223 optimal weight: 0.6980 chunk 169 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 453 HIS ** G 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 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 172 ASN K 179 GLN K 181 HIS ** M 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 90 ASN N 118 GLN O 18 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31815 Z= 0.177 Angle : 0.592 14.660 43242 Z= 0.291 Chirality : 0.041 0.211 4953 Planarity : 0.004 0.064 5317 Dihedral : 9.535 109.451 4884 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.43 % Favored : 92.54 % Rotamer: Outliers : 3.17 % Allowed : 18.01 % Favored : 78.83 % 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: -0.15 (0.14), residues: 3835 helix: 1.07 (0.11), residues: 2268 sheet: -1.71 (0.40), residues: 160 loop : -1.87 (0.17), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 107 HIS 0.006 0.001 HIS D 453 PHE 0.013 0.001 PHE A 321 TYR 0.021 0.001 TYR F 445 ARG 0.009 0.000 ARG D 498 *********************** 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 460 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 359 time to evaluate : 3.473 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7522 (tp30) REVERT: A 229 ARG cc_start: 0.6995 (mmm160) cc_final: 0.6583 (mmm160) REVERT: A 358 LEU cc_start: 0.8712 (tm) cc_final: 0.8420 (tp) REVERT: E 89 ASP cc_start: 0.7447 (t0) cc_final: 0.6988 (t0) REVERT: E 93 MET cc_start: 0.8950 (mmm) cc_final: 0.8731 (mmm) REVERT: F 382 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7827 (mtt180) REVERT: F 458 PHE cc_start: 0.7892 (t80) cc_final: 0.7347 (t80) REVERT: F 559 THR cc_start: 0.6824 (OUTLIER) cc_final: 0.6324 (m) REVERT: F 631 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.7265 (tm-30) REVERT: G 53 MET cc_start: 0.8690 (mtm) cc_final: 0.8371 (mtm) REVERT: H 36 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7377 (p0) REVERT: I 67 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.6834 (mp0) REVERT: I 141 MET cc_start: 0.8923 (ptm) cc_final: 0.8708 (ptm) REVERT: J 115 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8517 (mttm) REVERT: L 23 VAL cc_start: 0.9076 (t) cc_final: 0.8833 (t) REVERT: L 27 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8426 (mp) REVERT: L 66 ASN cc_start: 0.8901 (t0) cc_final: 0.8571 (t0) REVERT: M 67 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7545 (mt-10) REVERT: M 87 GLN cc_start: 0.8247 (mt0) cc_final: 0.7987 (mt0) REVERT: N 19 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8808 (pp) REVERT: N 104 ASP cc_start: 0.7751 (OUTLIER) cc_final: 0.7502 (m-30) REVERT: Q 10 MET cc_start: 0.7791 (mmt) cc_final: 0.7129 (mmt) REVERT: Q 11 LYS cc_start: 0.8598 (tttm) cc_final: 0.8394 (tttt) REVERT: S 43 MET cc_start: 0.2396 (ttt) cc_final: 0.2102 (ttp) outliers start: 101 outliers final: 46 residues processed: 429 average time/residue: 1.3368 time to fit residues: 685.2507 Evaluate side-chains 403 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 346 time to evaluate : 3.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 446 ASN Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain F residue 203 PHE Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 304 MET Chi-restraints excluded: chain F residue 382 ARG Chi-restraints excluded: chain F residue 559 THR Chi-restraints excluded: chain F residue 631 GLN Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 79 MET Chi-restraints excluded: chain G residue 83 LYS Chi-restraints excluded: chain H residue 36 ASP Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 67 GLU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 62 ARG Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 115 LYS Chi-restraints excluded: chain J residue 157 ILE Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain K residue 52 CYS Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 64 ASP Chi-restraints excluded: chain M residue 67 GLU Chi-restraints excluded: chain M residue 97 ARG Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 104 ASP Chi-restraints excluded: chain Q residue 3 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 226 optimal weight: 0.8980 chunk 146 optimal weight: 0.8980 chunk 218 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 232 optimal weight: 3.9990 chunk 249 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 287 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 453 HIS ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 135 ASN K 25 ASN K 181 HIS ** M 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 90 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31815 Z= 0.202 Angle : 0.606 15.434 43242 Z= 0.298 Chirality : 0.041 0.240 4953 Planarity : 0.004 0.065 5317 Dihedral : 9.376 109.572 4884 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.72 % Favored : 92.26 % Rotamer: Outliers : 3.01 % Allowed : 18.29 % Favored : 78.70 % 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: -0.09 (0.14), residues: 3835 helix: 1.10 (0.11), residues: 2271 sheet: -1.75 (0.40), residues: 164 loop : -1.82 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 107 HIS 0.006 0.001 HIS D 453 PHE 0.022 0.001 PHE H 131 TYR 0.019 0.001 TYR F 445 ARG 0.007 0.000 ARG D 498 *********************** 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 444 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 348 time to evaluate : 3.370 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 MET cc_start: 0.8147 (tpp) cc_final: 0.7909 (tpt) REVERT: A 52 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7372 (tp30) REVERT: A 173 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.8016 (mt-10) REVERT: A 358 LEU cc_start: 0.8724 (tm) cc_final: 0.8424 (tp) REVERT: D 392 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8156 (mtt) REVERT: E 89 ASP cc_start: 0.7455 (t0) cc_final: 0.7001 (t0) REVERT: E 93 MET cc_start: 0.8956 (mmm) cc_final: 0.8755 (mmm) REVERT: F 382 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7784 (mtt180) REVERT: F 441 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8749 (mp) REVERT: F 458 PHE cc_start: 0.7880 (t80) cc_final: 0.7347 (t80) REVERT: F 559 THR cc_start: 0.6811 (OUTLIER) cc_final: 0.6305 (m) REVERT: F 631 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.7225 (tm-30) REVERT: G 53 MET cc_start: 0.8751 (mtm) cc_final: 0.8424 (mtm) REVERT: H 36 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7305 (p0) REVERT: H 51 MET cc_start: 0.8626 (mmt) cc_final: 0.8412 (mmt) REVERT: I 16 GLN cc_start: 0.7702 (pp30) cc_final: 0.7410 (pp30) REVERT: I 67 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7044 (mp0) REVERT: I 141 MET cc_start: 0.8942 (ptm) cc_final: 0.8720 (ptm) REVERT: J 115 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8537 (mttm) REVERT: L 23 VAL cc_start: 0.9075 (t) cc_final: 0.8826 (t) REVERT: L 27 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8434 (mp) REVERT: L 66 ASN cc_start: 0.8962 (t0) cc_final: 0.8609 (t0) REVERT: M 67 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7530 (mt-10) REVERT: M 87 GLN cc_start: 0.8257 (mt0) cc_final: 0.7990 (mt0) REVERT: N 104 ASP cc_start: 0.7816 (OUTLIER) cc_final: 0.7534 (m-30) REVERT: S 43 MET cc_start: 0.2345 (ttt) cc_final: 0.2056 (ttp) outliers start: 96 outliers final: 55 residues processed: 415 average time/residue: 1.3324 time to fit residues: 665.3718 Evaluate side-chains 405 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 337 time to evaluate : 3.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 446 ASN Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain D residue 392 MET Chi-restraints excluded: chain D residue 453 HIS Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 203 PHE Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 304 MET Chi-restraints excluded: chain F residue 382 ARG Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 559 THR Chi-restraints excluded: chain F residue 631 GLN Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 79 MET Chi-restraints excluded: chain G residue 83 LYS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 36 ASP Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain I residue 67 GLU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 62 ARG Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 115 LYS Chi-restraints excluded: chain J residue 145 GLU Chi-restraints excluded: chain J residue 157 ILE Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain K residue 52 CYS Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 64 ASP Chi-restraints excluded: chain M residue 67 GLU Chi-restraints excluded: chain M residue 86 MET Chi-restraints excluded: chain M residue 97 ARG Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 61 GLN Chi-restraints excluded: chain N residue 104 ASP Chi-restraints excluded: chain P residue 29 ASN Chi-restraints excluded: chain Q residue 3 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 333 optimal weight: 0.7980 chunk 350 optimal weight: 4.9990 chunk 320 optimal weight: 5.9990 chunk 341 optimal weight: 0.9980 chunk 205 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 chunk 268 optimal weight: 0.6980 chunk 104 optimal weight: 6.9990 chunk 308 optimal weight: 8.9990 chunk 322 optimal weight: 0.6980 chunk 340 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 453 HIS ** 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 181 HIS ** M 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 90 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 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 0.048 31815 Z= 0.201 Angle : 0.607 16.500 43242 Z= 0.298 Chirality : 0.041 0.233 4953 Planarity : 0.004 0.065 5317 Dihedral : 9.296 109.525 4884 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.54 % Favored : 92.44 % Rotamer: Outliers : 3.01 % Allowed : 18.82 % Favored : 78.17 % 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: -0.04 (0.14), residues: 3835 helix: 1.15 (0.11), residues: 2272 sheet: -1.72 (0.40), residues: 164 loop : -1.80 (0.17), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 107 HIS 0.013 0.001 HIS D 453 PHE 0.017 0.001 PHE F 411 TYR 0.018 0.001 TYR F 445 ARG 0.007 0.000 ARG D 498 *********************** 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 445 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 349 time to evaluate : 3.390 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 MET cc_start: 0.8145 (tpp) cc_final: 0.7927 (tpt) REVERT: A 52 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7300 (tp30) REVERT: A 173 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.8016 (mt-10) REVERT: A 358 LEU cc_start: 0.8723 (tm) cc_final: 0.8421 (tp) REVERT: B 113 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7930 (mtp) REVERT: D 392 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.8182 (mtt) REVERT: E 89 ASP cc_start: 0.7414 (t0) cc_final: 0.6957 (t0) REVERT: E 93 MET cc_start: 0.8955 (mmm) cc_final: 0.8748 (mmm) REVERT: F 382 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7892 (ptt180) REVERT: F 391 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.7964 (mpt) REVERT: F 431 MET cc_start: 0.8592 (ptp) cc_final: 0.8392 (ptp) REVERT: F 441 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8775 (mp) REVERT: F 458 PHE cc_start: 0.7906 (t80) cc_final: 0.7327 (t80) REVERT: F 559 THR cc_start: 0.6802 (OUTLIER) cc_final: 0.6293 (m) REVERT: F 631 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.7221 (tm-30) REVERT: G 53 MET cc_start: 0.8736 (mtm) cc_final: 0.8428 (mtm) REVERT: G 113 LYS cc_start: 0.8533 (ttmt) cc_final: 0.8298 (tttt) REVERT: H 36 ASP cc_start: 0.7928 (OUTLIER) cc_final: 0.7497 (p0) REVERT: H 51 MET cc_start: 0.8622 (mmt) cc_final: 0.8364 (mmt) REVERT: H 202 ARG cc_start: 0.8144 (mtp180) cc_final: 0.7772 (ttp-110) REVERT: I 16 GLN cc_start: 0.7739 (pp30) cc_final: 0.7449 (pp30) REVERT: I 67 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.6975 (mp0) REVERT: J 115 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8546 (mttm) REVERT: L 23 VAL cc_start: 0.9074 (t) cc_final: 0.8822 (t) REVERT: L 27 ILE cc_start: 0.8914 (OUTLIER) cc_final: 0.8435 (mp) REVERT: L 66 ASN cc_start: 0.8888 (t0) cc_final: 0.8547 (t0) REVERT: M 67 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7530 (mt-10) REVERT: M 87 GLN cc_start: 0.8251 (mt0) cc_final: 0.7981 (mt0) REVERT: N 104 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.7495 (m-30) REVERT: Q 10 MET cc_start: 0.8134 (mmt) cc_final: 0.7118 (mmt) REVERT: S 43 MET cc_start: 0.2338 (ttt) cc_final: 0.2034 (ttp) outliers start: 96 outliers final: 53 residues processed: 416 average time/residue: 1.3254 time to fit residues: 658.5504 Evaluate side-chains 404 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 336 time to evaluate : 3.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain D residue 392 MET Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 203 PHE Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 304 MET Chi-restraints excluded: chain F residue 382 ARG Chi-restraints excluded: chain F residue 391 MET Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 559 THR Chi-restraints excluded: chain F residue 631 GLN Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 79 MET Chi-restraints excluded: chain G residue 83 LYS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 36 ASP Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain I residue 67 GLU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 62 ARG Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 115 LYS Chi-restraints excluded: chain J residue 145 GLU Chi-restraints excluded: chain J residue 157 ILE Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain K residue 52 CYS Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 64 ASP Chi-restraints excluded: chain M residue 67 GLU Chi-restraints excluded: chain M residue 86 MET Chi-restraints excluded: chain M residue 97 ARG Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 104 ASP Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 29 ASN Chi-restraints excluded: chain Q residue 3 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 224 optimal weight: 1.9990 chunk 360 optimal weight: 0.4980 chunk 220 optimal weight: 0.7980 chunk 171 optimal weight: 2.9990 chunk 250 optimal weight: 4.9990 chunk 378 optimal weight: 5.9990 chunk 348 optimal weight: 0.8980 chunk 301 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 232 optimal weight: 0.6980 chunk 184 optimal weight: 0.0470 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 453 HIS 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 25 ASN ** K 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 181 HIS M 11 HIS N 90 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 31815 Z= 0.177 Angle : 0.598 17.389 43242 Z= 0.294 Chirality : 0.041 0.227 4953 Planarity : 0.004 0.065 5317 Dihedral : 9.142 109.200 4884 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.43 % Favored : 92.54 % Rotamer: Outliers : 2.63 % Allowed : 19.07 % Favored : 78.29 % 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: 0.05 (0.14), residues: 3835 helix: 1.22 (0.11), residues: 2273 sheet: -1.63 (0.40), residues: 163 loop : -1.79 (0.17), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 107 HIS 0.006 0.001 HIS D 453 PHE 0.017 0.001 PHE F 411 TYR 0.021 0.001 TYR F 445 ARG 0.007 0.000 ARG G 167 ********************** 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 442 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 358 time to evaluate : 3.214 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 MET cc_start: 0.8121 (tpp) cc_final: 0.7897 (tpt) REVERT: A 52 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7291 (tp30) REVERT: A 173 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.8003 (mt-10) REVERT: A 358 LEU cc_start: 0.8709 (tm) cc_final: 0.8406 (tp) REVERT: B 113 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7769 (mtp) REVERT: D 392 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8178 (mtt) REVERT: E 89 ASP cc_start: 0.7529 (t0) cc_final: 0.7113 (t0) REVERT: F 382 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7870 (ptt180) REVERT: F 391 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.7895 (mpt) REVERT: F 431 MET cc_start: 0.8618 (ptp) cc_final: 0.8417 (ptp) REVERT: F 458 PHE cc_start: 0.7965 (t80) cc_final: 0.7418 (t80) REVERT: F 559 THR cc_start: 0.6761 (OUTLIER) cc_final: 0.6259 (m) REVERT: F 631 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.7208 (tm-30) REVERT: G 53 MET cc_start: 0.8706 (mtm) cc_final: 0.8426 (mtm) REVERT: G 113 LYS cc_start: 0.8508 (ttmt) cc_final: 0.8302 (tttt) REVERT: H 36 ASP cc_start: 0.7907 (OUTLIER) cc_final: 0.7474 (p0) REVERT: I 67 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.6887 (mt-10) REVERT: J 15 VAL cc_start: 0.7578 (OUTLIER) cc_final: 0.7275 (m) REVERT: L 23 VAL cc_start: 0.9067 (t) cc_final: 0.8820 (t) REVERT: L 27 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8443 (mp) REVERT: L 66 ASN cc_start: 0.8906 (t0) cc_final: 0.8585 (t0) REVERT: M 67 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7534 (mt-10) REVERT: M 87 GLN cc_start: 0.8241 (mt0) cc_final: 0.7971 (mt0) REVERT: N 104 ASP cc_start: 0.7768 (OUTLIER) cc_final: 0.7478 (m-30) REVERT: S 43 MET cc_start: 0.2322 (ttt) cc_final: 0.2026 (ttp) outliers start: 84 outliers final: 50 residues processed: 413 average time/residue: 1.3183 time to fit residues: 652.7342 Evaluate side-chains 403 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 339 time to evaluate : 3.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain D residue 392 MET Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 203 PHE Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 304 MET Chi-restraints excluded: chain F residue 355 MET Chi-restraints excluded: chain F residue 382 ARG Chi-restraints excluded: chain F residue 391 MET Chi-restraints excluded: chain F residue 559 THR Chi-restraints excluded: chain F residue 631 GLN Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 79 MET Chi-restraints excluded: chain G residue 83 LYS Chi-restraints excluded: chain H residue 36 ASP Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 151 MET Chi-restraints excluded: chain I residue 67 GLU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 62 ARG Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 157 ILE Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain K residue 52 CYS Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 64 ASP Chi-restraints excluded: chain M residue 67 GLU Chi-restraints excluded: chain M residue 86 MET Chi-restraints excluded: chain M residue 97 ARG Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 90 ASN Chi-restraints excluded: chain N residue 104 ASP Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 29 ASN Chi-restraints excluded: chain Q residue 3 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 239 optimal weight: 2.9990 chunk 321 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 277 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 301 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 310 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 453 HIS E 97 ASN ** G 117 GLN ** 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 ** K 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 181 HIS K 203 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.100163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.082143 restraints weight = 54862.356| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.72 r_work: 0.2961 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 31815 Z= 0.209 Angle : 0.711 59.188 43242 Z= 0.382 Chirality : 0.042 0.439 4953 Planarity : 0.004 0.065 5317 Dihedral : 9.146 109.185 4884 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.51 % Favored : 92.46 % Rotamer: Outliers : 2.32 % Allowed : 19.48 % Favored : 78.20 % Cbeta Deviations : 0.03 % 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: 0.04 (0.14), residues: 3835 helix: 1.22 (0.11), residues: 2273 sheet: -1.63 (0.40), residues: 163 loop : -1.80 (0.17), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 107 HIS 0.005 0.001 HIS D 453 PHE 0.017 0.001 PHE F 411 TYR 0.042 0.001 TYR H 309 ARG 0.007 0.000 ARG Q 7 =============================================================================== Job complete usr+sys time: 11213.19 seconds wall clock time: 199 minutes 9.34 seconds (11949.34 seconds total)