Starting phenix.real_space_refine on Sat Mar 16 22:03:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r8f_4759/03_2024/6r8f_4759.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r8f_4759/03_2024/6r8f_4759.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r8f_4759/03_2024/6r8f_4759.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r8f_4759/03_2024/6r8f_4759.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r8f_4759/03_2024/6r8f_4759.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r8f_4759/03_2024/6r8f_4759.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 66 5.16 5 C 9976 2.51 5 N 2858 2.21 5 O 2908 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 106": "NH1" <-> "NH2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 149": "NH1" <-> "NH2" Residue "B PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 62": "NH1" <-> "NH2" Residue "K ARG 82": "NH1" <-> "NH2" Residue "K ARG 160": "NH1" <-> "NH2" Residue "K ARG 219": "NH1" <-> "NH2" Residue "K TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 106": "NH1" <-> "NH2" Residue "D ARG 88": "NH1" <-> "NH2" Residue "D ARG 96": "NH1" <-> "NH2" Residue "D PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 149": "NH1" <-> "NH2" Residue "D PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 62": "NH1" <-> "NH2" Residue "L ARG 82": "NH1" <-> "NH2" Residue "L ARG 160": "NH1" <-> "NH2" Residue "L ARG 219": "NH1" <-> "NH2" Residue "L TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15810 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1797 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 8, 'TRANS': 229} Chain breaks: 4 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 4, 'ARG:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 71 Chain: "B" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1779 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 5, 'TRANS': 224} Chain breaks: 3 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 4, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 68 Chain: "K" Number of atoms: 2940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 2940 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 19, 'TRANS': 384} Chain breaks: 4 Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 285 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 143 Chain: "C" Number of atoms: 1797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1797 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 8, 'TRANS': 229} Chain breaks: 4 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 4, 'ARG:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 71 Chain: "D" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1779 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 5, 'TRANS': 224} Chain breaks: 3 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 4, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 68 Chain: "L" Number of atoms: 2940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 2940 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 19, 'TRANS': 384} Chain breaks: 4 Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 285 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 143 Chain: "E" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1388 Classifications: {'peptide': 210} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 86} Link IDs: {'PTRANS': 12, 'TRANS': 197} Chain breaks: 4 Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 288 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 2, 'UNK:plan-1': 82, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 101 Chain: "G" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1388 Classifications: {'peptide': 210} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 86} Link IDs: {'PTRANS': 12, 'TRANS': 197} Chain breaks: 4 Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 288 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 2, 'UNK:plan-1': 82, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 101 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.14, per 1000 atoms: 0.58 Number of scatterers: 15810 At special positions: 0 Unit cell: (145.919, 160.83, 105.445, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 66 16.00 O 2908 8.00 N 2858 7.00 C 9976 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: 5.42 Conformation dependent library (CDL) restraints added in 3.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" NE2 HIS A 124 " pdb="ZN ZN A 401 " - pdb=" NE2 HIS A 122 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" NE2 HIS C 124 " pdb="ZN ZN C 401 " - pdb=" NE2 HIS C 122 " 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4128 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 14 sheets defined 44.1% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 16 through 27 Processing helix chain 'A' and resid 93 through 112 removed outlier: 3.628A pdb=" N ALA A 99 " --> pdb=" O GLU A 95 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 141 removed outlier: 3.921A pdb=" N GLN A 139 " --> pdb=" O ASP A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 Processing helix chain 'A' and resid 233 through 250 removed outlier: 4.232A pdb=" N LYS A 237 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU A 243 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 264 Processing helix chain 'A' and resid 267 through 272 Processing helix chain 'A' and resid 283 through 311 removed outlier: 3.512A pdb=" N GLU A 288 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASP A 289 " --> pdb=" O GLN A 285 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU A 292 " --> pdb=" O GLU A 288 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN A 310 " --> pdb=" O GLU A 306 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU A 311 " --> pdb=" O GLU A 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 17 Processing helix chain 'B' and resid 76 through 81 removed outlier: 3.638A pdb=" N ASP B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 111 Processing helix chain 'B' and resid 112 through 120 removed outlier: 4.342A pdb=" N ARG B 118 " --> pdb=" O LYS B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 193 removed outlier: 3.556A pdb=" N ALA B 186 " --> pdb=" O SER B 182 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL B 188 " --> pdb=" O SER B 184 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLU B 191 " --> pdb=" O LYS B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 209 through 252 removed outlier: 3.514A pdb=" N GLU B 218 " --> pdb=" O ASN B 214 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LYS B 219 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA B 225 " --> pdb=" O GLN B 221 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B 229 " --> pdb=" O ALA B 225 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL B 233 " --> pdb=" O LYS B 229 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 234 " --> pdb=" O SER B 230 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA B 239 " --> pdb=" O GLU B 235 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL B 241 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG B 246 " --> pdb=" O ASN B 242 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN B 247 " --> pdb=" O LYS B 243 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE B 248 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 53 Processing helix chain 'K' and resid 53 through 69 removed outlier: 3.500A pdb=" N TRP K 57 " --> pdb=" O ASP K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 85 Processing helix chain 'K' and resid 115 through 125 removed outlier: 3.521A pdb=" N GLN K 120 " --> pdb=" O GLU K 116 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU K 124 " --> pdb=" O GLN K 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 150 through 155 Processing helix chain 'K' and resid 207 through 217 Processing helix chain 'K' and resid 235 through 244 removed outlier: 3.960A pdb=" N CYS K 241 " --> pdb=" O MET K 237 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU K 243 " --> pdb=" O GLU K 239 " (cutoff:3.500A) Processing helix chain 'K' and resid 266 through 270 removed outlier: 3.943A pdb=" N LYS K 269 " --> pdb=" O SER K 266 " (cutoff:3.500A) Processing helix chain 'K' and resid 311 through 316 Processing helix chain 'K' and resid 317 through 319 No H-bonds generated for 'chain 'K' and resid 317 through 319' Processing helix chain 'K' and resid 329 through 334 removed outlier: 3.787A pdb=" N ALA K 333 " --> pdb=" O ASN K 329 " (cutoff:3.500A) Processing helix chain 'K' and resid 339 through 344 removed outlier: 3.554A pdb=" N CYS K 343 " --> pdb=" O LEU K 339 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR K 344 " --> pdb=" O LYS K 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 339 through 344' Processing helix chain 'K' and resid 344 through 369 removed outlier: 3.550A pdb=" N ARG K 348 " --> pdb=" O THR K 344 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN K 353 " --> pdb=" O GLU K 349 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA K 364 " --> pdb=" O ALA K 360 " (cutoff:3.500A) Processing helix chain 'K' and resid 393 through 401 removed outlier: 3.917A pdb=" N VAL K 399 " --> pdb=" O ARG K 395 " (cutoff:3.500A) Processing helix chain 'K' and resid 429 through 434 removed outlier: 3.798A pdb=" N ARG K 434 " --> pdb=" O ALA K 430 " (cutoff:3.500A) Processing helix chain 'K' and resid 437 through 462 removed outlier: 3.729A pdb=" N PHE K 441 " --> pdb=" O ARG K 437 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ARG K 442 " --> pdb=" O GLU K 438 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ARG K 443 " --> pdb=" O ASP K 439 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN K 453 " --> pdb=" O ASP K 449 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL K 458 " --> pdb=" O ILE K 454 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER K 460 " --> pdb=" O LEU K 456 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS K 461 " --> pdb=" O GLU K 457 " (cutoff:3.500A) Processing helix chain 'K' and resid 464 through 472 removed outlier: 3.515A pdb=" N LYS K 469 " --> pdb=" O LEU K 465 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER K 470 " --> pdb=" O GLN K 466 " (cutoff:3.500A) Processing helix chain 'K' and resid 475 through 493 removed outlier: 3.967A pdb=" N ARG K 481 " --> pdb=" O GLU K 477 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU K 485 " --> pdb=" O ARG K 481 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG K 488 " --> pdb=" O ASN K 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 27 Processing helix chain 'C' and resid 93 through 112 removed outlier: 3.627A pdb=" N ALA C 99 " --> pdb=" O GLU C 95 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU C 109 " --> pdb=" O GLU C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 141 removed outlier: 3.921A pdb=" N GLN C 139 " --> pdb=" O ASP C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 231 Processing helix chain 'C' and resid 233 through 250 removed outlier: 4.232A pdb=" N LYS C 237 " --> pdb=" O VAL C 233 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU C 243 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE C 250 " --> pdb=" O ALA C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 264 Processing helix chain 'C' and resid 267 through 272 Processing helix chain 'C' and resid 283 through 311 removed outlier: 3.511A pdb=" N GLU C 288 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASP C 289 " --> pdb=" O GLN C 285 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU C 292 " --> pdb=" O GLU C 288 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN C 310 " --> pdb=" O GLU C 306 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU C 311 " --> pdb=" O GLU C 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 17 Processing helix chain 'D' and resid 76 through 81 removed outlier: 3.638A pdb=" N ASP D 81 " --> pdb=" O GLU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 111 Processing helix chain 'D' and resid 112 through 120 removed outlier: 4.341A pdb=" N ARG D 118 " --> pdb=" O LYS D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 193 removed outlier: 3.555A pdb=" N ALA D 186 " --> pdb=" O SER D 182 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL D 188 " --> pdb=" O SER D 184 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLU D 191 " --> pdb=" O LYS D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing helix chain 'D' and resid 209 through 252 removed outlier: 3.515A pdb=" N GLU D 218 " --> pdb=" O ASN D 214 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LYS D 219 " --> pdb=" O ALA D 215 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA D 225 " --> pdb=" O GLN D 221 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS D 229 " --> pdb=" O ALA D 225 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL D 233 " --> pdb=" O LYS D 229 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL D 234 " --> pdb=" O SER D 230 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA D 239 " --> pdb=" O GLU D 235 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL D 241 " --> pdb=" O CYS D 237 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG D 246 " --> pdb=" O ASN D 242 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN D 247 " --> pdb=" O LYS D 243 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE D 248 " --> pdb=" O LEU D 244 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 53 Processing helix chain 'L' and resid 53 through 69 removed outlier: 3.500A pdb=" N TRP L 57 " --> pdb=" O ASP L 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 85 Processing helix chain 'L' and resid 115 through 125 removed outlier: 3.520A pdb=" N GLN L 120 " --> pdb=" O GLU L 116 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU L 124 " --> pdb=" O GLN L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 150 through 155 Processing helix chain 'L' and resid 207 through 217 Processing helix chain 'L' and resid 235 through 244 removed outlier: 3.961A pdb=" N CYS L 241 " --> pdb=" O MET L 237 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU L 243 " --> pdb=" O GLU L 239 " (cutoff:3.500A) Processing helix chain 'L' and resid 266 through 270 removed outlier: 3.943A pdb=" N LYS L 269 " --> pdb=" O SER L 266 " (cutoff:3.500A) Processing helix chain 'L' and resid 311 through 316 Processing helix chain 'L' and resid 317 through 319 No H-bonds generated for 'chain 'L' and resid 317 through 319' Processing helix chain 'L' and resid 329 through 334 removed outlier: 3.786A pdb=" N ALA L 333 " --> pdb=" O ASN L 329 " (cutoff:3.500A) Processing helix chain 'L' and resid 339 through 344 removed outlier: 3.553A pdb=" N CYS L 343 " --> pdb=" O LEU L 339 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR L 344 " --> pdb=" O LYS L 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 339 through 344' Processing helix chain 'L' and resid 344 through 369 removed outlier: 3.550A pdb=" N ARG L 348 " --> pdb=" O THR L 344 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN L 353 " --> pdb=" O GLU L 349 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA L 364 " --> pdb=" O ALA L 360 " (cutoff:3.500A) Processing helix chain 'L' and resid 393 through 401 removed outlier: 3.917A pdb=" N VAL L 399 " --> pdb=" O ARG L 395 " (cutoff:3.500A) Processing helix chain 'L' and resid 429 through 434 removed outlier: 3.798A pdb=" N ARG L 434 " --> pdb=" O ALA L 430 " (cutoff:3.500A) Processing helix chain 'L' and resid 437 through 462 removed outlier: 3.731A pdb=" N PHE L 441 " --> pdb=" O ARG L 437 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ARG L 442 " --> pdb=" O GLU L 438 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ARG L 443 " --> pdb=" O ASP L 439 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN L 453 " --> pdb=" O ASP L 449 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL L 458 " --> pdb=" O ILE L 454 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER L 460 " --> pdb=" O LEU L 456 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS L 461 " --> pdb=" O GLU L 457 " (cutoff:3.500A) Processing helix chain 'L' and resid 464 through 472 removed outlier: 3.515A pdb=" N LYS L 469 " --> pdb=" O LEU L 465 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER L 470 " --> pdb=" O GLN L 466 " (cutoff:3.500A) Processing helix chain 'L' and resid 475 through 493 removed outlier: 3.968A pdb=" N ARG L 481 " --> pdb=" O GLU L 477 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU L 485 " --> pdb=" O ARG L 481 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG L 488 " --> pdb=" O ASN L 484 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 14 Processing helix chain 'E' and resid 15 through 25 removed outlier: 3.951A pdb=" N SER E 20 " --> pdb=" O PRO E 16 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N VAL E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL E 22 " --> pdb=" O ILE E 18 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN E 24 " --> pdb=" O SER E 20 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY E 25 " --> pdb=" O VAL E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 130 removed outlier: 3.624A pdb=" N GLU E 119 " --> pdb=" O LEU E 115 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER E 130 " --> pdb=" O GLN E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 149 Processing helix chain 'E' and resid 242 through 255 removed outlier: 4.035A pdb=" N UNK E 246 " --> pdb=" O UNK E 242 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N UNK E 255 " --> pdb=" O UNK E 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 14 Processing helix chain 'G' and resid 15 through 25 removed outlier: 3.950A pdb=" N SER G 20 " --> pdb=" O PRO G 16 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL G 21 " --> pdb=" O PHE G 17 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL G 22 " --> pdb=" O ILE G 18 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN G 24 " --> pdb=" O SER G 20 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY G 25 " --> pdb=" O VAL G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 130 removed outlier: 3.624A pdb=" N GLU G 119 " --> pdb=" O LEU G 115 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER G 130 " --> pdb=" O GLN G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 149 Processing helix chain 'G' and resid 242 through 255 removed outlier: 4.035A pdb=" N UNK G 246 " --> pdb=" O UNK G 242 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N UNK G 255 " --> pdb=" O UNK G 251 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 216 through 219 removed outlier: 6.621A pdb=" N SER A 76 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU A 41 " --> pdb=" O HIS A 73 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE A 39 " --> pdb=" O HIS A 75 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N VAL A 77 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU A 37 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ILE A 79 " --> pdb=" O MET A 35 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N MET A 35 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLY A 119 " --> pdb=" O CYS A 38 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLY A 40 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N VAL A 117 " --> pdb=" O GLY A 40 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N LEU A 152 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N TRP A 120 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N PHE A 154 " --> pdb=" O TRP A 120 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N HIS A 122 " --> pdb=" O PHE A 154 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N CYS A 156 " --> pdb=" O HIS A 122 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 169 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N PHE A 157 " --> pdb=" O ARG A 167 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ARG A 167 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER B 131 " --> pdb=" O GLU B 144 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE B 92 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU B 128 " --> pdb=" O ILE B 92 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TRP B 94 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N PHE B 130 " --> pdb=" O TRP B 94 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ARG B 96 " --> pdb=" O PHE B 130 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N VAL B 91 " --> pdb=" O GLY B 30 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N GLY B 30 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLY B 93 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY B 26 " --> pdb=" O TYR B 95 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N PHE B 27 " --> pdb=" O HIS B 57 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N HIS B 57 " --> pdb=" O PHE B 27 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU B 29 " --> pdb=" O GLU B 55 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N SER B 4 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N ILE B 56 " --> pdb=" O SER B 4 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 71 through 72 Processing sheet with id=AA3, first strand: chain 'K' and resid 134 through 136 removed outlier: 3.909A pdb=" N ILE K 273 " --> pdb=" O LEU K 248 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR K 275 " --> pdb=" O ALA K 250 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU K 220 " --> pdb=" O ARG K 160 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N LEU K 164 " --> pdb=" O ILE K 222 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 296 through 297 removed outlier: 4.029A pdb=" N LYS K 297 " --> pdb=" O ILE K 307 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE K 307 " --> pdb=" O LYS K 297 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'K' and resid 371 through 372 removed outlier: 4.415A pdb=" N SER K 371 " --> pdb=" O ASP K 385 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 216 through 219 removed outlier: 6.620A pdb=" N SER C 76 " --> pdb=" O GLU C 15 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU C 41 " --> pdb=" O HIS C 73 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE C 39 " --> pdb=" O HIS C 75 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N VAL C 77 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU C 37 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ILE C 79 " --> pdb=" O MET C 35 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N MET C 35 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLY C 119 " --> pdb=" O CYS C 38 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLY C 40 " --> pdb=" O VAL C 117 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N VAL C 117 " --> pdb=" O GLY C 40 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N LEU C 152 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N TRP C 120 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N PHE C 154 " --> pdb=" O TRP C 120 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N HIS C 122 " --> pdb=" O PHE C 154 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N CYS C 156 " --> pdb=" O HIS C 122 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU C 169 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N PHE C 157 " --> pdb=" O ARG C 167 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ARG C 167 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL C 168 " --> pdb=" O LEU D 143 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER D 131 " --> pdb=" O GLU D 144 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE D 92 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU D 128 " --> pdb=" O ILE D 92 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N TRP D 94 " --> pdb=" O LEU D 128 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N PHE D 130 " --> pdb=" O TRP D 94 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ARG D 96 " --> pdb=" O PHE D 130 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N VAL D 91 " --> pdb=" O GLY D 30 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N GLY D 30 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLY D 93 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY D 26 " --> pdb=" O TYR D 95 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N PHE D 27 " --> pdb=" O HIS D 57 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N HIS D 57 " --> pdb=" O PHE D 27 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU D 29 " --> pdb=" O GLU D 55 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N SER D 4 " --> pdb=" O ILE D 54 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N ILE D 56 " --> pdb=" O SER D 4 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 71 through 72 Processing sheet with id=AA8, first strand: chain 'L' and resid 134 through 136 removed outlier: 3.909A pdb=" N ILE L 273 " --> pdb=" O LEU L 248 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR L 275 " --> pdb=" O ALA L 250 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU L 220 " --> pdb=" O ARG L 160 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N LEU L 164 " --> pdb=" O ILE L 222 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 296 through 297 removed outlier: 4.029A pdb=" N LYS L 297 " --> pdb=" O ILE L 307 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE L 307 " --> pdb=" O LYS L 297 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'L' and resid 371 through 372 removed outlier: 4.415A pdb=" N SER L 371 " --> pdb=" O ASP L 385 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 37 through 38 Processing sheet with id=AB3, first strand: chain 'E' and resid 160 through 163 removed outlier: 3.953A pdb=" N UNK E 179 " --> pdb=" O UNK E 203 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N UNK E 203 " --> pdb=" O UNK E 179 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 37 through 38 Processing sheet with id=AB5, first strand: chain 'G' and resid 160 through 163 removed outlier: 3.953A pdb=" N UNK G 179 " --> pdb=" O UNK G 203 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N UNK G 203 " --> pdb=" O UNK G 179 " (cutoff:3.500A) 597 hydrogen bonds defined for protein. 1713 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: 4.77 Time building geometry restraints manager: 5.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5022 1.33 - 1.45: 3003 1.45 - 1.58: 7965 1.58 - 1.70: 0 1.70 - 1.82: 90 Bond restraints: 16080 Sorted by residual: bond pdb=" CA SER B 182 " pdb=" CB SER B 182 " ideal model delta sigma weight residual 1.529 1.478 0.051 1.38e-02 5.25e+03 1.36e+01 bond pdb=" CA SER D 182 " pdb=" CB SER D 182 " ideal model delta sigma weight residual 1.529 1.479 0.050 1.38e-02 5.25e+03 1.33e+01 bond pdb=" CB VAL A 129 " pdb=" CG1 VAL A 129 " ideal model delta sigma weight residual 1.521 1.409 0.112 3.30e-02 9.18e+02 1.14e+01 bond pdb=" CB VAL C 129 " pdb=" CG1 VAL C 129 " ideal model delta sigma weight residual 1.521 1.410 0.111 3.30e-02 9.18e+02 1.13e+01 bond pdb=" CA LEU D 80 " pdb=" C LEU D 80 " ideal model delta sigma weight residual 1.523 1.482 0.041 1.37e-02 5.33e+03 9.02e+00 ... (remaining 16075 not shown) Histogram of bond angle deviations from ideal: 96.37 - 103.93: 235 103.93 - 111.50: 7226 111.50 - 119.06: 5864 119.06 - 126.62: 8324 126.62 - 134.18: 217 Bond angle restraints: 21866 Sorted by residual: angle pdb=" C GLY K 427 " pdb=" N ALA K 428 " pdb=" CA ALA K 428 " ideal model delta sigma weight residual 122.85 115.35 7.50 1.10e+00 8.26e-01 4.64e+01 angle pdb=" C GLY L 427 " pdb=" N ALA L 428 " pdb=" CA ALA L 428 " ideal model delta sigma weight residual 122.85 115.38 7.47 1.10e+00 8.26e-01 4.62e+01 angle pdb=" C VAL C 129 " pdb=" CA VAL C 129 " pdb=" CB VAL C 129 " ideal model delta sigma weight residual 111.29 101.22 10.07 1.64e+00 3.72e-01 3.77e+01 angle pdb=" C VAL A 129 " pdb=" CA VAL A 129 " pdb=" CB VAL A 129 " ideal model delta sigma weight residual 111.29 101.23 10.06 1.64e+00 3.72e-01 3.77e+01 angle pdb=" N SER B 79 " pdb=" CA SER B 79 " pdb=" C SER B 79 " ideal model delta sigma weight residual 114.31 106.62 7.69 1.29e+00 6.01e-01 3.55e+01 ... (remaining 21861 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.33: 9015 14.33 - 28.67: 545 28.67 - 43.00: 96 43.00 - 57.33: 6 57.33 - 71.66: 10 Dihedral angle restraints: 9672 sinusoidal: 3368 harmonic: 6304 Sorted by residual: dihedral pdb=" CA CYS A 228 " pdb=" C CYS A 228 " pdb=" N LEU A 229 " pdb=" CA LEU A 229 " ideal model delta harmonic sigma weight residual 180.00 153.92 26.08 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA CYS C 228 " pdb=" C CYS C 228 " pdb=" N LEU C 229 " pdb=" CA LEU C 229 " ideal model delta harmonic sigma weight residual 180.00 153.93 26.07 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA ILE C 92 " pdb=" C ILE C 92 " pdb=" N SER C 93 " pdb=" CA SER C 93 " ideal model delta harmonic sigma weight residual -180.00 -154.08 -25.92 0 5.00e+00 4.00e-02 2.69e+01 ... (remaining 9669 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 2305 0.099 - 0.199: 255 0.199 - 0.298: 16 0.298 - 0.397: 2 0.397 - 0.497: 2 Chirality restraints: 2580 Sorted by residual: chirality pdb=" CB ILE C 218 " pdb=" CA ILE C 218 " pdb=" CG1 ILE C 218 " pdb=" CG2 ILE C 218 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.50 2.00e-01 2.50e+01 6.17e+00 chirality pdb=" CB ILE A 218 " pdb=" CA ILE A 218 " pdb=" CG1 ILE A 218 " pdb=" CG2 ILE A 218 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.49 2.00e-01 2.50e+01 6.09e+00 chirality pdb=" CB VAL C 34 " pdb=" CA VAL C 34 " pdb=" CG1 VAL C 34 " pdb=" CG2 VAL C 34 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.46e+00 ... (remaining 2577 not shown) Planarity restraints: 2848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 132 " 0.035 2.00e-02 2.50e+03 2.73e-02 1.31e+01 pdb=" CG PHE D 132 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 PHE D 132 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE D 132 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE D 132 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE D 132 " 0.011 2.00e-02 2.50e+03 pdb=" CZ PHE D 132 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 132 " 0.036 2.00e-02 2.50e+03 2.72e-02 1.30e+01 pdb=" CG PHE B 132 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 PHE B 132 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE B 132 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 132 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 132 " 0.011 2.00e-02 2.50e+03 pdb=" CZ PHE B 132 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 94 " 0.022 2.00e-02 2.50e+03 1.78e-02 7.89e+00 pdb=" CG TRP B 94 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP B 94 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP B 94 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 94 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 94 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 94 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 94 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 94 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 94 " 0.005 2.00e-02 2.50e+03 ... (remaining 2845 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 171 2.63 - 3.20: 13777 3.20 - 3.76: 22815 3.76 - 4.33: 30871 4.33 - 4.90: 50944 Nonbonded interactions: 118578 Sorted by model distance: nonbonded pdb=" OD2 ASP A 135 " pdb="ZN ZN A 401 " model vdw 2.059 2.230 nonbonded pdb=" OD1 ASP C 135 " pdb="ZN ZN C 401 " model vdw 2.091 2.230 nonbonded pdb=" OD1 ASP A 135 " pdb="ZN ZN A 401 " model vdw 2.097 2.230 nonbonded pdb=" OD2 ASP C 135 " pdb="ZN ZN C 401 " model vdw 2.102 2.230 nonbonded pdb=" OD1 ASN L 78 " pdb=" OG SER L 433 " model vdw 2.298 2.440 ... (remaining 118573 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 9.420 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 46.520 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.170 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: 0.020 Load rotamer database and sin/cos tables:3.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 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 : 0.013 0.112 16080 Z= 0.837 Angle : 1.145 10.075 21866 Z= 0.643 Chirality : 0.065 0.497 2580 Planarity : 0.008 0.064 2848 Dihedral : 10.253 71.665 5544 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % Rotamer: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.94 (0.13), residues: 1940 helix: -4.50 (0.08), residues: 840 sheet: -2.98 (0.29), residues: 292 loop : -3.47 (0.17), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.005 TRP B 94 HIS 0.016 0.003 HIS A 25 PHE 0.061 0.005 PHE D 132 TYR 0.040 0.003 TYR A 170 ARG 0.015 0.001 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 400 time to evaluate : 1.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.8567 (tmm) cc_final: 0.8287 (tmm) REVERT: A 158 ILE cc_start: 0.9211 (mm) cc_final: 0.8887 (mt) REVERT: A 241 GLN cc_start: 0.8269 (tp40) cc_final: 0.8061 (tt0) REVERT: A 295 GLN cc_start: 0.7815 (mt0) cc_final: 0.7531 (tm-30) REVERT: B 53 VAL cc_start: 0.8707 (t) cc_final: 0.8229 (m) REVERT: B 228 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7989 (tm-30) REVERT: K 128 ASP cc_start: 0.8024 (t0) cc_final: 0.7767 (t0) REVERT: K 200 LYS cc_start: 0.8454 (ptpt) cc_final: 0.8239 (ptpp) REVERT: K 343 CYS cc_start: 0.7972 (m) cc_final: 0.7171 (t) REVERT: K 346 MET cc_start: 0.8439 (tpp) cc_final: 0.8168 (tpp) REVERT: K 381 LEU cc_start: 0.9437 (pp) cc_final: 0.9193 (pt) REVERT: K 403 VAL cc_start: 0.9410 (m) cc_final: 0.9130 (p) REVERT: C 10 GLN cc_start: 0.8485 (mm110) cc_final: 0.8267 (mt0) REVERT: D 83 ILE cc_start: 0.8417 (mm) cc_final: 0.7569 (mm) REVERT: L 80 CYS cc_start: 0.8067 (m) cc_final: 0.7815 (m) REVERT: L 222 ILE cc_start: 0.8696 (pt) cc_final: 0.8416 (pt) REVERT: L 255 ILE cc_start: 0.9098 (mt) cc_final: 0.8758 (pt) REVERT: E 41 LYS cc_start: 0.8667 (mttt) cc_final: 0.8356 (mmtt) REVERT: E 119 GLU cc_start: 0.7328 (tp30) cc_final: 0.7114 (tp30) REVERT: G 105 TRP cc_start: 0.7809 (t60) cc_final: 0.7182 (t60) outliers start: 0 outliers final: 0 residues processed: 400 average time/residue: 0.3160 time to fit residues: 176.5130 Evaluate side-chains 237 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 1.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 72 optimal weight: 0.0770 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 134 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 81 optimal weight: 0.5980 chunk 100 optimal weight: 3.9990 chunk 156 optimal weight: 0.6980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 75 HIS ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 GLN B 214 ASN K 93 ASN K 254 HIS K 328 HIS ** K 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 435 GLN C 75 HIS C 241 GLN ** D 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 ASN L 254 HIS L 270 HIS E 100 GLN E 125 HIS G 24 ASN G 52 ASN G 125 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16080 Z= 0.193 Angle : 0.603 7.553 21866 Z= 0.317 Chirality : 0.043 0.192 2580 Planarity : 0.005 0.054 2848 Dihedral : 5.540 26.611 2286 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 2.34 % Allowed : 9.61 % Favored : 88.05 % 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: -4.13 (0.16), residues: 1940 helix: -2.47 (0.14), residues: 852 sheet: -2.15 (0.29), residues: 314 loop : -3.15 (0.19), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 94 HIS 0.009 0.001 HIS B 113 PHE 0.017 0.002 PHE E 86 TYR 0.019 0.002 TYR A 170 ARG 0.006 0.000 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 334 time to evaluate : 1.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.8397 (tmm) cc_final: 0.7860 (ttp) REVERT: A 80 LEU cc_start: 0.8999 (mp) cc_final: 0.8798 (mt) REVERT: A 158 ILE cc_start: 0.8958 (mm) cc_final: 0.8617 (mt) REVERT: A 213 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7453 (mp0) REVERT: B 135 THR cc_start: 0.9423 (p) cc_final: 0.9113 (m) REVERT: B 228 GLU cc_start: 0.8269 (tm-30) cc_final: 0.8012 (tm-30) REVERT: K 128 ASP cc_start: 0.8006 (t0) cc_final: 0.7747 (t0) REVERT: K 237 MET cc_start: 0.7965 (mtm) cc_final: 0.7672 (mtm) REVERT: K 343 CYS cc_start: 0.8041 (m) cc_final: 0.7093 (t) REVERT: K 382 VAL cc_start: 0.9480 (OUTLIER) cc_final: 0.9143 (m) REVERT: K 383 LEU cc_start: 0.9231 (tp) cc_final: 0.9030 (mt) REVERT: C 115 MET cc_start: 0.8134 (mmm) cc_final: 0.7649 (mmt) REVERT: C 226 LYS cc_start: 0.8879 (ttpt) cc_final: 0.8196 (ttmt) REVERT: D 143 LEU cc_start: 0.8533 (tp) cc_final: 0.7728 (mp) REVERT: L 80 CYS cc_start: 0.7913 (m) cc_final: 0.7624 (m) outliers start: 35 outliers final: 20 residues processed: 356 average time/residue: 0.2846 time to fit residues: 146.5425 Evaluate side-chains 271 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 249 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain K residue 58 GLU Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 243 GLU Chi-restraints excluded: chain K residue 382 VAL Chi-restraints excluded: chain K residue 406 THR Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain L residue 192 SER Chi-restraints excluded: chain L residue 290 ILE Chi-restraints excluded: chain L residue 433 SER Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain G residue 46 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 86 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 156 optimal weight: 1.9990 chunk 169 optimal weight: 0.0370 chunk 139 optimal weight: 0.5980 chunk 155 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 HIS A 293 GLN B 60 GLN B 138 ASN B 141 HIS K 328 HIS C 10 GLN ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 ASN D 141 HIS L 435 GLN E 24 ASN E 101 ASN G 52 ASN G 74 ASN G 101 ASN ** G 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16080 Z= 0.187 Angle : 0.563 8.283 21866 Z= 0.292 Chirality : 0.043 0.256 2580 Planarity : 0.004 0.048 2848 Dihedral : 4.977 24.345 2286 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 3.60 % Allowed : 13.35 % Favored : 83.04 % 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: -3.03 (0.18), residues: 1940 helix: -1.25 (0.17), residues: 852 sheet: -1.83 (0.30), residues: 318 loop : -2.88 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 130 HIS 0.008 0.001 HIS B 113 PHE 0.016 0.002 PHE D 132 TYR 0.018 0.001 TYR A 170 ARG 0.005 0.000 ARG D 245 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 273 time to evaluate : 1.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLN cc_start: 0.8328 (mp10) cc_final: 0.7539 (mp10) REVERT: A 35 MET cc_start: 0.8318 (tmm) cc_final: 0.7899 (ttp) REVERT: A 158 ILE cc_start: 0.8979 (mm) cc_final: 0.8692 (mt) REVERT: A 213 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7684 (mp0) REVERT: B 53 VAL cc_start: 0.8325 (t) cc_final: 0.7995 (m) REVERT: B 228 GLU cc_start: 0.8299 (tm-30) cc_final: 0.8045 (tm-30) REVERT: K 128 ASP cc_start: 0.8050 (t0) cc_final: 0.7761 (t0) REVERT: K 343 CYS cc_start: 0.7985 (m) cc_final: 0.7029 (t) REVERT: K 382 VAL cc_start: 0.9381 (OUTLIER) cc_final: 0.9014 (m) REVERT: C 115 MET cc_start: 0.8113 (mmm) cc_final: 0.7763 (mmm) REVERT: C 289 ASP cc_start: 0.7333 (t70) cc_final: 0.6953 (t0) REVERT: D 25 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7329 (mt-10) REVERT: D 231 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6465 (tt0) REVERT: L 80 CYS cc_start: 0.7734 (m) cc_final: 0.7488 (m) REVERT: L 162 MET cc_start: 0.8591 (ttp) cc_final: 0.8376 (ttt) REVERT: L 242 ASP cc_start: 0.8179 (m-30) cc_final: 0.7878 (m-30) REVERT: E 101 ASN cc_start: 0.8229 (m-40) cc_final: 0.7902 (m110) REVERT: E 119 GLU cc_start: 0.6419 (mt-10) cc_final: 0.6211 (mt-10) outliers start: 54 outliers final: 32 residues processed: 300 average time/residue: 0.2785 time to fit residues: 121.3643 Evaluate side-chains 271 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 236 time to evaluate : 1.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 33 ARG Chi-restraints excluded: chain B residue 59 HIS Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 382 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 132 PHE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain L residue 192 SER Chi-restraints excluded: chain L residue 244 VAL Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain G residue 56 PHE Chi-restraints excluded: chain G residue 71 ILE Chi-restraints excluded: chain G residue 115 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 0.4980 chunk 117 optimal weight: 0.0970 chunk 81 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 157 optimal weight: 0.5980 chunk 166 optimal weight: 0.8980 chunk 82 optimal weight: 7.9990 chunk 148 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 279 HIS K 328 HIS ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 HIS G 52 ASN G 101 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16080 Z= 0.167 Angle : 0.535 6.829 21866 Z= 0.275 Chirality : 0.041 0.156 2580 Planarity : 0.004 0.043 2848 Dihedral : 4.574 23.092 2286 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.54 % Allowed : 15.75 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.35 (0.19), residues: 1940 helix: -0.44 (0.18), residues: 834 sheet: -1.94 (0.32), residues: 274 loop : -2.57 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 105 HIS 0.008 0.001 HIS B 113 PHE 0.012 0.001 PHE G 86 TYR 0.018 0.001 TYR L 195 ARG 0.006 0.000 ARG C 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 249 time to evaluate : 1.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLN cc_start: 0.8323 (mp10) cc_final: 0.7540 (mp10) REVERT: A 35 MET cc_start: 0.8172 (tmm) cc_final: 0.7737 (ttp) REVERT: B 53 VAL cc_start: 0.8335 (t) cc_final: 0.8023 (m) REVERT: B 135 THR cc_start: 0.9313 (p) cc_final: 0.9082 (m) REVERT: B 228 GLU cc_start: 0.8303 (tm-30) cc_final: 0.8085 (tm-30) REVERT: B 229 LYS cc_start: 0.8535 (mttt) cc_final: 0.7841 (mtmm) REVERT: K 128 ASP cc_start: 0.8034 (t0) cc_final: 0.7671 (t0) REVERT: K 343 CYS cc_start: 0.7857 (m) cc_final: 0.6897 (t) REVERT: K 382 VAL cc_start: 0.9208 (OUTLIER) cc_final: 0.8855 (m) REVERT: K 383 LEU cc_start: 0.9276 (mt) cc_final: 0.8889 (mp) REVERT: C 14 LEU cc_start: 0.7980 (tp) cc_final: 0.7440 (tp) REVERT: C 115 MET cc_start: 0.7936 (mmm) cc_final: 0.7592 (mmm) REVERT: C 289 ASP cc_start: 0.7371 (t70) cc_final: 0.7117 (t0) REVERT: D 64 LYS cc_start: 0.6927 (mttp) cc_final: 0.6251 (mmmt) REVERT: D 231 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6480 (tt0) REVERT: L 237 MET cc_start: 0.7504 (mtt) cc_final: 0.7239 (mtp) REVERT: E 101 ASN cc_start: 0.8121 (m-40) cc_final: 0.7719 (m110) outliers start: 53 outliers final: 33 residues processed: 283 average time/residue: 0.2788 time to fit residues: 115.9073 Evaluate side-chains 265 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 230 time to evaluate : 2.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 33 ARG Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain K residue 68 CYS Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 382 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 244 GLN Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 132 PHE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain L residue 192 SER Chi-restraints excluded: chain L residue 221 ILE Chi-restraints excluded: chain L residue 244 VAL Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 71 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 123 optimal weight: 0.0020 chunk 68 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 149 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN ** K 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 328 HIS C 10 GLN ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 ASN G 101 ASN ** G 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 16080 Z= 0.298 Angle : 0.590 6.897 21866 Z= 0.303 Chirality : 0.043 0.151 2580 Planarity : 0.004 0.042 2848 Dihedral : 4.832 23.687 2286 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 4.54 % Allowed : 16.62 % Favored : 78.84 % 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: -2.21 (0.19), residues: 1940 helix: -0.26 (0.18), residues: 860 sheet: -1.95 (0.31), residues: 274 loop : -2.63 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 94 HIS 0.010 0.001 HIS B 113 PHE 0.029 0.002 PHE D 132 TYR 0.022 0.002 TYR B 185 ARG 0.006 0.000 ARG C 167 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 243 time to evaluate : 1.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLN cc_start: 0.8400 (mp10) cc_final: 0.7554 (mp10) REVERT: A 35 MET cc_start: 0.8281 (tmm) cc_final: 0.7937 (ptm) REVERT: A 158 ILE cc_start: 0.8949 (mm) cc_final: 0.8748 (mt) REVERT: A 289 ASP cc_start: 0.8268 (t70) cc_final: 0.8005 (t0) REVERT: A 295 GLN cc_start: 0.7945 (tm-30) cc_final: 0.7624 (tm-30) REVERT: B 53 VAL cc_start: 0.8470 (t) cc_final: 0.8137 (m) REVERT: B 228 GLU cc_start: 0.8355 (tm-30) cc_final: 0.8034 (tm-30) REVERT: B 229 LYS cc_start: 0.8486 (mttt) cc_final: 0.7898 (mtmm) REVERT: K 128 ASP cc_start: 0.8050 (t0) cc_final: 0.7690 (t0) REVERT: K 343 CYS cc_start: 0.8069 (m) cc_final: 0.7159 (t) REVERT: K 382 VAL cc_start: 0.9296 (OUTLIER) cc_final: 0.8925 (m) REVERT: K 383 LEU cc_start: 0.9360 (mt) cc_final: 0.9021 (mp) REVERT: C 17 ASP cc_start: 0.7686 (p0) cc_final: 0.7009 (p0) REVERT: D 64 LYS cc_start: 0.6656 (mttp) cc_final: 0.6116 (mmmt) REVERT: D 144 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7745 (mm-30) REVERT: D 231 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6511 (tt0) REVERT: L 228 TYR cc_start: 0.8331 (t80) cc_final: 0.8118 (t80) REVERT: L 242 ASP cc_start: 0.8268 (m-30) cc_final: 0.8041 (m-30) REVERT: E 68 LYS cc_start: 0.8767 (mtpt) cc_final: 0.8336 (mtpp) REVERT: E 101 ASN cc_start: 0.8175 (m-40) cc_final: 0.7815 (m110) REVERT: G 105 TRP cc_start: 0.8001 (t60) cc_final: 0.7735 (t60) outliers start: 68 outliers final: 45 residues processed: 291 average time/residue: 0.2840 time to fit residues: 120.7855 Evaluate side-chains 277 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 229 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 33 ARG Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain K residue 68 CYS Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 241 CYS Chi-restraints excluded: chain K residue 276 THR Chi-restraints excluded: chain K residue 382 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 132 PHE Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain L residue 192 SER Chi-restraints excluded: chain L residue 221 ILE Chi-restraints excluded: chain L residue 244 VAL Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 71 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 0.8980 chunk 149 optimal weight: 0.9980 chunk 32 optimal weight: 0.2980 chunk 97 optimal weight: 1.9990 chunk 41 optimal weight: 0.0170 chunk 166 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 overall best weight: 0.8420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 328 HIS G 52 ASN G 101 ASN ** G 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16080 Z= 0.223 Angle : 0.558 9.216 21866 Z= 0.286 Chirality : 0.042 0.165 2580 Planarity : 0.004 0.043 2848 Dihedral : 4.602 22.536 2286 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.60 % Allowed : 18.16 % Favored : 78.24 % 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: -1.91 (0.19), residues: 1940 helix: 0.09 (0.19), residues: 854 sheet: -1.80 (0.32), residues: 270 loop : -2.57 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 105 HIS 0.009 0.001 HIS B 113 PHE 0.022 0.001 PHE D 132 TYR 0.020 0.001 TYR L 195 ARG 0.008 0.000 ARG E 23 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 235 time to evaluate : 1.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLN cc_start: 0.8346 (mp10) cc_final: 0.7552 (mp10) REVERT: A 35 MET cc_start: 0.8195 (tmm) cc_final: 0.7876 (ptm) REVERT: A 295 GLN cc_start: 0.8006 (tm-30) cc_final: 0.7611 (tm-30) REVERT: B 53 VAL cc_start: 0.8444 (t) cc_final: 0.8096 (m) REVERT: B 129 LEU cc_start: 0.8894 (tt) cc_final: 0.8608 (tp) REVERT: B 228 GLU cc_start: 0.8382 (tm-30) cc_final: 0.8087 (tm-30) REVERT: B 229 LYS cc_start: 0.8442 (mttt) cc_final: 0.7837 (mtmm) REVERT: K 128 ASP cc_start: 0.8038 (t0) cc_final: 0.7660 (t0) REVERT: K 343 CYS cc_start: 0.7976 (m) cc_final: 0.7115 (t) REVERT: K 382 VAL cc_start: 0.9248 (OUTLIER) cc_final: 0.8862 (m) REVERT: C 17 ASP cc_start: 0.7687 (p0) cc_final: 0.7026 (p0) REVERT: D 64 LYS cc_start: 0.6629 (mttp) cc_final: 0.6172 (mmmt) REVERT: D 144 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7856 (mt-10) REVERT: D 231 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6510 (tt0) REVERT: L 228 TYR cc_start: 0.8330 (t80) cc_final: 0.8064 (t80) REVERT: E 68 LYS cc_start: 0.8766 (mtpt) cc_final: 0.8349 (mtpp) REVERT: G 105 TRP cc_start: 0.7996 (t60) cc_final: 0.7688 (t60) outliers start: 54 outliers final: 41 residues processed: 274 average time/residue: 0.2792 time to fit residues: 111.9216 Evaluate side-chains 267 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 223 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 33 ARG Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain K residue 68 CYS Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 276 THR Chi-restraints excluded: chain K residue 382 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 244 GLN Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 132 PHE Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 224 CYS Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain L residue 192 SER Chi-restraints excluded: chain L residue 221 ILE Chi-restraints excluded: chain L residue 244 VAL Chi-restraints excluded: chain L residue 264 ILE Chi-restraints excluded: chain L residue 290 ILE Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 71 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 0.0270 chunk 94 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 140 optimal weight: 0.1980 chunk 92 optimal weight: 3.9990 chunk 165 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 76 optimal weight: 0.0370 chunk 102 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 GLN G 24 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16080 Z= 0.155 Angle : 0.532 10.343 21866 Z= 0.269 Chirality : 0.041 0.195 2580 Planarity : 0.004 0.042 2848 Dihedral : 4.287 21.118 2286 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 3.87 % Allowed : 18.49 % Favored : 77.64 % 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: -1.61 (0.20), residues: 1940 helix: 0.35 (0.19), residues: 864 sheet: -1.68 (0.34), residues: 250 loop : -2.43 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 105 HIS 0.006 0.001 HIS B 113 PHE 0.017 0.001 PHE D 132 TYR 0.018 0.001 TYR B 185 ARG 0.010 0.000 ARG E 23 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 252 time to evaluate : 1.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLN cc_start: 0.8384 (mp10) cc_final: 0.7766 (mp10) REVERT: A 35 MET cc_start: 0.8114 (tmm) cc_final: 0.7558 (ptt) REVERT: A 295 GLN cc_start: 0.8053 (tm-30) cc_final: 0.7642 (tm-30) REVERT: B 53 VAL cc_start: 0.8453 (t) cc_final: 0.8101 (m) REVERT: B 228 GLU cc_start: 0.8360 (tm-30) cc_final: 0.8087 (tm-30) REVERT: B 229 LYS cc_start: 0.8396 (mttt) cc_final: 0.7728 (mtmm) REVERT: K 128 ASP cc_start: 0.8017 (t0) cc_final: 0.7670 (t0) REVERT: K 343 CYS cc_start: 0.7851 (m) cc_final: 0.7025 (t) REVERT: K 382 VAL cc_start: 0.9115 (OUTLIER) cc_final: 0.8827 (m) REVERT: C 14 LEU cc_start: 0.8081 (tp) cc_final: 0.7622 (tp) REVERT: C 17 ASP cc_start: 0.7621 (p0) cc_final: 0.7029 (p0) REVERT: C 105 GLU cc_start: 0.8381 (tp30) cc_final: 0.8169 (mm-30) REVERT: D 64 LYS cc_start: 0.6818 (mttp) cc_final: 0.6364 (mmmt) REVERT: D 231 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.6471 (tt0) REVERT: L 242 ASP cc_start: 0.8138 (m-30) cc_final: 0.7888 (m-30) REVERT: L 292 TYR cc_start: 0.9042 (p90) cc_final: 0.8838 (p90) REVERT: L 371 SER cc_start: 0.8215 (OUTLIER) cc_final: 0.7716 (p) REVERT: L 381 LEU cc_start: 0.9183 (pp) cc_final: 0.8971 (pp) REVERT: E 68 LYS cc_start: 0.8751 (mtpt) cc_final: 0.8332 (mtpp) REVERT: G 101 ASN cc_start: 0.6203 (t160) cc_final: 0.5849 (t0) REVERT: G 105 TRP cc_start: 0.8021 (t60) cc_final: 0.7664 (t60) outliers start: 58 outliers final: 40 residues processed: 289 average time/residue: 0.2798 time to fit residues: 118.2383 Evaluate side-chains 271 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 228 time to evaluate : 1.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 221 HIS Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 33 ARG Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain K residue 68 CYS Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 382 VAL Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 132 PHE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain L residue 192 SER Chi-restraints excluded: chain L residue 221 ILE Chi-restraints excluded: chain L residue 371 SER Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 71 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 15 optimal weight: 0.0570 chunk 130 optimal weight: 0.9990 chunk 150 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 chunk 144 optimal weight: 0.0980 overall best weight: 0.5700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 HIS ** E 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.4692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16080 Z= 0.180 Angle : 0.556 9.531 21866 Z= 0.278 Chirality : 0.041 0.177 2580 Planarity : 0.004 0.045 2848 Dihedral : 4.254 22.979 2286 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 3.60 % Allowed : 19.23 % Favored : 77.17 % 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: -1.43 (0.20), residues: 1940 helix: 0.52 (0.19), residues: 860 sheet: -1.57 (0.34), residues: 252 loop : -2.37 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 94 HIS 0.007 0.001 HIS B 113 PHE 0.033 0.001 PHE G 17 TYR 0.018 0.001 TYR L 195 ARG 0.009 0.000 ARG E 23 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 233 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLN cc_start: 0.8375 (mp10) cc_final: 0.7744 (mp10) REVERT: A 35 MET cc_start: 0.8151 (tmm) cc_final: 0.7578 (ptt) REVERT: A 295 GLN cc_start: 0.8045 (tm-30) cc_final: 0.7649 (tm-30) REVERT: B 53 VAL cc_start: 0.8512 (t) cc_final: 0.8163 (m) REVERT: B 228 GLU cc_start: 0.8366 (tm-30) cc_final: 0.8130 (tm-30) REVERT: B 229 LYS cc_start: 0.8356 (mttt) cc_final: 0.7694 (mtmm) REVERT: K 128 ASP cc_start: 0.8023 (t0) cc_final: 0.7653 (t0) REVERT: K 382 VAL cc_start: 0.9164 (OUTLIER) cc_final: 0.8806 (m) REVERT: C 17 ASP cc_start: 0.7740 (p0) cc_final: 0.7080 (p0) REVERT: C 105 GLU cc_start: 0.8381 (tp30) cc_final: 0.8163 (mm-30) REVERT: D 64 LYS cc_start: 0.6801 (mttp) cc_final: 0.6354 (mmmt) REVERT: D 231 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6544 (tt0) REVERT: L 242 ASP cc_start: 0.8163 (m-30) cc_final: 0.7904 (m-30) REVERT: L 292 TYR cc_start: 0.9043 (p90) cc_final: 0.8794 (p90) REVERT: L 371 SER cc_start: 0.8210 (OUTLIER) cc_final: 0.7702 (p) REVERT: E 68 LYS cc_start: 0.8792 (mtpt) cc_final: 0.8371 (mtpp) REVERT: G 105 TRP cc_start: 0.8063 (t60) cc_final: 0.7729 (t60) outliers start: 54 outliers final: 46 residues processed: 265 average time/residue: 0.2771 time to fit residues: 107.5341 Evaluate side-chains 274 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 225 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 221 HIS Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 33 ARG Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 276 THR Chi-restraints excluded: chain K residue 382 VAL Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 137 ARG Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 221 HIS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 132 PHE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain L residue 192 SER Chi-restraints excluded: chain L residue 221 ILE Chi-restraints excluded: chain L residue 264 ILE Chi-restraints excluded: chain L residue 371 SER Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 125 HIS Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 71 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 47 optimal weight: 0.0670 chunk 139 optimal weight: 0.0980 chunk 146 optimal weight: 0.8980 chunk 153 optimal weight: 0.0980 chunk 101 optimal weight: 0.9990 chunk 163 optimal weight: 0.0570 overall best weight: 0.2236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 294 ASN ** D 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 101 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.4920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16080 Z= 0.138 Angle : 0.533 9.357 21866 Z= 0.266 Chirality : 0.040 0.173 2580 Planarity : 0.004 0.050 2848 Dihedral : 4.026 20.621 2286 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.80 % Allowed : 19.96 % Favored : 77.24 % 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: -1.11 (0.20), residues: 1940 helix: 0.81 (0.19), residues: 844 sheet: -1.44 (0.34), residues: 252 loop : -2.17 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 105 HIS 0.005 0.001 HIS B 113 PHE 0.028 0.001 PHE G 17 TYR 0.020 0.001 TYR L 195 ARG 0.010 0.000 ARG E 23 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 250 time to evaluate : 1.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLN cc_start: 0.8352 (mp10) cc_final: 0.7758 (mp10) REVERT: A 81 ARG cc_start: 0.8075 (ptm-80) cc_final: 0.7827 (ttt-90) REVERT: A 164 LYS cc_start: 0.8515 (ptpt) cc_final: 0.8228 (mttp) REVERT: A 295 GLN cc_start: 0.8101 (tm-30) cc_final: 0.7686 (tm-30) REVERT: B 53 VAL cc_start: 0.8415 (t) cc_final: 0.8057 (m) REVERT: B 228 GLU cc_start: 0.8356 (tm-30) cc_final: 0.8112 (tm-30) REVERT: B 229 LYS cc_start: 0.8313 (mttt) cc_final: 0.7657 (mtmm) REVERT: K 128 ASP cc_start: 0.8002 (t0) cc_final: 0.7621 (t0) REVERT: K 382 VAL cc_start: 0.8972 (OUTLIER) cc_final: 0.8576 (m) REVERT: C 14 LEU cc_start: 0.8055 (tp) cc_final: 0.7496 (tp) REVERT: C 17 ASP cc_start: 0.7711 (p0) cc_final: 0.7044 (p0) REVERT: C 276 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7827 (mtm) REVERT: D 64 LYS cc_start: 0.6833 (mttp) cc_final: 0.6450 (mmmt) REVERT: D 231 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.6489 (tt0) REVERT: L 242 ASP cc_start: 0.8018 (m-30) cc_final: 0.7796 (m-30) REVERT: E 68 LYS cc_start: 0.8720 (mtpt) cc_final: 0.8308 (mtpp) outliers start: 42 outliers final: 32 residues processed: 275 average time/residue: 0.2696 time to fit residues: 109.2706 Evaluate side-chains 270 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 235 time to evaluate : 1.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 276 THR Chi-restraints excluded: chain K residue 382 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 221 HIS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 132 PHE Chi-restraints excluded: chain D residue 210 TYR Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain L residue 264 ILE Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 71 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 113 optimal weight: 8.9990 chunk 171 optimal weight: 0.9990 chunk 157 optimal weight: 0.2980 chunk 136 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16080 Z= 0.195 Angle : 0.566 9.766 21866 Z= 0.283 Chirality : 0.041 0.172 2580 Planarity : 0.004 0.042 2848 Dihedral : 4.132 21.589 2286 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 2.74 % Allowed : 20.43 % Favored : 76.84 % 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: -1.04 (0.20), residues: 1940 helix: 0.88 (0.19), residues: 844 sheet: -1.34 (0.34), residues: 252 loop : -2.15 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 94 HIS 0.007 0.001 HIS D 113 PHE 0.032 0.001 PHE G 17 TYR 0.019 0.001 TYR L 195 ARG 0.010 0.000 ARG C 167 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 229 time to evaluate : 1.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLN cc_start: 0.8331 (mp10) cc_final: 0.7651 (mp10) REVERT: A 295 GLN cc_start: 0.8098 (tm-30) cc_final: 0.7720 (tm-30) REVERT: B 53 VAL cc_start: 0.8426 (t) cc_final: 0.8066 (m) REVERT: B 229 LYS cc_start: 0.8281 (mttt) cc_final: 0.7850 (mtmm) REVERT: K 128 ASP cc_start: 0.8011 (t0) cc_final: 0.7626 (t0) REVERT: K 346 MET cc_start: 0.7478 (tpp) cc_final: 0.7265 (tpp) REVERT: K 382 VAL cc_start: 0.8912 (OUTLIER) cc_final: 0.8569 (m) REVERT: C 17 ASP cc_start: 0.7861 (p0) cc_final: 0.7217 (p0) REVERT: C 226 LYS cc_start: 0.8772 (tppt) cc_final: 0.8565 (tppt) REVERT: D 64 LYS cc_start: 0.6843 (mttp) cc_final: 0.6500 (mmmt) REVERT: D 231 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6557 (tt0) REVERT: L 242 ASP cc_start: 0.8093 (m-30) cc_final: 0.7855 (m-30) REVERT: E 68 LYS cc_start: 0.8789 (mtpt) cc_final: 0.8362 (mtpp) outliers start: 41 outliers final: 38 residues processed: 251 average time/residue: 0.2838 time to fit residues: 103.7003 Evaluate side-chains 264 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 224 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 276 THR Chi-restraints excluded: chain K residue 290 ILE Chi-restraints excluded: chain K residue 382 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 221 HIS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 241 GLN Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 132 PHE Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 210 TYR Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain L residue 221 ILE Chi-restraints excluded: chain L residue 264 ILE Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 71 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 0.0050 chunk 125 optimal weight: 0.7980 chunk 20 optimal weight: 0.0070 chunk 37 optimal weight: 0.8980 chunk 136 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 140 optimal weight: 0.0980 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 119 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.3012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN B 141 HIS C 244 GLN ** D 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 101 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.146432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.122004 restraints weight = 24909.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.121691 restraints weight = 28617.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.123572 restraints weight = 24260.259| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.5096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16080 Z= 0.144 Angle : 0.539 9.496 21866 Z= 0.268 Chirality : 0.040 0.163 2580 Planarity : 0.004 0.042 2848 Dihedral : 3.958 20.637 2286 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.54 % Allowed : 20.89 % Favored : 76.57 % 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: -0.89 (0.20), residues: 1940 helix: 1.02 (0.19), residues: 844 sheet: -1.25 (0.34), residues: 252 loop : -2.10 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 105 HIS 0.005 0.001 HIS B 113 PHE 0.028 0.001 PHE G 17 TYR 0.019 0.001 TYR L 195 ARG 0.010 0.000 ARG C 167 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3295.33 seconds wall clock time: 60 minutes 2.66 seconds (3602.66 seconds total)