Starting phenix.real_space_refine on Sun Jun 15 00:48:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wsq_32764/06_2025/7wsq_32764.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wsq_32764/06_2025/7wsq_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/cci-nas-00/data/ceres_data/7wsq_32764/06_2025/7wsq_32764.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wsq_32764/06_2025/7wsq_32764.map" model { file = "/net/cci-nas-00/data/ceres_data/7wsq_32764/06_2025/7wsq_32764.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wsq_32764/06_2025/7wsq_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. Time to flip 17 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 10.83, per 1000 atoms: 0.66 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=32, symmetry=0 Number of additional bonds: simple=32, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.96 Conformation dependent library (CDL) restraints added in 2.7 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: 2.12 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: 7.06 Time building geometry restraints manager: 5.60 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: 0.00 - 15.48: 23172 15.48 - 30.96: 24 30.96 - 46.45: 2 46.45 - 61.93: 0 61.93 - 77.41: 4 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: 0.04 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: 150.000 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: 0.680 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 46.300 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 201.650 ------------------------------------------------------------------------------- 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 : 0.039 2.035 17010 Z= 1.954 Angle : 1.699 77.412 23220 Z= 0.565 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 Details of bonding type rmsd hydrogen bonds : bond 0.25501 ( 513) hydrogen bonds : angle 8.25616 ( 1431) metal coordination : bond 0.00232 ( 6) metal coordination : angle 27.24183 ( 18) covalent geometry : bond 0.03848 (16972) covalent geometry : angle 1.52060 (23202) Misc. bond : bond 0.09011 ( 32) *********************** 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 to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 2.353 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: 0.3025 time to fit residues: 128.0476 Evaluate side-chains 213 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 1.997 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.172636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.149413 restraints weight = 25116.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.149497 restraints weight = 26526.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.151190 restraints weight = 22011.523| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 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 17010 Z= 0.165 Angle : 1.509 85.402 23220 Z= 0.442 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 Details of bonding type rmsd hydrogen bonds : bond 0.04602 ( 513) hydrogen bonds : angle 5.90518 ( 1431) metal coordination : bond 0.01484 ( 6) metal coordination : angle 36.99906 ( 18) covalent geometry : bond 0.00374 (16972) covalent geometry : angle 1.10292 (23202) Misc. bond : bond 0.00703 ( 32) *********************** 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 to be fit. rotamer outliers: 10 poor density : 246 time to evaluate : 1.742 Fit side-chains REVERT: A 70 SER cc_start: 0.7692 (t) cc_final: 0.7260 (p) REVERT: A 156 MET cc_start: 0.8339 (ttm) cc_final: 0.8108 (mtp) REVERT: A 497 TRP cc_start: 0.7313 (m100) cc_final: 0.7061 (m100) REVERT: C 187 ASP cc_start: 0.7663 (t70) cc_final: 0.7372 (t70) REVERT: C 352 LYS cc_start: 0.8376 (mmtt) cc_final: 0.8094 (tppt) REVERT: D 526 MET cc_start: 0.7604 (mtm) cc_final: 0.7310 (mtm) REVERT: F 352 LYS cc_start: 0.8344 (mmtt) cc_final: 0.8074 (tppt) outliers start: 10 outliers final: 8 residues processed: 251 average time/residue: 0.2587 time to fit residues: 101.1460 Evaluate side-chains 225 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 217 time to evaluate : 1.729 ------------------------------------------------------------------------------- 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 79 optimal weight: 2.9990 chunk 165 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 192 optimal weight: 1.9990 chunk 74 optimal weight: 0.0010 chunk 170 optimal weight: 0.7980 chunk 81 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 191 optimal weight: 0.0040 overall best weight: 0.7200 ------------------------------------------------------------------------------- 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** ** D 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.172331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.149868 restraints weight = 24754.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.150626 restraints weight = 25308.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.152259 restraints weight = 20654.764| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 17010 Z= 0.142 Angle : 1.438 83.787 23220 Z= 0.419 Chirality : 0.059 1.420 2478 Planarity : 0.005 0.060 2986 Dihedral : 9.458 97.403 2432 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.17 % Allowed : 15.08 % Favored : 83.74 % 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: -0.32 (0.19), residues: 2072 helix: 0.72 (0.20), residues: 710 sheet: -0.03 (0.41), residues: 180 loop : -0.81 (0.19), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 111 HIS 0.006 0.001 HIS A 110 PHE 0.015 0.001 PHE A 507 TYR 0.027 0.001 TYR D 79 ARG 0.007 0.000 ARG D 396 Details of bonding type rmsd hydrogen bonds : bond 0.03234 ( 513) hydrogen bonds : angle 5.33267 ( 1431) metal coordination : bond 0.00300 ( 6) metal coordination : angle 34.48595 ( 18) covalent geometry : bond 0.00321 (16972) covalent geometry : angle 1.07032 (23202) Misc. bond : bond 0.01851 ( 32) *********************** 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 262 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 242 time to evaluate : 1.758 Fit side-chains REVERT: A 70 SER cc_start: 0.7667 (t) cc_final: 0.7251 (p) REVERT: A 156 MET cc_start: 0.8298 (ttm) cc_final: 0.7961 (mtp) REVERT: A 221 ASN cc_start: 0.8713 (t0) cc_final: 0.8328 (t0) REVERT: C 187 ASP cc_start: 0.7481 (t70) cc_final: 0.7264 (t70) REVERT: C 352 LYS cc_start: 0.8301 (mmtt) cc_final: 0.8045 (tppt) REVERT: D 221 ASN cc_start: 0.8687 (t0) cc_final: 0.8294 (t0) REVERT: D 329 MET cc_start: 0.7403 (ttm) cc_final: 0.7065 (ttt) REVERT: D 523 THR cc_start: 0.8978 (OUTLIER) cc_final: 0.8756 (t) REVERT: F 352 LYS cc_start: 0.8271 (mmtt) cc_final: 0.8020 (tppt) outliers start: 20 outliers final: 8 residues processed: 257 average time/residue: 0.2745 time to fit residues: 110.9506 Evaluate side-chains 227 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 218 time to evaluate : 1.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain F residue 345 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 155 optimal weight: 5.9990 chunk 150 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 199 optimal weight: 5.9990 chunk 197 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 204 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 141 optimal weight: 0.9990 chunk 115 optimal weight: 10.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 345 GLN ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN D 345 GLN D 503 HIS ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 ASN ** F 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.167023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.148222 restraints weight = 25260.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.148118 restraints weight = 28690.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.148767 restraints weight = 26012.495| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 17010 Z= 0.200 Angle : 1.505 83.963 23220 Z= 0.445 Chirality : 0.062 1.470 2478 Planarity : 0.005 0.059 2986 Dihedral : 9.691 105.389 2432 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.05 % Allowed : 16.31 % Favored : 81.63 % 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: -0.49 (0.19), residues: 2072 helix: 0.61 (0.20), residues: 710 sheet: -0.27 (0.40), residues: 184 loop : -0.92 (0.18), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 111 HIS 0.007 0.001 HIS A 110 PHE 0.018 0.002 PHE A 507 TYR 0.024 0.002 TYR D 79 ARG 0.006 0.000 ARG D 396 Details of bonding type rmsd hydrogen bonds : bond 0.03352 ( 513) hydrogen bonds : angle 5.26305 ( 1431) metal coordination : bond 0.00423 ( 6) metal coordination : angle 35.98635 ( 18) covalent geometry : bond 0.00474 (16972) covalent geometry : angle 1.12315 (23202) Misc. bond : bond 0.02713 ( 32) *********************** 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 266 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 231 time to evaluate : 1.918 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 SER cc_start: 0.7732 (t) cc_final: 0.7182 (p) REVERT: A 156 MET cc_start: 0.8302 (ttm) cc_final: 0.7977 (mtp) REVERT: A 221 ASN cc_start: 0.8790 (t0) cc_final: 0.8442 (t0) REVERT: C 352 LYS cc_start: 0.8454 (mmtt) cc_final: 0.8195 (tppt) REVERT: D 221 ASN cc_start: 0.8807 (t0) cc_final: 0.8433 (t0) REVERT: D 329 MET cc_start: 0.7477 (ttm) cc_final: 0.7092 (ttt) REVERT: E 134 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6967 (pt0) REVERT: F 124 ASN cc_start: 0.8696 (OUTLIER) cc_final: 0.8413 (t0) REVERT: F 352 LYS cc_start: 0.8426 (mmtt) cc_final: 0.8169 (tppt) outliers start: 35 outliers final: 24 residues processed: 252 average time/residue: 0.2607 time to fit residues: 103.7226 Evaluate side-chains 238 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 212 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 440 VAL 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 149 MET Chi-restraints excluded: chain B residue 159 ILE 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 D residue 60 SER Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 133 ILE Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 149 MET Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain F residue 124 ASN 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 35 optimal weight: 7.9990 chunk 158 optimal weight: 10.0000 chunk 114 optimal weight: 8.9990 chunk 79 optimal weight: 0.2980 chunk 18 optimal weight: 0.9990 chunk 49 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 chunk 34 optimal weight: 9.9990 chunk 94 optimal weight: 0.5980 chunk 155 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 HIS ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 GLN ** D 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 HIS F 58 ASN ** F 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.170114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.147389 restraints weight = 25487.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.147711 restraints weight = 26098.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.149275 restraints weight = 22274.518| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 17010 Z= 0.150 Angle : 1.441 83.954 23220 Z= 0.423 Chirality : 0.060 1.437 2478 Planarity : 0.005 0.059 2986 Dihedral : 9.628 103.497 2432 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.35 % Allowed : 18.43 % Favored : 79.23 % 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: -0.39 (0.19), residues: 2072 helix: 0.69 (0.20), residues: 712 sheet: -0.24 (0.41), residues: 184 loop : -0.86 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 111 HIS 0.010 0.001 HIS F 308 PHE 0.014 0.001 PHE E 144 TYR 0.024 0.001 TYR D 79 ARG 0.004 0.000 ARG D 396 Details of bonding type rmsd hydrogen bonds : bond 0.02942 ( 513) hydrogen bonds : angle 5.04791 ( 1431) metal coordination : bond 0.00365 ( 6) metal coordination : angle 34.01110 ( 18) covalent geometry : bond 0.00348 (16972) covalent geometry : angle 1.08615 (23202) Misc. bond : bond 0.01726 ( 32) *********************** 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 264 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 224 time to evaluate : 2.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 SER cc_start: 0.7760 (t) cc_final: 0.7287 (p) REVERT: A 98 GLN cc_start: 0.7889 (pp30) cc_final: 0.7619 (pp30) REVERT: A 156 MET cc_start: 0.8315 (ttm) cc_final: 0.7972 (mtp) REVERT: A 221 ASN cc_start: 0.8761 (t0) cc_final: 0.8387 (t0) REVERT: A 346 MET cc_start: 0.7900 (mmm) cc_final: 0.7598 (mtm) REVERT: A 497 TRP cc_start: 0.7273 (m100) cc_final: 0.6380 (m-10) REVERT: B 134 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7154 (pt0) REVERT: C 124 ASN cc_start: 0.8652 (OUTLIER) cc_final: 0.8419 (t0) REVERT: C 352 LYS cc_start: 0.8370 (mmtt) cc_final: 0.8133 (tppt) REVERT: D 70 SER cc_start: 0.7697 (t) cc_final: 0.7238 (p) REVERT: D 98 GLN cc_start: 0.7658 (pp30) cc_final: 0.7434 (pp30) REVERT: D 156 MET cc_start: 0.8327 (ttm) cc_final: 0.8089 (mtp) REVERT: D 221 ASN cc_start: 0.8790 (t0) cc_final: 0.8381 (t0) REVERT: D 329 MET cc_start: 0.7369 (ttm) cc_final: 0.7021 (ttt) REVERT: D 497 TRP cc_start: 0.7201 (m100) cc_final: 0.6539 (m-10) REVERT: F 352 LYS cc_start: 0.8349 (mmtt) cc_final: 0.8124 (tppt) outliers start: 40 outliers final: 27 residues processed: 249 average time/residue: 0.2887 time to fit residues: 111.3093 Evaluate side-chains 244 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 215 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 268 ILE 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 493 VAL 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 46 LEU Chi-restraints excluded: chain C residue 124 ASN 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 D residue 60 SER Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 411 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 133 ILE Chi-restraints excluded: chain E residue 149 MET Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain F residue 384 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 180 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 28 optimal weight: 0.3980 chunk 83 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 123 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- 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** ** D 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 ASN ** F 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.165672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.142596 restraints weight = 25517.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.142265 restraints weight = 27110.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.143906 restraints weight = 23429.339| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 17010 Z= 0.200 Angle : 1.505 83.975 23220 Z= 0.443 Chirality : 0.062 1.475 2478 Planarity : 0.005 0.060 2986 Dihedral : 9.634 107.270 2432 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.17 % Allowed : 18.43 % Favored : 78.40 % 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: -0.50 (0.19), residues: 2072 helix: 0.64 (0.20), residues: 712 sheet: -0.23 (0.41), residues: 184 loop : -0.96 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 111 HIS 0.010 0.001 HIS C 308 PHE 0.016 0.002 PHE E 144 TYR 0.022 0.002 TYR D 79 ARG 0.003 0.000 ARG D 396 Details of bonding type rmsd hydrogen bonds : bond 0.03194 ( 513) hydrogen bonds : angle 5.10919 ( 1431) metal coordination : bond 0.00497 ( 6) metal coordination : angle 35.89873 ( 18) covalent geometry : bond 0.00472 (16972) covalent geometry : angle 1.12578 (23202) Misc. bond : bond 0.02821 ( 32) *********************** 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 285 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 231 time to evaluate : 2.083 Fit side-chains revert: symmetry clash REVERT: A 70 SER cc_start: 0.7866 (t) cc_final: 0.7296 (p) REVERT: A 98 GLN cc_start: 0.7964 (pp30) cc_final: 0.7629 (pp30) REVERT: A 156 MET cc_start: 0.8395 (ttm) cc_final: 0.8089 (mtp) REVERT: A 221 ASN cc_start: 0.8840 (t0) cc_final: 0.8504 (t0) REVERT: A 497 TRP cc_start: 0.7367 (m100) cc_final: 0.6507 (m-10) REVERT: B 55 MET cc_start: 0.7718 (mmt) cc_final: 0.7234 (mmt) REVERT: B 134 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7088 (pt0) REVERT: C 124 ASN cc_start: 0.8731 (OUTLIER) cc_final: 0.8481 (t0) REVERT: C 352 LYS cc_start: 0.8464 (mmtt) cc_final: 0.8189 (tppt) REVERT: D 70 SER cc_start: 0.7708 (t) cc_final: 0.7116 (p) REVERT: D 98 GLN cc_start: 0.7759 (pp30) cc_final: 0.7475 (pp30) REVERT: D 156 MET cc_start: 0.8323 (ttm) cc_final: 0.8083 (mtp) REVERT: D 221 ASN cc_start: 0.8857 (t0) cc_final: 0.8499 (t0) REVERT: D 497 TRP cc_start: 0.7306 (m100) cc_final: 0.6591 (m-10) REVERT: E 134 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.7104 (pt0) REVERT: F 124 ASN cc_start: 0.8735 (OUTLIER) cc_final: 0.8394 (t0) REVERT: F 352 LYS cc_start: 0.8457 (mmtt) cc_final: 0.8179 (tppt) outliers start: 54 outliers final: 40 residues processed: 267 average time/residue: 0.2921 time to fit residues: 122.3027 Evaluate side-chains 257 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 213 time to evaluate : 1.790 ------------------------------------------------------------------------------- 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 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 429 LEU Chi-restraints excluded: chain A residue 440 VAL 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 134 GLU Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 124 ASN 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 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 178 MET Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 268 ILE 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 470 THR Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 133 ILE Chi-restraints excluded: chain E residue 134 GLU 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 152 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 154 optimal weight: 6.9990 chunk 193 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 161 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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** ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.167445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.144844 restraints weight = 25314.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.144804 restraints weight = 25965.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.146488 restraints weight = 22258.591| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 17010 Z= 0.166 Angle : 1.470 84.006 23220 Z= 0.431 Chirality : 0.060 1.444 2478 Planarity : 0.005 0.060 2986 Dihedral : 9.552 108.231 2432 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.99 % Allowed : 18.31 % Favored : 78.70 % 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: 0.69 (0.20), residues: 712 sheet: -0.26 (0.41), residues: 184 loop : -0.94 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 111 HIS 0.012 0.001 HIS F 308 PHE 0.022 0.002 PHE C 306 TYR 0.023 0.002 TYR A 79 ARG 0.003 0.000 ARG A 205 Details of bonding type rmsd hydrogen bonds : bond 0.02952 ( 513) hydrogen bonds : angle 5.01479 ( 1431) metal coordination : bond 0.00392 ( 6) metal coordination : angle 34.79368 ( 18) covalent geometry : bond 0.00390 (16972) covalent geometry : angle 1.10601 (23202) Misc. bond : bond 0.02249 ( 32) *********************** REFINEMENT MACRO_CYCLE 7 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 to be fit. rotamer outliers: 51 poor density : 222 time to evaluate : 2.026 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 SER cc_start: 0.7827 (t) cc_final: 0.7308 (p) REVERT: A 98 GLN cc_start: 0.7903 (pp30) cc_final: 0.7573 (pp30) REVERT: A 109 TRP cc_start: 0.8077 (m100) cc_final: 0.7807 (m100) REVERT: A 156 MET cc_start: 0.8384 (ttm) cc_final: 0.8021 (mtp) REVERT: A 221 ASN cc_start: 0.8811 (t0) cc_final: 0.8416 (t0) REVERT: A 329 MET cc_start: 0.8026 (mmm) cc_final: 0.7624 (mtp) REVERT: A 497 TRP cc_start: 0.7325 (m100) cc_final: 0.6503 (m-10) REVERT: B 134 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7120 (pt0) REVERT: C 124 ASN cc_start: 0.8704 (OUTLIER) cc_final: 0.8396 (t0) REVERT: C 352 LYS cc_start: 0.8461 (mmtt) cc_final: 0.8190 (tppt) REVERT: D 70 SER cc_start: 0.7740 (t) cc_final: 0.7269 (p) REVERT: D 98 GLN cc_start: 0.7655 (pp30) cc_final: 0.7412 (pp30) REVERT: D 156 MET cc_start: 0.8329 (ttm) cc_final: 0.8076 (mtp) REVERT: D 221 ASN cc_start: 0.8822 (t0) cc_final: 0.8425 (t0) REVERT: D 329 MET cc_start: 0.7375 (ttm) cc_final: 0.6929 (ttt) REVERT: D 497 TRP cc_start: 0.7276 (m100) cc_final: 0.6607 (m-10) REVERT: F 124 ASN cc_start: 0.8707 (OUTLIER) cc_final: 0.8392 (t0) REVERT: F 352 LYS cc_start: 0.8448 (mmtt) cc_final: 0.8184 (tppt) outliers start: 51 outliers final: 37 residues processed: 257 average time/residue: 0.4352 time to fit residues: 179.6230 Evaluate side-chains 254 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 214 time to evaluate : 1.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 268 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 429 LEU 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 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 159 ILE Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 124 ASN 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 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 337 ILE 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 470 THR Chi-restraints excluded: chain D residue 493 VAL 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 E residue 159 ILE 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 115 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 197 optimal weight: 0.6980 chunk 114 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 104 optimal weight: 0.9990 chunk 48 optimal weight: 0.4980 chunk 110 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 chunk 46 optimal weight: 0.0020 overall best weight: 0.5188 ------------------------------------------------------------------------------- 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** B 123 GLN ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 ASN E 123 GLN ** F 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.172211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.149606 restraints weight = 25068.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.150025 restraints weight = 26189.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.151897 restraints weight = 20452.815| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.118 17010 Z= 0.137 Angle : 1.414 83.941 23220 Z= 0.419 Chirality : 0.059 1.422 2478 Planarity : 0.005 0.062 2986 Dihedral : 9.338 103.860 2432 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.97 % Favored : 94.98 % Rotamer: Outliers : 2.52 % Allowed : 18.90 % Favored : 78.58 % 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: -0.37 (0.19), residues: 2072 helix: 0.74 (0.20), residues: 724 sheet: -0.31 (0.41), residues: 184 loop : -0.86 (0.19), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 111 HIS 0.012 0.001 HIS C 308 PHE 0.018 0.001 PHE C 306 TYR 0.024 0.001 TYR D 68 ARG 0.004 0.000 ARG A 205 Details of bonding type rmsd hydrogen bonds : bond 0.02689 ( 513) hydrogen bonds : angle 4.87956 ( 1431) metal coordination : bond 0.00334 ( 6) metal coordination : angle 32.66948 ( 18) covalent geometry : bond 0.00307 (16972) covalent geometry : angle 1.08258 (23202) Misc. bond : bond 0.03283 ( 32) *********************** REFINEMENT MACRO_CYCLE 8 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 275 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 232 time to evaluate : 1.859 Fit side-chains revert: symmetry clash REVERT: A 70 SER cc_start: 0.7670 (t) cc_final: 0.7220 (p) REVERT: A 98 GLN cc_start: 0.7776 (pp30) cc_final: 0.7509 (pp30) REVERT: A 109 TRP cc_start: 0.8000 (m100) cc_final: 0.7795 (m100) REVERT: A 156 MET cc_start: 0.8330 (ttm) cc_final: 0.7834 (mtp) REVERT: A 221 ASN cc_start: 0.8686 (t0) cc_final: 0.8263 (t0) REVERT: A 329 MET cc_start: 0.7952 (mmm) cc_final: 0.7647 (mtp) REVERT: A 497 TRP cc_start: 0.7332 (m100) cc_final: 0.6473 (m-10) REVERT: B 134 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6989 (pt0) REVERT: C 124 ASN cc_start: 0.8603 (OUTLIER) cc_final: 0.8400 (t0) REVERT: C 352 LYS cc_start: 0.8297 (mmtt) cc_final: 0.8007 (tppt) REVERT: D 156 MET cc_start: 0.8368 (ttm) cc_final: 0.8036 (mtp) REVERT: D 221 ASN cc_start: 0.8735 (t0) cc_final: 0.8346 (t0) REVERT: D 329 MET cc_start: 0.7355 (ttm) cc_final: 0.6868 (ttt) REVERT: D 346 MET cc_start: 0.7668 (mmm) cc_final: 0.7349 (mtm) REVERT: D 497 TRP cc_start: 0.7205 (m100) cc_final: 0.6529 (m-10) REVERT: F 124 ASN cc_start: 0.8608 (OUTLIER) cc_final: 0.8385 (t0) REVERT: F 352 LYS cc_start: 0.8287 (mmtt) cc_final: 0.7993 (tppt) outliers start: 43 outliers final: 30 residues processed: 267 average time/residue: 0.2621 time to fit residues: 109.0608 Evaluate side-chains 243 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 210 time to evaluate : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 VAL 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 421 LEU Chi-restraints excluded: chain A residue 429 LEU 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 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 169 TYR Chi-restraints excluded: chain C residue 124 ASN 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 D residue 60 SER Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 429 LEU 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 133 ILE Chi-restraints excluded: chain F residue 124 ASN Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 345 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 58 optimal weight: 0.0020 chunk 142 optimal weight: 8.9990 chunk 174 optimal weight: 3.9990 chunk 184 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 79 optimal weight: 0.0970 chunk 132 optimal weight: 0.0270 chunk 127 optimal weight: 0.0270 chunk 36 optimal weight: 0.9990 chunk 191 optimal weight: 6.9990 chunk 90 optimal weight: 0.0970 overall best weight: 0.0500 ------------------------------------------------------------------------------- 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** ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.176192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.152109 restraints weight = 25060.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.153184 restraints weight = 23994.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.154792 restraints weight = 19009.959| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.128 17010 Z= 0.137 Angle : 1.392 83.900 23220 Z= 0.419 Chirality : 0.059 1.422 2478 Planarity : 0.005 0.058 2986 Dihedral : 9.036 96.394 2432 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.63 % Favored : 95.32 % Rotamer: Outliers : 1.88 % Allowed : 20.13 % Favored : 77.99 % 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: -0.44 (0.19), residues: 2072 helix: 0.66 (0.20), residues: 738 sheet: -0.12 (0.43), residues: 164 loop : -0.95 (0.19), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 111 HIS 0.013 0.001 HIS C 308 PHE 0.018 0.001 PHE C 306 TYR 0.026 0.001 TYR B 162 ARG 0.004 0.000 ARG A 279 Details of bonding type rmsd hydrogen bonds : bond 0.02560 ( 513) hydrogen bonds : angle 4.79481 ( 1431) metal coordination : bond 0.00318 ( 6) metal coordination : angle 31.61727 ( 18) covalent geometry : bond 0.00304 (16972) covalent geometry : angle 1.07848 (23202) Misc. bond : bond 0.04021 ( 32) *********************** REFINEMENT MACRO_CYCLE 9 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 266 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 234 time to evaluate : 1.736 Fit side-chains REVERT: A 98 GLN cc_start: 0.7770 (pp30) cc_final: 0.7506 (pp30) REVERT: A 109 TRP cc_start: 0.8014 (m100) cc_final: 0.7794 (m100) REVERT: A 156 MET cc_start: 0.8341 (ttm) cc_final: 0.7985 (mtp) REVERT: A 497 TRP cc_start: 0.7256 (m100) cc_final: 0.6359 (m-10) REVERT: B 134 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6921 (pt0) REVERT: C 352 LYS cc_start: 0.8277 (mmtt) cc_final: 0.8046 (tppt) REVERT: D 156 MET cc_start: 0.8167 (ttm) cc_final: 0.7530 (mtp) REVERT: D 221 ASN cc_start: 0.8612 (t0) cc_final: 0.8238 (t0) REVERT: D 497 TRP cc_start: 0.7184 (m100) cc_final: 0.6423 (m-10) REVERT: D 526 MET cc_start: 0.6964 (mtm) cc_final: 0.6744 (mtm) REVERT: F 45 TYR cc_start: 0.8945 (OUTLIER) cc_final: 0.8107 (t80) REVERT: F 352 LYS cc_start: 0.8273 (mmtt) cc_final: 0.8046 (tppt) outliers start: 32 outliers final: 21 residues processed: 258 average time/residue: 0.2804 time to fit residues: 113.7495 Evaluate side-chains 236 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 213 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 421 LEU 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 B residue 93 LEU Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain C residue 293 VAL 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 368 TYR Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 421 LEU 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 F residue 45 TYR Chi-restraints excluded: chain F residue 293 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 107 optimal weight: 0.9990 chunk 25 optimal weight: 8.9990 chunk 48 optimal weight: 20.0000 chunk 114 optimal weight: 3.9990 chunk 162 optimal weight: 7.9990 chunk 65 optimal weight: 8.9990 chunk 127 optimal weight: 0.5980 chunk 129 optimal weight: 8.9990 chunk 94 optimal weight: 0.8980 chunk 133 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 221 ASN ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 HIS ** F 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 189 ASN ** F 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.170526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.148076 restraints weight = 25242.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.148431 restraints weight = 26748.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.150298 restraints weight = 21062.740| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.145 17010 Z= 0.163 Angle : 1.451 83.994 23220 Z= 0.432 Chirality : 0.060 1.456 2478 Planarity : 0.005 0.058 2986 Dihedral : 9.108 99.659 2432 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.76 % Allowed : 20.25 % Favored : 77.99 % 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: -0.41 (0.19), residues: 2072 helix: 0.71 (0.20), residues: 726 sheet: -0.40 (0.40), residues: 180 loop : -0.88 (0.18), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 111 HIS 0.013 0.001 HIS C 308 PHE 0.018 0.002 PHE C 306 TYR 0.022 0.002 TYR D 68 ARG 0.008 0.000 ARG C 190 Details of bonding type rmsd hydrogen bonds : bond 0.02813 ( 513) hydrogen bonds : angle 4.88457 ( 1431) metal coordination : bond 0.00304 ( 6) metal coordination : angle 33.84706 ( 18) covalent geometry : bond 0.00385 (16972) covalent geometry : angle 1.10351 (23202) Misc. bond : bond 0.03000 ( 32) ********************** REFINEMENT MACRO_CYCLE 10 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 244 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 214 time to evaluate : 1.861 Fit side-chains REVERT: A 156 MET cc_start: 0.8433 (ttm) cc_final: 0.7987 (mtp) REVERT: A 497 TRP cc_start: 0.7299 (m100) cc_final: 0.6425 (m-10) REVERT: B 134 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6993 (pt0) REVERT: C 352 LYS cc_start: 0.8356 (mmtt) cc_final: 0.8110 (tppt) REVERT: D 156 MET cc_start: 0.8343 (ttm) cc_final: 0.8001 (mtp) REVERT: D 221 ASN cc_start: 0.8732 (t0) cc_final: 0.8361 (t0) REVERT: D 346 MET cc_start: 0.7608 (mmm) cc_final: 0.7281 (mtm) REVERT: D 497 TRP cc_start: 0.7262 (m100) cc_final: 0.6482 (m-10) REVERT: E 134 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6957 (pt0) REVERT: F 352 LYS cc_start: 0.8337 (mmtt) cc_final: 0.8090 (tppt) outliers start: 30 outliers final: 23 residues processed: 237 average time/residue: 0.2684 time to fit residues: 98.6053 Evaluate side-chains 230 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 205 time to evaluate : 1.900 ------------------------------------------------------------------------------- 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 421 LEU 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 B residue 93 LEU Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 384 VAL 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 337 ILE Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 421 LEU 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 134 GLU Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 384 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 25 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 197 optimal weight: 0.6980 chunk 111 optimal weight: 9.9990 chunk 54 optimal weight: 0.0000 chunk 166 optimal weight: 0.9990 chunk 191 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- 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** ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.173169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.150615 restraints weight = 25163.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.151203 restraints weight = 25826.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.153114 restraints weight = 20497.638| |-----------------------------------------------------------------------------| r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.119 17010 Z= 0.141 Angle : 1.423 84.020 23220 Z= 0.424 Chirality : 0.059 1.429 2478 Planarity : 0.005 0.057 2986 Dihedral : 9.068 99.431 2432 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.64 % Allowed : 20.25 % 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: -0.40 (0.19), residues: 2072 helix: 0.70 (0.20), residues: 728 sheet: -0.12 (0.42), residues: 164 loop : -0.91 (0.19), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 111 HIS 0.012 0.001 HIS C 308 PHE 0.018 0.001 PHE C 306 TYR 0.021 0.001 TYR D 68 ARG 0.009 0.000 ARG C 190 Details of bonding type rmsd hydrogen bonds : bond 0.02659 ( 513) hydrogen bonds : angle 4.83693 ( 1431) metal coordination : bond 0.00333 ( 6) metal coordination : angle 32.85987 ( 18) covalent geometry : bond 0.00319 (16972) covalent geometry : angle 1.08986 (23202) Misc. bond : bond 0.03261 ( 32) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5519.16 seconds wall clock time: 101 minutes 20.79 seconds (6080.79 seconds total)