Starting phenix.real_space_refine on Tue Aug 6 14:47:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsq_32764/08_2024/7wsq_32764.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsq_32764/08_2024/7wsq_32764.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/7wsq_32764/08_2024/7wsq_32764.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsq_32764/08_2024/7wsq_32764.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsq_32764/08_2024/7wsq_32764.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsq_32764/08_2024/7wsq_32764.cif" } 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 12 7.16 5 P 4 5.49 5 S 90 5.16 5 C 10438 2.51 5 N 2856 2.21 5 O 3122 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 184": "OD1" <-> "OD2" Residue "A TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 136": "OE1" <-> "OE2" Residue "B TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 61": "OD1" <-> "OD2" Residue "C TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 61": "OD1" <-> "OD2" Residue "F TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 16522 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4143 Classifications: {'peptide': 537} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 500} Chain: "B" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 780 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain breaks: 4 Chain: "C" Number of atoms: 3149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3149 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 391} Chain breaks: 1 Chain: "D" Number of atoms: 4143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4143 Classifications: {'peptide': 537} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 500} Chain: "E" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 780 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain breaks: 4 Chain: "F" Number of atoms: 3149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3149 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 391} Chain breaks: 1 Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'F3S': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'HEC': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'F3S': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'HEC': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1743 SG CYS A 226 56.402 34.924 73.094 1.00 11.67 S ATOM 1714 SG CYS A 222 54.539 31.327 76.966 1.00 16.07 S ATOM 1674 SG CYS A 216 56.131 28.347 72.238 1.00 12.67 S ATOM 9815 SG CYS D 226 49.725 95.575 73.082 1.00 12.69 S ATOM 9786 SG CYS D 222 51.584 99.211 76.969 1.00 16.63 S ATOM 9746 SG CYS D 216 50.012 102.154 72.238 1.00 15.48 S Time building chain proxies: 9.95, per 1000 atoms: 0.60 Number of scatterers: 16522 At special positions: 0 Unit cell: (106.14, 131.37, 116.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 12 26.01 S 90 16.00 P 4 15.00 O 3122 8.00 N 2856 7.00 C 10438 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=32, symmetry=0 Number of additional bonds: simple=32, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.60 Conformation dependent library (CDL) restraints added in 3.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S A 602 " pdb="FE1 F3S A 602 " - pdb=" SG CYS A 226 " pdb="FE4 F3S A 602 " - pdb=" SG CYS A 216 " pdb="FE3 F3S A 602 " - pdb=" SG CYS A 222 " pdb=" F3S D 602 " pdb="FE1 F3S D 602 " - pdb=" SG CYS D 226 " pdb="FE4 F3S D 602 " - pdb=" SG CYS D 216 " pdb="FE3 F3S D 602 " - pdb=" SG CYS D 222 " Number of angles added : 18 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3860 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 16 sheets defined 40.2% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 16 through 30 Processing helix chain 'A' and resid 43 through 54 Processing helix chain 'A' and resid 56 through 61 removed outlier: 3.975A pdb=" N GLN A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 97 Processing helix chain 'A' and resid 105 through 110 Processing helix chain 'A' and resid 119 through 124 removed outlier: 3.735A pdb=" N PHE A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS A 124 " --> pdb=" O PRO A 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 119 through 124' Processing helix chain 'A' and resid 124 through 130 Processing helix chain 'A' and resid 142 through 154 Processing helix chain 'A' and resid 181 through 195 Processing helix chain 'A' and resid 233 through 245 removed outlier: 4.170A pdb=" N ALA A 237 " --> pdb=" O ASN A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 301 Processing helix chain 'A' and resid 351 through 354 removed outlier: 4.404A pdb=" N ASP A 354 " --> pdb=" O ASN A 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 351 through 354' Processing helix chain 'A' and resid 355 through 360 removed outlier: 3.733A pdb=" N ARG A 358 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER A 359 " --> pdb=" O ASP A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 384 Processing helix chain 'A' and resid 388 through 401 Processing helix chain 'A' and resid 440 through 462 removed outlier: 4.573A pdb=" N VAL A 444 " --> pdb=" O VAL A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 541 removed outlier: 4.129A pdb=" N MET A 526 " --> pdb=" O SER A 522 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ASP A 535 " --> pdb=" O LEU A 531 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA A 536 " --> pdb=" O ARG A 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 56 Processing helix chain 'B' and resid 70 through 83 removed outlier: 3.547A pdb=" N ALA B 74 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ALA B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 98 removed outlier: 3.553A pdb=" N ILE B 90 " --> pdb=" O PHE B 86 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LYS B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA B 92 " --> pdb=" O THR B 88 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ARG B 94 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLU B 95 " --> pdb=" O LYS B 91 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N HIS B 96 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE B 97 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR B 98 " --> pdb=" O ARG B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 124 No H-bonds generated for 'chain 'B' and resid 122 through 124' Processing helix chain 'B' and resid 125 through 130 Processing helix chain 'C' and resid 41 through 50 Processing helix chain 'C' and resid 51 through 56 removed outlier: 4.038A pdb=" N CYS C 55 " --> pdb=" O ASP C 51 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N HIS C 56 " --> pdb=" O CYS C 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 51 through 56' Processing helix chain 'C' and resid 95 through 104 Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.776A pdb=" N ARG C 125 " --> pdb=" O ALA C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 141 removed outlier: 4.021A pdb=" N SER C 133 " --> pdb=" O GLU C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 162 No H-bonds generated for 'chain 'C' and resid 160 through 162' Processing helix chain 'C' and resid 163 through 172 removed outlier: 3.811A pdb=" N TRP C 167 " --> pdb=" O SER C 163 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE C 169 " --> pdb=" O GLY C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 197 removed outlier: 3.666A pdb=" N GLU C 197 " --> pdb=" O TYR C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 206 removed outlier: 4.068A pdb=" N CYS C 204 " --> pdb=" O HIS C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 256 Processing helix chain 'C' and resid 265 through 274 Processing helix chain 'C' and resid 275 through 278 Processing helix chain 'C' and resid 279 through 291 Processing helix chain 'C' and resid 334 through 343 removed outlier: 3.714A pdb=" N VAL C 342 " --> pdb=" O LEU C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 383 Processing helix chain 'C' and resid 408 through 423 Processing helix chain 'C' and resid 431 through 441 removed outlier: 3.894A pdb=" N VAL C 435 " --> pdb=" O SER C 431 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS C 436 " --> pdb=" O ALA C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 451 removed outlier: 3.540A pdb=" N LYS C 449 " --> pdb=" O PRO C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 471 removed outlier: 3.555A pdb=" N MET C 456 " --> pdb=" O SER C 452 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY C 462 " --> pdb=" O LEU C 458 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL C 471 " --> pdb=" O ALA C 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 30 Processing helix chain 'D' and resid 43 through 54 Processing helix chain 'D' and resid 56 through 61 removed outlier: 3.887A pdb=" N GLN D 61 " --> pdb=" O ASP D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 97 Processing helix chain 'D' and resid 105 through 110 Processing helix chain 'D' and resid 119 through 124 removed outlier: 3.758A pdb=" N PHE D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS D 124 " --> pdb=" O PRO D 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 119 through 124' Processing helix chain 'D' and resid 124 through 130 Processing helix chain 'D' and resid 138 through 154 Proline residue: D 144 - end of helix Processing helix chain 'D' and resid 181 through 195 Processing helix chain 'D' and resid 234 through 245 Processing helix chain 'D' and resid 293 through 301 Processing helix chain 'D' and resid 351 through 354 removed outlier: 4.456A pdb=" N ASP D 354 " --> pdb=" O ASN D 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 351 through 354' Processing helix chain 'D' and resid 355 through 360 removed outlier: 3.724A pdb=" N ARG D 358 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER D 359 " --> pdb=" O ASP D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 383 removed outlier: 3.764A pdb=" N MET D 379 " --> pdb=" O SER D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 401 removed outlier: 3.901A pdb=" N ASP D 392 " --> pdb=" O GLY D 388 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU D 393 " --> pdb=" O LYS D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 462 removed outlier: 4.538A pdb=" N VAL D 444 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG D 445 " --> pdb=" O GLY D 441 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS D 446 " --> pdb=" O GLU D 442 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER D 447 " --> pdb=" O TYR D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 541 removed outlier: 4.031A pdb=" N MET D 526 " --> pdb=" O SER D 522 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA D 534 " --> pdb=" O SER D 530 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASP D 535 " --> pdb=" O LEU D 531 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA D 536 " --> pdb=" O ARG D 532 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 56 Processing helix chain 'E' and resid 70 through 83 removed outlier: 3.583A pdb=" N ALA E 74 " --> pdb=" O ASN E 70 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ALA E 81 " --> pdb=" O LEU E 77 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN E 82 " --> pdb=" O ALA E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 98 removed outlier: 3.558A pdb=" N ILE E 90 " --> pdb=" O PHE E 86 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LYS E 91 " --> pdb=" O SER E 87 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA E 92 " --> pdb=" O THR E 88 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ARG E 94 " --> pdb=" O ILE E 90 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLU E 95 " --> pdb=" O LYS E 91 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS E 96 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE E 97 " --> pdb=" O LEU E 93 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR E 98 " --> pdb=" O ARG E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 124 No H-bonds generated for 'chain 'E' and resid 122 through 124' Processing helix chain 'E' and resid 125 through 130 Processing helix chain 'F' and resid 41 through 50 removed outlier: 3.501A pdb=" N LEU F 46 " --> pdb=" O ARG F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 56 removed outlier: 4.039A pdb=" N CYS F 55 " --> pdb=" O ASP F 51 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N HIS F 56 " --> pdb=" O CYS F 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 51 through 56' Processing helix chain 'F' and resid 95 through 104 Processing helix chain 'F' and resid 122 through 126 removed outlier: 3.772A pdb=" N ARG F 125 " --> pdb=" O ALA F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 141 removed outlier: 4.021A pdb=" N SER F 133 " --> pdb=" O GLU F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 162 No H-bonds generated for 'chain 'F' and resid 160 through 162' Processing helix chain 'F' and resid 163 through 172 removed outlier: 3.758A pdb=" N TRP F 167 " --> pdb=" O SER F 163 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE F 169 " --> pdb=" O GLY F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 197 removed outlier: 3.667A pdb=" N GLU F 197 " --> pdb=" O TYR F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 206 removed outlier: 4.069A pdb=" N CYS F 204 " --> pdb=" O HIS F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 256 Processing helix chain 'F' and resid 265 through 274 Processing helix chain 'F' and resid 275 through 278 Processing helix chain 'F' and resid 279 through 291 Processing helix chain 'F' and resid 334 through 341 Processing helix chain 'F' and resid 373 through 383 Processing helix chain 'F' and resid 408 through 423 Processing helix chain 'F' and resid 431 through 441 removed outlier: 3.891A pdb=" N VAL F 435 " --> pdb=" O SER F 431 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS F 436 " --> pdb=" O ALA F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 445 through 451 removed outlier: 3.539A pdb=" N LYS F 449 " --> pdb=" O PRO F 446 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 471 removed outlier: 3.564A pdb=" N MET F 456 " --> pdb=" O SER F 452 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL F 471 " --> pdb=" O ALA F 467 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 247 through 249 removed outlier: 6.607A pdb=" N VAL A 33 " --> pdb=" O LYS A 247 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N ILE A 249 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU A 35 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N VAL A 11 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N PHE A 285 " --> pdb=" O PHE A 507 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.386A pdb=" N ILE A 87 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N HIS A 433 " --> pdb=" O SER A 422 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 198 through 200 Processing sheet with id=AA4, first strand: chain 'A' and resid 253 through 258 removed outlier: 7.328A pdb=" N SER A 269 " --> pdb=" O TYR A 255 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N MET A 257 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ALA A 267 " --> pdb=" O MET A 257 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 329 through 332 removed outlier: 3.540A pdb=" N ILE A 405 " --> pdb=" O MET A 329 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ASP A 404 " --> pdb=" O ASN A 369 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 70 through 73 removed outlier: 3.506A pdb=" N ILE C 71 " --> pdb=" O ILE C 78 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE C 78 " --> pdb=" O ILE C 71 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 224 through 225 Processing sheet with id=AA8, first strand: chain 'C' and resid 385 through 388 Processing sheet with id=AA9, first strand: chain 'D' and resid 247 through 249 removed outlier: 6.607A pdb=" N VAL D 33 " --> pdb=" O LYS D 247 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N ILE D 249 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU D 35 " --> pdb=" O ILE D 249 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N VAL D 11 " --> pdb=" O VAL D 286 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N PHE D 285 " --> pdb=" O PHE D 507 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 87 through 89 removed outlier: 6.379A pdb=" N ILE D 87 " --> pdb=" O VAL D 436 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N HIS D 433 " --> pdb=" O SER D 422 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 198 through 200 Processing sheet with id=AB3, first strand: chain 'D' and resid 253 through 258 removed outlier: 7.279A pdb=" N SER D 269 " --> pdb=" O TYR D 255 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N MET D 257 " --> pdb=" O ALA D 267 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ALA D 267 " --> pdb=" O MET D 257 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 329 through 332 removed outlier: 4.528A pdb=" N ASP D 404 " --> pdb=" O ASN D 369 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 70 through 73 removed outlier: 3.505A pdb=" N ILE F 71 " --> pdb=" O ILE F 78 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE F 78 " --> pdb=" O ILE F 71 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 224 through 225 Processing sheet with id=AB7, first strand: chain 'F' and resid 385 through 388 513 hydrogen bonds defined for protein. 1431 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: 4.64 Time building geometry restraints manager: 8.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.83: 16930 1.83 - 2.45: 36 2.45 - 3.06: 0 3.06 - 3.68: 0 3.68 - 4.29: 6 Bond restraints: 16972 Sorted by residual: bond pdb=" S4 F3S A 602 " pdb="FE1 F3S A 602 " ideal model delta sigma weight residual 2.233 4.268 -2.035 2.00e-02 2.50e+03 1.04e+04 bond pdb=" S4 F3S D 602 " pdb="FE1 F3S D 602 " ideal model delta sigma weight residual 2.233 4.268 -2.035 2.00e-02 2.50e+03 1.04e+04 bond pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " ideal model delta sigma weight residual 2.258 4.291 -2.033 2.00e-02 2.50e+03 1.03e+04 bond pdb=" S1 F3S D 602 " pdb="FE4 F3S D 602 " ideal model delta sigma weight residual 2.258 4.290 -2.032 2.00e-02 2.50e+03 1.03e+04 bond pdb=" S2 F3S A 602 " pdb="FE3 F3S A 602 " ideal model delta sigma weight residual 2.300 4.248 -1.948 2.00e-02 2.50e+03 9.49e+03 ... (remaining 16967 not shown) Histogram of bond angle deviations from ideal: 37.34 - 65.68: 12 65.68 - 94.02: 40 94.02 - 122.36: 20398 122.36 - 150.70: 2740 150.70 - 179.04: 12 Bond angle restraints: 23202 Sorted by residual: angle pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " pdb=" S3 F3S A 602 " ideal model delta sigma weight residual 114.75 37.34 77.41 3.00e+00 1.11e-01 6.66e+02 angle pdb=" S1 F3S D 602 " pdb="FE4 F3S D 602 " pdb=" S3 F3S D 602 " ideal model delta sigma weight residual 114.75 37.36 77.39 3.00e+00 1.11e-01 6.65e+02 angle pdb=" S3 F3S A 602 " pdb="FE1 F3S A 602 " pdb=" S4 F3S A 602 " ideal model delta sigma weight residual 112.59 38.05 74.54 3.00e+00 1.11e-01 6.17e+02 angle pdb=" S3 F3S D 602 " pdb="FE1 F3S D 602 " pdb=" S4 F3S D 602 " ideal model delta sigma weight residual 112.59 38.07 74.52 3.00e+00 1.11e-01 6.17e+02 angle pdb=" S1 F3S D 602 " pdb="FE4 F3S D 602 " pdb=" S2 F3S D 602 " ideal model delta sigma weight residual 103.63 72.19 31.44 3.00e+00 1.11e-01 1.10e+02 ... (remaining 23197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.27: 9275 22.27 - 44.53: 609 44.53 - 66.80: 70 66.80 - 89.06: 26 89.06 - 111.33: 2 Dihedral angle restraints: 9982 sinusoidal: 3928 harmonic: 6054 Sorted by residual: dihedral pdb=" CA HIS E 118 " pdb=" C HIS E 118 " pdb=" N PRO E 119 " pdb=" CA PRO E 119 " ideal model delta harmonic sigma weight residual 180.00 133.29 46.71 0 5.00e+00 4.00e-02 8.73e+01 dihedral pdb=" CA HIS B 118 " pdb=" C HIS B 118 " pdb=" N PRO B 119 " pdb=" CA PRO B 119 " ideal model delta harmonic sigma weight residual 180.00 134.44 45.56 0 5.00e+00 4.00e-02 8.30e+01 dihedral pdb=" CA PHE D 80 " pdb=" C PHE D 80 " pdb=" N PRO D 81 " pdb=" CA PRO D 81 " ideal model delta harmonic sigma weight residual -180.00 -140.76 -39.24 0 5.00e+00 4.00e-02 6.16e+01 ... (remaining 9979 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 3.128: 2476 3.128 - 6.256: 0 6.256 - 9.384: 0 9.384 - 12.512: 0 12.512 - 15.640: 2 Chirality restraints: 2478 Sorted by residual: chirality pdb=" S2 F3S D 602 " pdb="FE1 F3S D 602 " pdb="FE3 F3S D 602 " pdb="FE4 F3S D 602 " both_signs ideal model delta sigma weight residual False 10.77 -4.87 15.64 2.00e-01 2.50e+01 6.12e+03 chirality pdb=" S2 F3S A 602 " pdb="FE1 F3S A 602 " pdb="FE3 F3S A 602 " pdb="FE4 F3S A 602 " both_signs ideal model delta sigma weight residual False 10.77 -4.87 15.64 2.00e-01 2.50e+01 6.11e+03 chirality pdb=" CB ILE B 133 " pdb=" CA ILE B 133 " pdb=" CG1 ILE B 133 " pdb=" CG2 ILE B 133 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 2475 not shown) Planarity restraints: 2986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CBD HEC F 501 " -0.023 2.00e-02 2.50e+03 4.93e-02 2.43e+01 pdb=" CGD HEC F 501 " 0.085 2.00e-02 2.50e+03 pdb=" O1D HEC F 501 " -0.030 2.00e-02 2.50e+03 pdb=" O2D HEC F 501 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CBD HEC C 501 " -0.023 2.00e-02 2.50e+03 4.90e-02 2.40e+01 pdb=" CGD HEC C 501 " 0.085 2.00e-02 2.50e+03 pdb=" O1D HEC C 501 " -0.030 2.00e-02 2.50e+03 pdb=" O2D HEC C 501 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 111 " -0.029 2.00e-02 2.50e+03 2.95e-02 2.17e+01 pdb=" CG TRP A 111 " 0.078 2.00e-02 2.50e+03 pdb=" CD1 TRP A 111 " -0.041 2.00e-02 2.50e+03 pdb=" CD2 TRP A 111 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 111 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 111 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 111 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 111 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 111 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 111 " -0.001 2.00e-02 2.50e+03 ... (remaining 2983 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 100 2.44 - 3.06: 11043 3.06 - 3.67: 26340 3.67 - 4.29: 38200 4.29 - 4.90: 61868 Nonbonded interactions: 137551 Sorted by model distance: nonbonded pdb=" SG CYS A 226 " pdb=" S1 F3S A 602 " model vdw 1.827 3.760 nonbonded pdb=" SG CYS D 226 " pdb=" S1 F3S D 602 " model vdw 1.850 3.760 nonbonded pdb=" CG ASN D 521 " pdb=" C4 FAD D 601 " model vdw 2.070 2.792 nonbonded pdb=" CG ASN A 521 " pdb=" C4 FAD A 601 " model vdw 2.079 2.792 nonbonded pdb=" O ARG A 358 " pdb=" OH TYR A 443 " model vdw 2.112 3.040 ... (remaining 137546 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } 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: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 50.940 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 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 : 0.038 2.035 16972 Z= 2.117 Angle : 1.521 77.412 23202 Z= 0.562 Chirality : 0.446 15.640 2478 Planarity : 0.006 0.065 2986 Dihedral : 14.723 111.326 6122 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.10 % Twisted Proline : 3.12 % 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: -0.66 (0.19), residues: 2072 helix: 0.35 (0.21), residues: 646 sheet: 0.17 (0.43), residues: 176 loop : -0.96 (0.18), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.002 TRP A 111 HIS 0.006 0.001 HIS B 118 PHE 0.015 0.001 PHE B 144 TYR 0.032 0.001 TYR D 79 ARG 0.007 0.000 ARG D 396 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 1.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 LYS cc_start: 0.5338 (ttmm) cc_final: 0.5090 (mtpp) REVERT: A 321 MET cc_start: 0.7044 (tpp) cc_final: 0.6784 (mmt) REVERT: C 130 ASP cc_start: 0.7306 (m-30) cc_final: 0.7101 (m-30) REVERT: C 352 LYS cc_start: 0.8330 (mmtt) cc_final: 0.8002 (tppt) REVERT: D 321 MET cc_start: 0.7370 (tpp) cc_final: 0.7095 (mmt) REVERT: D 329 MET cc_start: 0.7587 (tpp) cc_final: 0.7208 (mtp) REVERT: F 130 ASP cc_start: 0.7282 (m-30) cc_final: 0.7078 (m-30) REVERT: F 352 LYS cc_start: 0.8300 (mmtt) cc_final: 0.7964 (tppt) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.2563 time to fit residues: 108.2518 Evaluate side-chains 213 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 173 optimal weight: 0.9990 chunk 156 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 161 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 187 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 ASN ** D 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 ASN E 165 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 16972 Z= 0.247 Angle : 1.103 85.401 23202 Z= 0.434 Chirality : 0.061 1.492 2478 Planarity : 0.005 0.062 2986 Dihedral : 9.571 100.440 2432 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.59 % Allowed : 11.74 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.10 % Twisted Proline : 3.12 % 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: -0.46 (0.19), residues: 2072 helix: 0.62 (0.21), residues: 696 sheet: 0.10 (0.42), residues: 180 loop : -0.93 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 111 HIS 0.008 0.001 HIS A 110 PHE 0.014 0.001 PHE C 64 TYR 0.026 0.001 TYR D 79 ARG 0.007 0.000 ARG A 499 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 246 time to evaluate : 1.747 Fit side-chains REVERT: A 70 SER cc_start: 0.7514 (t) cc_final: 0.7094 (p) REVERT: A 156 MET cc_start: 0.8316 (ttm) cc_final: 0.8071 (mtp) REVERT: A 497 TRP cc_start: 0.7222 (m100) cc_final: 0.6987 (m100) REVERT: C 187 ASP cc_start: 0.7528 (t70) cc_final: 0.7307 (t70) REVERT: C 352 LYS cc_start: 0.8351 (mmtt) cc_final: 0.8074 (tppt) REVERT: D 526 MET cc_start: 0.7618 (mtm) cc_final: 0.7325 (mtm) REVERT: F 352 LYS cc_start: 0.8317 (mmtt) cc_final: 0.8048 (tppt) outliers start: 10 outliers final: 8 residues processed: 251 average time/residue: 0.2523 time to fit residues: 98.6309 Evaluate side-chains 225 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 217 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain E residue 93 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 103 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 155 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 187 optimal weight: 10.0000 chunk 202 optimal weight: 0.0050 chunk 166 optimal weight: 8.9990 chunk 185 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 150 optimal weight: 6.9990 overall best weight: 5.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 ASN ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 ASN ** C 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 ASN D 263 ASN ** D 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 503 HIS ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 189 ASN ** F 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.128 16972 Z= 0.520 Angle : 1.257 84.695 23202 Z= 0.509 Chirality : 0.067 1.507 2478 Planarity : 0.007 0.064 2986 Dihedral : 10.221 118.401 2432 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 3.11 % Allowed : 15.96 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.10 % Twisted Proline : 3.12 % 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: -1.05 (0.18), residues: 2072 helix: 0.09 (0.20), residues: 712 sheet: -0.25 (0.41), residues: 184 loop : -1.28 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 111 HIS 0.009 0.002 HIS C 308 PHE 0.024 0.003 PHE B 144 TYR 0.030 0.003 TYR D 79 ARG 0.007 0.001 ARG D 396 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 230 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.8375 (ttm) cc_final: 0.8072 (mtp) REVERT: A 221 ASN cc_start: 0.8900 (t0) cc_final: 0.8542 (t0) REVERT: A 242 GLU cc_start: 0.7615 (tm-30) cc_final: 0.7312 (tm-30) REVERT: A 329 MET cc_start: 0.7973 (tpp) cc_final: 0.7763 (mmm) REVERT: C 124 ASN cc_start: 0.8834 (OUTLIER) cc_final: 0.8455 (t0) REVERT: D 221 ASN cc_start: 0.8929 (t0) cc_final: 0.8558 (t0) REVERT: D 242 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7462 (tm-30) REVERT: D 329 MET cc_start: 0.7517 (ttm) cc_final: 0.7098 (ttt) REVERT: D 406 TYR cc_start: 0.8423 (p90) cc_final: 0.8206 (p90) REVERT: F 124 ASN cc_start: 0.8855 (OUTLIER) cc_final: 0.8472 (t0) outliers start: 53 outliers final: 36 residues processed: 273 average time/residue: 0.2481 time to fit residues: 107.0248 Evaluate side-chains 242 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 204 time to evaluate : 1.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 13 ILE Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 133 ILE Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain F residue 124 ASN Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain F residue 445 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 185 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 188 optimal weight: 0.8980 chunk 199 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 ASN A 345 GLN B 118 HIS C 58 ASN C 347 HIS D 46 GLN ** D 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 ASN D 345 GLN E 118 HIS F 58 ASN ** F 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 16972 Z= 0.233 Angle : 1.120 84.249 23202 Z= 0.430 Chirality : 0.060 1.402 2478 Planarity : 0.005 0.062 2986 Dihedral : 9.850 110.679 2432 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.88 % Allowed : 19.48 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.10 % Twisted Proline : 3.12 % 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: -0.64 (0.19), residues: 2072 helix: 0.53 (0.20), residues: 710 sheet: -0.32 (0.40), residues: 184 loop : -1.04 (0.18), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 111 HIS 0.008 0.001 HIS A 110 PHE 0.027 0.001 PHE E 54 TYR 0.027 0.002 TYR A 79 ARG 0.007 0.000 ARG D 396 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 237 time to evaluate : 1.721 Fit side-chains revert: symmetry clash REVERT: A 70 SER cc_start: 0.7663 (t) cc_final: 0.7196 (p) REVERT: A 98 GLN cc_start: 0.7781 (pp30) cc_final: 0.7496 (pp30) REVERT: A 156 MET cc_start: 0.8313 (ttm) cc_final: 0.8031 (mtp) REVERT: A 221 ASN cc_start: 0.8827 (t0) cc_final: 0.8437 (t0) REVERT: A 329 MET cc_start: 0.7714 (tpp) cc_final: 0.7251 (mtp) REVERT: B 134 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7348 (pt0) REVERT: C 187 ASP cc_start: 0.7353 (t70) cc_final: 0.7130 (t70) REVERT: C 352 LYS cc_start: 0.8412 (mmtt) cc_final: 0.8125 (tppt) REVERT: D 98 GLN cc_start: 0.7727 (pp30) cc_final: 0.7440 (pp30) REVERT: D 221 ASN cc_start: 0.8860 (t0) cc_final: 0.8472 (t0) REVERT: D 368 TYR cc_start: 0.7607 (OUTLIER) cc_final: 0.6317 (p90) REVERT: E 134 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7287 (pt0) REVERT: F 187 ASP cc_start: 0.7339 (t70) cc_final: 0.7117 (t70) REVERT: F 352 LYS cc_start: 0.8363 (mmtt) cc_final: 0.8084 (tppt) outliers start: 32 outliers final: 14 residues processed: 258 average time/residue: 0.2671 time to fit residues: 107.0507 Evaluate side-chains 238 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 221 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain E residue 133 ILE Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 345 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 165 optimal weight: 5.9990 chunk 113 optimal weight: 0.0670 chunk 2 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 169 optimal weight: 7.9990 chunk 137 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 178 optimal weight: 9.9990 chunk 50 optimal weight: 7.9990 overall best weight: 3.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN A 219 ASN ** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 ASN ** D 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 ASN ** F 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 16972 Z= 0.395 Angle : 1.179 84.108 23202 Z= 0.465 Chirality : 0.064 1.502 2478 Planarity : 0.006 0.063 2986 Dihedral : 9.929 114.286 2432 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 4.05 % Allowed : 17.66 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.10 % Twisted Proline : 3.12 % 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: -0.85 (0.19), residues: 2072 helix: 0.36 (0.20), residues: 716 sheet: -0.36 (0.40), residues: 184 loop : -1.20 (0.18), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 111 HIS 0.010 0.001 HIS F 308 PHE 0.018 0.002 PHE A 507 TYR 0.024 0.002 TYR D 79 ARG 0.006 0.000 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 217 time to evaluate : 1.885 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 GLN cc_start: 0.7946 (pp30) cc_final: 0.7589 (pp30) REVERT: A 156 MET cc_start: 0.8437 (ttm) cc_final: 0.8083 (mtp) REVERT: A 221 ASN cc_start: 0.8859 (t0) cc_final: 0.8499 (t0) REVERT: A 329 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.7442 (mtp) REVERT: B 134 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7360 (pt0) REVERT: D 98 GLN cc_start: 0.7938 (pp30) cc_final: 0.7637 (pp30) REVERT: D 221 ASN cc_start: 0.8899 (t0) cc_final: 0.8526 (t0) REVERT: D 329 MET cc_start: 0.7656 (tpp) cc_final: 0.7238 (ttt) REVERT: F 124 ASN cc_start: 0.8781 (OUTLIER) cc_final: 0.8440 (t0) REVERT: F 187 ASP cc_start: 0.7437 (t70) cc_final: 0.7135 (t70) outliers start: 69 outliers final: 46 residues processed: 266 average time/residue: 0.2491 time to fit residues: 104.6502 Evaluate side-chains 253 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 204 time to evaluate : 1.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 13 ILE Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 469 MET Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 133 ILE Chi-restraints excluded: chain E residue 149 MET Chi-restraints excluded: chain F residue 124 ASN Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 445 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 66 optimal weight: 2.9990 chunk 179 optimal weight: 0.3980 chunk 39 optimal weight: 5.9990 chunk 116 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 199 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 92 optimal weight: 0.2980 chunk 16 optimal weight: 5.9990 chunk 65 optimal weight: 0.0050 chunk 104 optimal weight: 0.7980 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 ASN ** D 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 ASN ** D 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 HIS F 347 HIS ** F 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 16972 Z= 0.224 Angle : 1.111 84.083 23202 Z= 0.425 Chirality : 0.060 1.418 2478 Planarity : 0.005 0.062 2986 Dihedral : 9.757 111.151 2432 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.99 % Allowed : 18.90 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.10 % Twisted Proline : 3.12 % 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: -0.60 (0.19), residues: 2072 helix: 0.58 (0.20), residues: 708 sheet: -0.44 (0.40), residues: 184 loop : -1.00 (0.18), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 497 HIS 0.006 0.001 HIS B 64 PHE 0.014 0.001 PHE C 306 TYR 0.025 0.002 TYR D 79 ARG 0.005 0.000 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 226 time to evaluate : 1.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 GLN cc_start: 0.7807 (pp30) cc_final: 0.7497 (pp30) REVERT: A 156 MET cc_start: 0.8364 (ttm) cc_final: 0.7956 (mtp) REVERT: A 221 ASN cc_start: 0.8786 (t0) cc_final: 0.8403 (t0) REVERT: A 329 MET cc_start: 0.7646 (tpp) cc_final: 0.7141 (mtp) REVERT: B 134 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7251 (pt0) REVERT: C 187 ASP cc_start: 0.7277 (t70) cc_final: 0.7066 (t70) REVERT: C 352 LYS cc_start: 0.8411 (mmtt) cc_final: 0.8099 (tppt) REVERT: D 98 GLN cc_start: 0.7725 (pp30) cc_final: 0.7438 (pp30) REVERT: D 221 ASN cc_start: 0.8808 (t0) cc_final: 0.8425 (t0) REVERT: D 329 MET cc_start: 0.7527 (tpp) cc_final: 0.7269 (ttt) REVERT: F 352 LYS cc_start: 0.8413 (mmtt) cc_final: 0.8091 (tppt) outliers start: 51 outliers final: 40 residues processed: 261 average time/residue: 0.2391 time to fit residues: 98.3703 Evaluate side-chains 247 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 206 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 133 ILE Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain E residue 149 MET Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain F residue 445 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.89 > 50: distance: 75 - 80: 35.783 distance: 81 - 84: 39.129 distance: 82 - 83: 39.680 distance: 82 - 89: 39.564 distance: 86 - 87: 40.094 distance: 86 - 88: 40.255 distance: 89 - 90: 56.311 distance: 90 - 91: 41.039 distance: 91 - 92: 56.498 distance: 91 - 95: 56.521 distance: 93 - 94: 23.476 distance: 94 - 259: 28.281 distance: 95 - 96: 39.702 distance: 96 - 97: 34.169 distance: 96 - 99: 40.286 distance: 97 - 98: 25.311 distance: 97 - 101: 44.569 distance: 99 - 100: 40.683 distance: 101 - 102: 37.190 distance: 102 - 103: 45.961 distance: 103 - 104: 58.815 distance: 103 - 105: 42.798 distance: 106 - 109: 39.652 distance: 107 - 108: 43.566 distance: 107 - 113: 25.229 distance: 109 - 110: 21.379 distance: 110 - 111: 31.975 distance: 110 - 112: 43.107 distance: 113 - 114: 15.248 distance: 114 - 115: 17.274 distance: 114 - 117: 18.354 distance: 115 - 116: 25.556 distance: 115 - 121: 37.113 distance: 117 - 118: 20.513 distance: 118 - 119: 23.840 distance: 121 - 122: 18.987 distance: 122 - 123: 23.739 distance: 122 - 125: 14.996 distance: 123 - 124: 43.533 distance: 123 - 129: 34.551 distance: 125 - 126: 40.127 distance: 126 - 127: 29.872 distance: 126 - 128: 20.999 distance: 129 - 130: 40.323 distance: 130 - 131: 31.044 distance: 130 - 133: 44.434 distance: 131 - 132: 50.626 distance: 131 - 135: 41.979 distance: 133 - 134: 11.312 distance: 134 - 258: 29.054 distance: 137 - 143: 40.149 distance: 139 - 140: 6.932 distance: 140 - 141: 36.544 distance: 141 - 142: 15.280 distance: 143 - 144: 40.639 distance: 143 - 149: 40.540 distance: 144 - 147: 39.166 distance: 145 - 146: 47.102 distance: 145 - 150: 35.408 distance: 147 - 148: 57.009 distance: 148 - 149: 38.746