Starting phenix.real_space_refine on Fri Jul 3 22:52:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wsq_32764/07_2026/7wsq_32764.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wsq_32764/07_2026/7wsq_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_32764/07_2026/7wsq_32764.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wsq_32764/07_2026/7wsq_32764.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7wsq_32764/07_2026/7wsq_32764.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wsq_32764/07_2026/7wsq_32764.cif" model { file = "/net/cci-nas-00/data/ceres_data/7wsq_32764/07_2026/7wsq_32764.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wsq_32764/07_2026/7wsq_32764.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 3.52, per 1000 atoms: 0.21 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: 1.71 Conformation dependent library (CDL) restraints added in 729.9 milliseconds 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: 0.46 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: 2.62 Time building geometry restraints manager: 2.06 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: 9211 22.27 - 44.53: 591 44.53 - 66.80: 70 66.80 - 89.06: 22 89.06 - 111.33: 2 Dihedral angle restraints: 9896 sinusoidal: 3842 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 9893 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.690 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 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 : 14.515 111.326 6036 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 11.62 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.007 0.000 ARG D 396 TYR 0.032 0.001 TYR D 79 PHE 0.015 0.001 PHE B 144 TRP 0.078 0.002 TRP A 111 HIS 0.006 0.001 HIS B 118 Details of bonding type rmsd/Z covalent geometry : bond 0.03848 / 1.92 (16972) covalent geometry : angle 1.52060 / 0.56 (23202) hydrogen bonds : bond 0.25501 / 17.12 ( 513) hydrogen bonds : angle 8.25616 / 6.10 ( 1431) metal coordination : bond 0.00232 / 0.12 ( 6) metal coordination : angle 27.24183 / 13.71 ( 18) Misc. bond : bond 0.09011 / 5.88 ( 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 : 0.592 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: 0.7281 (m-30) cc_final: 0.7078 (m-30) REVERT: F 352 LYS cc_start: 0.8300 (mmtt) cc_final: 0.7963 (tppt) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.1236 time to fit residues: 52.7753 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 : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.167837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.143235 restraints weight = 25484.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.143670 restraints weight = 23105.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.145048 restraints weight = 21294.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.145363 restraints weight = 15535.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.145560 restraints weight = 14627.690| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.152 17010 Z= 0.225 Angle : 1.654 90.950 23220 Z= 0.479 Chirality : 0.058 1.240 2478 Planarity : 0.006 0.063 2986 Dihedral : 8.744 103.475 2346 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 0.94 % Allowed : 13.03 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.10 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.19), residues: 2072 helix: 0.49 (0.20), residues: 696 sheet: 0.10 (0.43), residues: 180 loop : -1.06 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 499 TYR 0.026 0.002 TYR D 79 PHE 0.019 0.002 PHE C 64 TRP 0.041 0.002 TRP A 111 HIS 0.009 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.22 (16972) covalent geometry : angle 1.18865 / 0.47 (23202) hydrogen bonds : bond 0.04404 / 3.07 ( 513) hydrogen bonds : angle 5.85498 / 4.21 ( 1431) metal coordination : bond 0.01416 / 0.74 ( 6) metal coordination : angle 41.33001 / 18.58 ( 18) Misc. bond : bond 0.03768 / 2.16 ( 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 251 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 235 time to evaluate : 0.501 Fit side-chains revert: symmetry clash REVERT: A 70 SER cc_start: 0.7802 (t) cc_final: 0.7274 (p) REVERT: A 156 MET cc_start: 0.8317 (ttm) cc_final: 0.8065 (mtp) REVERT: C 352 LYS cc_start: 0.8473 (mmtt) cc_final: 0.8198 (tppt) REVERT: D 329 MET cc_start: 0.7599 (tpp) cc_final: 0.7280 (ttt) REVERT: D 526 MET cc_start: 0.7980 (mtt) cc_final: 0.7679 (mtm) REVERT: F 352 LYS cc_start: 0.8442 (mmtt) cc_final: 0.8169 (tppt) outliers start: 16 outliers final: 14 residues processed: 240 average time/residue: 0.1162 time to fit residues: 44.2547 Evaluate side-chains 225 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 211 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 ILE 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 C residue 345 SER Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 133 ILE Chi-restraints excluded: chain F residue 345 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 121 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 chunk 58 optimal weight: 9.9990 chunk 61 optimal weight: 0.0070 chunk 157 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 178 optimal weight: 10.0000 chunk 145 optimal weight: 4.9990 chunk 169 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 overall best weight: 2.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 ASN C 427 GLN ** D 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN D 503 HIS E 118 HIS F 58 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.165117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.141930 restraints weight = 25543.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.142578 restraints weight = 25666.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.144072 restraints weight = 20147.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.144493 restraints weight = 15423.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.144688 restraints weight = 14416.107| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.171 17010 Z= 0.210 Angle : 1.546 84.414 23220 Z= 0.453 Chirality : 0.062 1.472 2478 Planarity : 0.006 0.062 2986 Dihedral : 8.663 109.396 2346 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.70 % Allowed : 16.08 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.10 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.19), residues: 2072 helix: 0.51 (0.20), residues: 698 sheet: -0.13 (0.41), residues: 184 loop : -1.09 (0.18), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 396 TYR 0.026 0.002 TYR D 79 PHE 0.014 0.002 PHE B 144 TRP 0.027 0.002 TRP A 111 HIS 0.006 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.21 (16972) covalent geometry : angle 1.14323 / 0.44 (23202) hydrogen bonds : bond 0.03708 / 2.58 ( 513) hydrogen bonds : angle 5.45530 / 3.94 ( 1431) metal coordination : bond 0.00581 / 0.30 ( 6) metal coordination : angle 37.40859 / 16.49 ( 18) Misc. bond : bond 0.04291 / 2.48 ( 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 281 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 235 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.8370 (ttm) cc_final: 0.8028 (mtp) REVERT: A 221 ASN cc_start: 0.8934 (t0) cc_final: 0.8564 (t0) REVERT: A 329 MET cc_start: 0.7929 (OUTLIER) cc_final: 0.7463 (mtp) REVERT: A 523 THR cc_start: 0.9255 (OUTLIER) cc_final: 0.9049 (t) REVERT: C 352 LYS cc_start: 0.8500 (mmtt) cc_final: 0.8177 (tppt) REVERT: D 221 ASN cc_start: 0.8927 (t0) cc_final: 0.8569 (t0) REVERT: D 526 MET cc_start: 0.8019 (mtt) cc_final: 0.7721 (mtm) REVERT: F 124 ASN cc_start: 0.8754 (OUTLIER) cc_final: 0.8392 (t0) REVERT: F 352 LYS cc_start: 0.8472 (mmtt) cc_final: 0.8162 (tppt) outliers start: 46 outliers final: 27 residues processed: 267 average time/residue: 0.1158 time to fit residues: 49.1743 Evaluate side-chains 250 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 220 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain D residue 54 MET Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 337 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 159 ILE Chi-restraints excluded: chain F residue 124 ASN Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 393 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 120 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 chunk 190 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 201 optimal weight: 3.9990 chunk 187 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 GLN B 118 HIS ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 GLN ** D 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 GLN ** F 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.166173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.142122 restraints weight = 25337.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.142206 restraints weight = 24878.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.143819 restraints weight = 20543.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.144509 restraints weight = 14573.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.144622 restraints weight = 13885.129| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.131 17010 Z= 0.190 Angle : 1.520 84.134 23220 Z= 0.446 Chirality : 0.062 1.452 2478 Planarity : 0.005 0.061 2986 Dihedral : 8.633 108.743 2346 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.76 % Allowed : 17.25 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.10 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.19), residues: 2072 helix: 0.47 (0.20), residues: 708 sheet: -0.30 (0.40), residues: 184 loop : -1.05 (0.18), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 396 TYR 0.025 0.002 TYR D 79 PHE 0.026 0.002 PHE E 54 TRP 0.022 0.002 TRP A 111 HIS 0.008 0.001 HIS F 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 (16972) covalent geometry : angle 1.13101 / 0.44 (23202) hydrogen bonds : bond 0.03278 / 2.27 ( 513) hydrogen bonds : angle 5.30579 / 3.83 ( 1431) metal coordination : bond 0.00383 / 0.20 ( 6) metal coordination : angle 36.49988 / 15.99 ( 18) Misc. bond : bond 0.03312 / 1.91 ( 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 270 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 223 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.8399 (ttm) cc_final: 0.8068 (mtp) REVERT: A 221 ASN cc_start: 0.8906 (t0) cc_final: 0.8509 (t0) REVERT: A 329 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7320 (mtp) REVERT: B 134 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7278 (pt0) REVERT: C 124 ASN cc_start: 0.8791 (OUTLIER) cc_final: 0.8465 (t0) REVERT: C 187 ASP cc_start: 0.7442 (t70) cc_final: 0.7208 (t70) REVERT: C 352 LYS cc_start: 0.8485 (mmtt) cc_final: 0.8166 (tppt) REVERT: D 221 ASN cc_start: 0.8913 (t0) cc_final: 0.8499 (t0) REVERT: D 329 MET cc_start: 0.7383 (ttm) cc_final: 0.7017 (ttt) REVERT: E 134 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7322 (pt0) REVERT: F 124 ASN cc_start: 0.8751 (OUTLIER) cc_final: 0.8381 (t0) REVERT: F 352 LYS cc_start: 0.8461 (mmtt) cc_final: 0.8161 (tppt) outliers start: 47 outliers final: 31 residues processed: 252 average time/residue: 0.1193 time to fit residues: 47.7144 Evaluate side-chains 243 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 207 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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 329 MET Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 411 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 133 ILE Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain C residue 103 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 54 MET Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 458 ILE 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 F residue 103 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 154 optimal weight: 2.9990 chunk 167 optimal weight: 10.0000 chunk 163 optimal weight: 4.9990 chunk 200 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 119 optimal weight: 7.9990 chunk 147 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 GLN ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 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 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3947 r_free = 0.3947 target = 0.160552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.136364 restraints weight = 25630.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.137593 restraints weight = 25558.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.139134 restraints weight = 20853.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.139194 restraints weight = 15629.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.139301 restraints weight = 14810.615| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.284 17010 Z= 0.273 Angle : 1.614 84.192 23220 Z= 0.485 Chirality : 0.065 1.506 2478 Planarity : 0.006 0.064 2986 Dihedral : 8.934 116.379 2346 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 4.64 % Allowed : 17.84 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.10 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.18), residues: 2072 helix: 0.28 (0.20), residues: 708 sheet: -0.42 (0.40), residues: 184 loop : -1.30 (0.18), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 396 TYR 0.025 0.002 TYR D 79 PHE 0.017 0.002 PHE A 80 TRP 0.020 0.002 TRP D 111 HIS 0.007 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00646 / 0.27 (16972) covalent geometry : angle 1.20598 / 0.48 (23202) hydrogen bonds : bond 0.03701 / 2.59 ( 513) hydrogen bonds : angle 5.48936 / 3.96 ( 1431) metal coordination : bond 0.00629 / 0.33 ( 6) metal coordination : angle 38.53910 / 16.68 ( 18) Misc. bond : bond 0.07011 / 3.99 ( 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 292 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 213 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.8423 (ttm) cc_final: 0.8103 (mtp) REVERT: A 221 ASN cc_start: 0.8926 (t0) cc_final: 0.8527 (t0) REVERT: A 329 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7434 (mtp) REVERT: B 134 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7464 (pt0) REVERT: C 124 ASN cc_start: 0.8836 (OUTLIER) cc_final: 0.8488 (t0) REVERT: D 221 ASN cc_start: 0.8942 (t0) cc_final: 0.8537 (t0) REVERT: D 329 MET cc_start: 0.7439 (ttm) cc_final: 0.7051 (ttt) REVERT: E 134 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7410 (pt0) REVERT: F 124 ASN cc_start: 0.8831 (OUTLIER) cc_final: 0.8479 (t0) outliers start: 79 outliers final: 54 residues processed: 271 average time/residue: 0.1222 time to fit residues: 52.7055 Evaluate side-chains 259 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 200 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 469 MET 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 156 VAL Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain D residue 13 ILE Chi-restraints excluded: chain D residue 54 MET 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 153 MET Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 316 LEU 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 458 ILE 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 156 VAL Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 124 ASN Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 393 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 21 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 164 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 170 optimal weight: 0.6980 chunk 172 optimal weight: 9.9990 chunk 84 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 ASN ** D 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 HIS F 425 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.167938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.143976 restraints weight = 25224.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.144828 restraints weight = 21969.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.146385 restraints weight = 19075.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.146659 restraints weight = 13858.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.146972 restraints weight = 14074.036| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2575 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= 0.148 Angle : 1.478 84.190 23220 Z= 0.433 Chirality : 0.060 1.405 2478 Planarity : 0.005 0.063 2986 Dihedral : 8.675 112.053 2346 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.17 % Allowed : 19.25 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.10 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.19), residues: 2072 helix: 0.47 (0.20), residues: 720 sheet: -0.56 (0.39), residues: 184 loop : -1.04 (0.19), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 28 TYR 0.024 0.001 TYR A 79 PHE 0.013 0.001 PHE C 210 TRP 0.020 0.001 TRP D 497 HIS 0.006 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (16972) covalent geometry : angle 1.11618 / 0.43 (23202) hydrogen bonds : bond 0.02925 / 2.02 ( 513) hydrogen bonds : angle 5.11191 / 3.70 ( 1431) metal coordination : bond 0.00215 / 0.12 ( 6) metal coordination : angle 34.79407 / 15.45 ( 18) Misc. bond : bond 0.02127 / 1.05 ( 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 284 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 230 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 GLN cc_start: 0.7826 (pp30) cc_final: 0.7361 (pp30) REVERT: A 156 MET cc_start: 0.8398 (ttm) cc_final: 0.8007 (mtp) REVERT: A 221 ASN cc_start: 0.8861 (t0) cc_final: 0.8510 (t0) REVERT: A 329 MET cc_start: 0.7653 (OUTLIER) cc_final: 0.7306 (mtp) REVERT: A 421 LEU cc_start: 0.7054 (OUTLIER) cc_final: 0.6775 (pt) REVERT: C 124 ASN cc_start: 0.8763 (OUTLIER) cc_final: 0.8451 (t0) REVERT: C 187 ASP cc_start: 0.7308 (t70) cc_final: 0.7035 (t70) REVERT: C 352 LYS cc_start: 0.8414 (mmtt) cc_final: 0.8096 (tppt) REVERT: D 98 GLN cc_start: 0.7664 (pp30) cc_final: 0.7397 (pp30) REVERT: D 221 ASN cc_start: 0.8873 (t0) cc_final: 0.8457 (t0) REVERT: D 329 MET cc_start: 0.7344 (ttm) cc_final: 0.6968 (ttt) REVERT: D 421 LEU cc_start: 0.7044 (OUTLIER) cc_final: 0.6747 (pt) REVERT: F 187 ASP cc_start: 0.7261 (t70) cc_final: 0.6997 (t70) REVERT: F 352 LYS cc_start: 0.8383 (mmtt) cc_final: 0.8066 (tppt) outliers start: 54 outliers final: 36 residues processed: 267 average time/residue: 0.1229 time to fit residues: 51.8213 Evaluate side-chains 253 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 213 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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 329 MET Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 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 169 TYR Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain D residue 54 MET Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 469 MET 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 293 VAL Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 425 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 23 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 131 optimal weight: 6.9990 chunk 1 optimal weight: 0.6980 chunk 168 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 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 501 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 = 0.3987 r_free = 0.3987 target = 0.163686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.141022 restraints weight = 25474.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.141237 restraints weight = 26079.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.142801 restraints weight = 22172.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.143296 restraints weight = 16035.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.143462 restraints weight = 16835.866| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.176 17010 Z= 0.198 Angle : 1.525 84.052 23220 Z= 0.447 Chirality : 0.062 1.475 2478 Planarity : 0.006 0.064 2986 Dihedral : 8.552 110.671 2346 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 3.64 % Allowed : 19.42 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.10 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.19), residues: 2072 helix: 0.48 (0.20), residues: 720 sheet: -0.59 (0.39), residues: 184 loop : -1.11 (0.18), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 28 TYR 0.053 0.002 TYR A 79 PHE 0.015 0.002 PHE F 210 TRP 0.016 0.002 TRP D 497 HIS 0.008 0.001 HIS E 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.20 (16972) covalent geometry : angle 1.13735 / 0.44 (23202) hydrogen bonds : bond 0.03192 / 2.21 ( 513) hydrogen bonds : angle 5.13946 / 3.70 ( 1431) metal coordination : bond 0.00564 / 0.30 ( 6) metal coordination : angle 36.53119 / 15.98 ( 18) Misc. bond : bond 0.04668 / 2.55 ( 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 283 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 221 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 GLN cc_start: 0.7835 (pp30) cc_final: 0.7544 (pp30) REVERT: A 156 MET cc_start: 0.8413 (ttm) cc_final: 0.7955 (mtp) REVERT: A 221 ASN cc_start: 0.8884 (t0) cc_final: 0.8541 (t0) REVERT: A 469 MET cc_start: 0.6150 (mtp) cc_final: 0.5876 (mtm) REVERT: B 150 TYR cc_start: 0.4868 (t80) cc_final: 0.4646 (t80) REVERT: C 124 ASN cc_start: 0.8802 (OUTLIER) cc_final: 0.8477 (t0) REVERT: C 187 ASP cc_start: 0.7271 (t70) cc_final: 0.6967 (t70) REVERT: D 98 GLN cc_start: 0.7713 (pp30) cc_final: 0.7369 (pp30) REVERT: D 156 MET cc_start: 0.8341 (ttm) cc_final: 0.8039 (mtp) REVERT: D 221 ASN cc_start: 0.8900 (t0) cc_final: 0.8562 (t0) REVERT: D 329 MET cc_start: 0.7382 (ttm) cc_final: 0.6986 (ttt) REVERT: F 124 ASN cc_start: 0.8814 (OUTLIER) cc_final: 0.8457 (t0) REVERT: F 187 ASP cc_start: 0.7236 (t70) cc_final: 0.6933 (t70) outliers start: 62 outliers final: 47 residues processed: 262 average time/residue: 0.1151 time to fit residues: 48.0823 Evaluate side-chains 260 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 211 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 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 149 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain C residue 103 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 C residue 393 ILE Chi-restraints excluded: chain D residue 54 MET Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 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 122 ILE Chi-restraints excluded: chain E residue 133 ILE Chi-restraints excluded: chain E residue 149 MET Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 124 ASN Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 393 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 138 optimal weight: 0.9980 chunk 163 optimal weight: 7.9990 chunk 43 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 199 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 200 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 HIS B 123 GLN C 425 ASN ** D 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.167761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.146499 restraints weight = 25125.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.146798 restraints weight = 26788.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.148295 restraints weight = 23507.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.148567 restraints weight = 16634.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.148696 restraints weight = 16648.310| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.123 17010 Z= 0.148 Angle : 1.469 84.070 23220 Z= 0.429 Chirality : 0.060 1.425 2478 Planarity : 0.005 0.064 2986 Dihedral : 8.414 109.313 2346 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.23 % Allowed : 20.13 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.10 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.19), residues: 2072 helix: 0.59 (0.20), residues: 722 sheet: -0.61 (0.39), residues: 184 loop : -1.05 (0.18), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 28 TYR 0.041 0.002 TYR A 79 PHE 0.019 0.001 PHE F 306 TRP 0.016 0.001 TRP D 497 HIS 0.006 0.001 HIS E 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (16972) covalent geometry : angle 1.10836 / 0.42 (23202) hydrogen bonds : bond 0.02830 / 1.95 ( 513) hydrogen bonds : angle 4.95975 / 3.57 ( 1431) metal coordination : bond 0.00302 / 0.17 ( 6) metal coordination : angle 34.63380 / 15.42 ( 18) Misc. bond : bond 0.02668 / 1.22 ( 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 278 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 223 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 GLN cc_start: 0.7735 (pp30) cc_final: 0.7467 (pp30) REVERT: A 109 TRP cc_start: 0.8019 (m100) cc_final: 0.7740 (m100) REVERT: A 156 MET cc_start: 0.8390 (ttm) cc_final: 0.7981 (mtp) REVERT: A 221 ASN cc_start: 0.8808 (t0) cc_final: 0.8458 (t0) REVERT: B 94 ARG cc_start: 0.4999 (mtt90) cc_final: 0.4540 (mtt90) REVERT: C 124 ASN cc_start: 0.8686 (OUTLIER) cc_final: 0.8460 (t0) REVERT: C 187 ASP cc_start: 0.7156 (t70) cc_final: 0.6940 (t70) REVERT: C 352 LYS cc_start: 0.8381 (mmtt) cc_final: 0.8048 (tppt) REVERT: C 405 GLN cc_start: 0.8534 (tm-30) cc_final: 0.7835 (tt0) REVERT: D 98 GLN cc_start: 0.7485 (pp30) cc_final: 0.7280 (pp30) REVERT: D 156 MET cc_start: 0.8255 (ttm) cc_final: 0.7942 (mtp) REVERT: D 221 ASN cc_start: 0.8798 (t0) cc_final: 0.8419 (t0) REVERT: D 329 MET cc_start: 0.7368 (ttm) cc_final: 0.6983 (ttt) REVERT: F 124 ASN cc_start: 0.8733 (OUTLIER) cc_final: 0.8405 (t0) REVERT: F 352 LYS cc_start: 0.8373 (mmtt) cc_final: 0.8049 (tppt) outliers start: 55 outliers final: 37 residues processed: 262 average time/residue: 0.1189 time to fit residues: 49.0329 Evaluate side-chains 252 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 213 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 411 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 169 TYR Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 429 LEU 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 384 VAL Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain F residue 425 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 102 optimal weight: 0.5980 chunk 63 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 chunk 163 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 chunk 151 optimal weight: 4.9990 chunk 190 optimal weight: 3.9990 chunk 181 optimal weight: 0.1980 chunk 108 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 174 optimal weight: 0.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 ASN ** D 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.165151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.143204 restraints weight = 25332.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.142929 restraints weight = 27028.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.144626 restraints weight = 24756.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.144669 restraints weight = 18049.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.144842 restraints weight = 17116.583| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.137 17010 Z= 0.181 Angle : 1.505 84.046 23220 Z= 0.441 Chirality : 0.061 1.455 2478 Planarity : 0.005 0.068 2986 Dihedral : 8.288 108.993 2346 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 3.05 % Allowed : 20.54 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.10 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.19), residues: 2072 helix: 0.57 (0.20), residues: 722 sheet: -0.61 (0.39), residues: 184 loop : -1.09 (0.18), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 28 TYR 0.041 0.002 TYR A 79 PHE 0.018 0.002 PHE F 306 TRP 0.016 0.001 TRP D 497 HIS 0.006 0.001 HIS D 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.18 (16972) covalent geometry : angle 1.12559 / 0.43 (23202) hydrogen bonds : bond 0.03017 / 2.09 ( 513) hydrogen bonds : angle 5.02046 / 3.61 ( 1431) metal coordination : bond 0.00386 / 0.21 ( 6) metal coordination : angle 35.89549 / 15.84 ( 18) Misc. bond : bond 0.04027 / 2.12 ( 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 270 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 218 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 GLN cc_start: 0.7804 (pp30) cc_final: 0.7512 (pp30) REVERT: A 156 MET cc_start: 0.8392 (ttm) cc_final: 0.8016 (mtp) REVERT: A 221 ASN cc_start: 0.8819 (t0) cc_final: 0.8508 (t0) REVERT: A 469 MET cc_start: 0.6217 (mtp) cc_final: 0.5978 (mtm) REVERT: C 124 ASN cc_start: 0.8730 (OUTLIER) cc_final: 0.8467 (t0) REVERT: C 187 ASP cc_start: 0.7158 (t70) cc_final: 0.6930 (t70) REVERT: C 352 LYS cc_start: 0.8516 (mmtt) cc_final: 0.8156 (tppt) REVERT: D 98 GLN cc_start: 0.7648 (pp30) cc_final: 0.7420 (pp30) REVERT: D 156 MET cc_start: 0.8216 (ttm) cc_final: 0.7901 (mtp) REVERT: D 221 ASN cc_start: 0.8818 (t0) cc_final: 0.8449 (t0) REVERT: E 150 TYR cc_start: 0.4787 (t80) cc_final: 0.4578 (t80) REVERT: F 124 ASN cc_start: 0.8756 (OUTLIER) cc_final: 0.8403 (t0) REVERT: F 352 LYS cc_start: 0.8448 (mmtt) cc_final: 0.8082 (tppt) outliers start: 52 outliers final: 41 residues processed: 253 average time/residue: 0.1225 time to fit residues: 49.3403 Evaluate side-chains 255 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 212 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 411 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 149 MET 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 C residue 393 ILE Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 429 LEU 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 Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain F residue 425 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 104 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 25 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 chunk 193 optimal weight: 2.9990 chunk 160 optimal weight: 9.9990 chunk 90 optimal weight: 4.9990 chunk 132 optimal weight: 0.0980 chunk 67 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 184 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.168308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.145382 restraints weight = 25140.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.146027 restraints weight = 25921.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.147633 restraints weight = 21035.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.148046 restraints weight = 15216.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.148188 restraints weight = 15351.589| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.127 17010 Z= 0.147 Angle : 1.471 83.996 23220 Z= 0.431 Chirality : 0.060 1.439 2478 Planarity : 0.005 0.067 2986 Dihedral : 8.214 108.205 2346 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.52 % Allowed : 21.07 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.10 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.19), residues: 2072 helix: 0.64 (0.20), residues: 720 sheet: -0.64 (0.39), residues: 184 loop : -1.06 (0.18), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 28 TYR 0.039 0.001 TYR A 79 PHE 0.017 0.001 PHE F 306 TRP 0.017 0.001 TRP D 497 HIS 0.005 0.001 HIS D 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (16972) covalent geometry : angle 1.10876 / 0.42 (23202) hydrogen bonds : bond 0.02795 / 1.93 ( 513) hydrogen bonds : angle 4.95190 / 3.56 ( 1431) metal coordination : bond 0.00350 / 0.18 ( 6) metal coordination : angle 34.72612 / 15.46 ( 18) Misc. bond : bond 0.02749 / 1.24 ( 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 267 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 224 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 GLN cc_start: 0.7772 (pp30) cc_final: 0.7493 (pp30) REVERT: A 156 MET cc_start: 0.8459 (ttm) cc_final: 0.8106 (mtp) REVERT: A 221 ASN cc_start: 0.8791 (t0) cc_final: 0.8434 (t0) REVERT: C 124 ASN cc_start: 0.8713 (OUTLIER) cc_final: 0.8483 (t0) REVERT: C 187 ASP cc_start: 0.7229 (t70) cc_final: 0.6968 (t70) REVERT: C 352 LYS cc_start: 0.8405 (mmtt) cc_final: 0.8077 (tppt) REVERT: C 405 GLN cc_start: 0.8520 (tm-30) cc_final: 0.7852 (tt0) REVERT: D 98 GLN cc_start: 0.7628 (pp30) cc_final: 0.7410 (pp30) REVERT: D 156 MET cc_start: 0.8303 (ttm) cc_final: 0.7907 (mtp) REVERT: D 221 ASN cc_start: 0.8758 (t0) cc_final: 0.8347 (t0) REVERT: F 124 ASN cc_start: 0.8762 (OUTLIER) cc_final: 0.8429 (t0) REVERT: F 352 LYS cc_start: 0.8386 (mmtt) cc_final: 0.8059 (tppt) outliers start: 43 outliers final: 32 residues processed: 254 average time/residue: 0.1222 time to fit residues: 48.4683 Evaluate side-chains 249 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 215 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 294 THR 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 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 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 87 ILE Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 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 384 VAL Chi-restraints excluded: chain F residue 425 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 141 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 42 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 135 optimal weight: 0.7980 chunk 132 optimal weight: 10.0000 chunk 187 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 29 optimal weight: 0.3980 chunk 82 optimal weight: 0.8980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 ASN ** D 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 189 ASN F 425 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.165850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.143990 restraints weight = 25289.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.144313 restraints weight = 25088.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.145681 restraints weight = 22141.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.145651 restraints weight = 16492.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.145959 restraints weight = 16495.181| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 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 : 0.005 0.129 17010 Z= 0.177 Angle : 1.502 84.038 23220 Z= 0.441 Chirality : 0.061 1.457 2478 Planarity : 0.005 0.067 2986 Dihedral : 8.178 108.067 2346 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 2.99 % Allowed : 20.95 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.10 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.19), residues: 2072 helix: 0.58 (0.20), residues: 722 sheet: -0.62 (0.39), residues: 184 loop : -1.09 (0.18), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 190 TYR 0.038 0.002 TYR A 79 PHE 0.017 0.002 PHE F 306 TRP 0.016 0.001 TRP A 111 HIS 0.007 0.001 HIS D 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (16972) covalent geometry : angle 1.12390 / 0.43 (23202) hydrogen bonds : bond 0.02959 / 2.04 ( 513) hydrogen bonds : angle 4.98755 / 3.59 ( 1431) metal coordination : bond 0.00381 / 0.20 ( 6) metal coordination : angle 35.78160 / 15.82 ( 18) Misc. bond : bond 0.03948 / 2.11 ( 32) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2327.51 seconds wall clock time: 41 minutes 32.46 seconds (2492.46 seconds total)