Starting phenix.real_space_refine on Thu May 15 12:55:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j5s_35992/05_2025/8j5s_35992.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j5s_35992/05_2025/8j5s_35992.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j5s_35992/05_2025/8j5s_35992.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j5s_35992/05_2025/8j5s_35992.map" model { file = "/net/cci-nas-00/data/ceres_data/8j5s_35992/05_2025/8j5s_35992.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j5s_35992/05_2025/8j5s_35992.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.002 sd= 0.070 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: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 P 6 5.49 5 Mg 2 5.21 5 S 41 5.16 5 C 8402 2.51 5 N 2368 2.21 5 O 2452 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 173 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13275 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4003 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 28, 'TRANS': 498} Chain: "B" Number of atoms: 2475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2475 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 11, 'TRANS': 313} Chain: "C" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2130 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 13, 'TRANS': 268} Chain: "D" Number of atoms: 4555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4555 Classifications: {'peptide': 608} Link IDs: {'PTRANS': 35, 'TRANS': 572} Chain: "E" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 40 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'UNK:plan-1': 8} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 72 Unusual residues: {' MG': 2, 'ANP': 2, 'SF4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10814 SG CYS D 299 20.668 26.978 21.695 1.00 42.55 S ATOM 10947 SG CYS D 317 26.841 25.253 20.106 1.00 37.75 S ATOM 10714 SG CYS D 286 25.527 27.181 26.537 1.00 34.10 S ATOM 10761 SG CYS D 292 25.576 31.656 21.276 1.00 32.40 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N GLU A 510 " occ=0.94 ... (7 atoms not shown) pdb=" OE2 GLU A 510 " occ=0.94 Time building chain proxies: 8.23, per 1000 atoms: 0.62 Number of scatterers: 13275 At special positions: 0 Unit cell: (86.528, 95.68, 168.064, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 S 41 16.00 P 6 15.00 Mg 2 11.99 O 2452 8.00 N 2368 7.00 C 8402 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=0, symmetry=0 Time building additional restraints: 3.53 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 D 705 " pdb="FE4 SF4 D 705 " - pdb=" SG CYS D 292 " pdb="FE3 SF4 D 705 " - pdb=" SG CYS D 286 " pdb="FE1 SF4 D 705 " - pdb=" SG CYS D 299 " pdb="FE2 SF4 D 705 " - pdb=" SG CYS D 317 " Number of angles added : 12 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3190 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 12 sheets defined 50.1% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 111 through 119 removed outlier: 5.243A pdb=" N MET A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 182 removed outlier: 3.593A pdb=" N ILE A 175 " --> pdb=" O THR A 171 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 226 removed outlier: 3.884A pdb=" N GLY A 225 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N MET A 226 " --> pdb=" O TRP A 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 222 through 226' Processing helix chain 'A' and resid 235 through 239 Processing helix chain 'A' and resid 241 through 248 Processing helix chain 'A' and resid 296 through 299 removed outlier: 3.523A pdb=" N ALA A 299 " --> pdb=" O ASP A 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 296 through 299' Processing helix chain 'A' and resid 300 through 306 Processing helix chain 'A' and resid 316 through 325 removed outlier: 3.837A pdb=" N ALA A 323 " --> pdb=" O GLN A 319 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA A 324 " --> pdb=" O LEU A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 363 removed outlier: 3.749A pdb=" N LYS A 363 " --> pdb=" O LEU A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 375 Processing helix chain 'A' and resid 401 through 405 removed outlier: 3.633A pdb=" N ALA A 405 " --> pdb=" O GLY A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 417 Processing helix chain 'A' and resid 445 through 459 removed outlier: 3.980A pdb=" N PHE A 449 " --> pdb=" O SER A 445 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA A 450 " --> pdb=" O THR A 446 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN A 459 " --> pdb=" O HIS A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 499 through 505 removed outlier: 3.967A pdb=" N GLN A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 530 Processing helix chain 'A' and resid 533 through 550 removed outlier: 3.577A pdb=" N ALA A 539 " --> pdb=" O GLY A 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 30 removed outlier: 3.956A pdb=" N ASN B 11 " --> pdb=" O ARG B 7 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL B 14 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 39 Processing helix chain 'B' and resid 45 through 55 Processing helix chain 'B' and resid 61 through 74 removed outlier: 3.781A pdb=" N ASN B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N HIS B 72 " --> pdb=" O ASN B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 123 removed outlier: 3.925A pdb=" N GLY B 92 " --> pdb=" O GLY B 88 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ARG B 93 " --> pdb=" O THR B 89 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL B 97 " --> pdb=" O ARG B 93 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU B 101 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL B 111 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 141 removed outlier: 3.777A pdb=" N MET B 132 " --> pdb=" O SER B 128 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 138 " --> pdb=" O THR B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 163 removed outlier: 4.829A pdb=" N ARG B 157 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL B 158 " --> pdb=" O GLY B 154 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 221 removed outlier: 3.768A pdb=" N ARG B 188 " --> pdb=" O ARG B 184 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N LEU B 194 " --> pdb=" O GLN B 190 " (cutoff:3.500A) Proline residue: B 195 - end of helix removed outlier: 3.626A pdb=" N ALA B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG B 209 " --> pdb=" O ALA B 205 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR B 210 " --> pdb=" O GLY B 206 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN B 213 " --> pdb=" O ARG B 209 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 229 removed outlier: 3.888A pdb=" N THR B 226 " --> pdb=" O ASP B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 241 removed outlier: 3.653A pdb=" N LEU B 238 " --> pdb=" O ARG B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 247 Processing helix chain 'B' and resid 248 through 252 Processing helix chain 'B' and resid 253 through 273 removed outlier: 3.776A pdb=" N VAL B 266 " --> pdb=" O VAL B 262 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N PHE B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 287 Processing helix chain 'B' and resid 289 through 319 removed outlier: 3.576A pdb=" N VAL B 293 " --> pdb=" O ASP B 289 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL B 298 " --> pdb=" O ALA B 294 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 17 removed outlier: 4.186A pdb=" N ARG C 13 " --> pdb=" O THR C 9 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG C 14 " --> pdb=" O LEU C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 38 removed outlier: 4.062A pdb=" N TYR C 36 " --> pdb=" O PHE C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 42 Processing helix chain 'C' and resid 72 through 110 removed outlier: 3.532A pdb=" N THR C 77 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY C 88 " --> pdb=" O SER C 84 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE C 105 " --> pdb=" O THR C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 125 removed outlier: 3.591A pdb=" N ASP C 114 " --> pdb=" O GLY C 110 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL C 121 " --> pdb=" O LEU C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 137 removed outlier: 3.714A pdb=" N VAL C 136 " --> pdb=" O LEU C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 155 Processing helix chain 'C' and resid 158 through 174 removed outlier: 3.738A pdb=" N SER C 171 " --> pdb=" O GLY C 167 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU C 174 " --> pdb=" O MET C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 185 Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'C' and resid 202 through 225 removed outlier: 3.994A pdb=" N ALA C 209 " --> pdb=" O ILE C 205 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU C 210 " --> pdb=" O ILE C 206 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N VAL C 212 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU C 225 " --> pdb=" O GLY C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 244 Processing helix chain 'C' and resid 245 through 247 No H-bonds generated for 'chain 'C' and resid 245 through 247' Processing helix chain 'C' and resid 251 through 280 removed outlier: 3.808A pdb=" N PHE C 256 " --> pdb=" O TRP C 252 " (cutoff:3.500A) Proline residue: C 257 - end of helix Processing helix chain 'D' and resid 47 through 52 Processing helix chain 'D' and resid 82 through 87 Processing helix chain 'D' and resid 108 through 120 removed outlier: 3.685A pdb=" N GLU D 114 " --> pdb=" O ASP D 110 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE D 116 " --> pdb=" O ILE D 112 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N HIS D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 140 removed outlier: 3.709A pdb=" N ASP D 137 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU D 138 " --> pdb=" O GLU D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 148 Processing helix chain 'D' and resid 149 through 150 No H-bonds generated for 'chain 'D' and resid 149 through 150' Processing helix chain 'D' and resid 151 through 155 Processing helix chain 'D' and resid 159 through 170 removed outlier: 3.685A pdb=" N VAL D 164 " --> pdb=" O ARG D 160 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE D 165 " --> pdb=" O GLN D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 204 Processing helix chain 'D' and resid 214 through 222 removed outlier: 4.102A pdb=" N VAL D 218 " --> pdb=" O ASP D 214 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA D 219 " --> pdb=" O LEU D 215 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU D 220 " --> pdb=" O GLY D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 243 Processing helix chain 'D' and resid 248 through 256 Processing helix chain 'D' and resid 327 through 332 Processing helix chain 'D' and resid 399 through 409 Processing helix chain 'D' and resid 419 through 423 Processing helix chain 'D' and resid 429 through 436 removed outlier: 3.739A pdb=" N SER D 435 " --> pdb=" O ALA D 431 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU D 436 " --> pdb=" O GLU D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 451 removed outlier: 3.672A pdb=" N SER D 450 " --> pdb=" O ASP D 446 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU D 451 " --> pdb=" O PRO D 447 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 446 through 451' Processing helix chain 'D' and resid 456 through 462 Processing helix chain 'D' and resid 462 through 467 Processing helix chain 'D' and resid 472 through 486 removed outlier: 3.848A pdb=" N ALA D 477 " --> pdb=" O ASN D 473 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL D 486 " --> pdb=" O LEU D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 495 Processing helix chain 'D' and resid 496 through 500 Processing helix chain 'D' and resid 501 through 514 removed outlier: 3.626A pdb=" N ARG D 507 " --> pdb=" O GLY D 503 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE D 508 " --> pdb=" O GLN D 504 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY D 509 " --> pdb=" O LYS D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 550 removed outlier: 3.591A pdb=" N ALA D 536 " --> pdb=" O VAL D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 567 removed outlier: 4.222A pdb=" N VAL D 563 " --> pdb=" O ASP D 559 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HIS D 565 " --> pdb=" O SER D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 602 Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 95 removed outlier: 6.524A pdb=" N ARG A 271 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LEU A 265 " --> pdb=" O ARG A 271 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL A 273 " --> pdb=" O SER A 263 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 126 through 128 Processing sheet with id=AA3, first strand: chain 'A' and resid 141 through 146 removed outlier: 3.759A pdb=" N SER A 143 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU A 145 " --> pdb=" O THR A 155 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER A 202 " --> pdb=" O THR A 215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 313 Processing sheet with id=AA5, first strand: chain 'A' and resid 463 through 469 removed outlier: 4.578A pdb=" N TYR A 441 " --> pdb=" O GLN A 488 " (cutoff:3.500A) removed outlier: 10.333A pdb=" N GLY A 490 " --> pdb=" O TYR A 441 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE A 489 " --> pdb=" O HIS A 341 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N SER A 338 " --> pdb=" O GLN A 559 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N GLN A 559 " --> pdb=" O SER A 338 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TYR A 340 " --> pdb=" O LEU A 557 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 463 through 469 removed outlier: 4.578A pdb=" N TYR A 441 " --> pdb=" O GLN A 488 " (cutoff:3.500A) removed outlier: 10.333A pdb=" N GLY A 490 " --> pdb=" O TYR A 441 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 428 through 429 Processing sheet with id=AA8, first strand: chain 'A' and resid 570 through 571 removed outlier: 3.609A pdb=" N GLY A 587 " --> pdb=" O ALA A 571 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 21 through 29 removed outlier: 6.826A pdb=" N ALA D 23 " --> pdb=" O PHE D 14 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N PHE D 14 " --> pdb=" O ALA D 23 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ARG D 25 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N VAL D 12 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N TYR D 29 " --> pdb=" O THR D 8 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N THR D 8 " --> pdb=" O TYR D 29 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 92 through 94 removed outlier: 6.062A pdb=" N GLY D 92 " --> pdb=" O ILE D 177 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ASP D 179 " --> pdb=" O GLY D 92 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL D 94 " --> pdb=" O ASP D 179 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N LEU D 176 " --> pdb=" O LEU D 209 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N ILE D 211 " --> pdb=" O LEU D 176 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N CYS D 178 " --> pdb=" O ILE D 211 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL D 36 " --> pdb=" O ARG D 224 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N LEU D 226 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA D 38 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N MET D 228 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL D 40 " --> pdb=" O MET D 228 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA D 225 " --> pdb=" O SER D 236 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N SER D 236 " --> pdb=" O ALA D 225 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL D 227 " --> pdb=" O VAL D 234 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N HIS D 313 " --> pdb=" O VAL D 309 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU D 307 " --> pdb=" O ALA D 315 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 355 through 359 removed outlier: 4.712A pdb=" N LEU D 355 " --> pdb=" O GLY D 379 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS D 357 " --> pdb=" O VAL D 377 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N TYR D 359 " --> pdb=" O ARG D 375 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ARG D 375 " --> pdb=" O TYR D 359 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 440 through 443 removed outlier: 6.464A pdb=" N THR D 389 " --> pdb=" O GLN D 569 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ALA D 571 " --> pdb=" O THR D 389 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLY D 391 " --> pdb=" O ALA D 571 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N MET D 573 " --> pdb=" O GLY D 391 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL D 393 " --> pdb=" O MET D 573 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL D 570 " --> pdb=" O GLN D 581 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLN D 581 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL D 572 " --> pdb=" O VAL D 579 " (cutoff:3.500A) 593 hydrogen bonds defined for protein. 1716 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.28 Time building geometry restraints manager: 4.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.41: 5394 1.41 - 1.63: 8051 1.63 - 1.85: 70 1.85 - 2.07: 0 2.07 - 2.29: 12 Bond restraints: 13527 Sorted by residual: bond pdb=" N3B ANP D 703 " pdb=" PG ANP D 703 " ideal model delta sigma weight residual 1.795 1.633 0.162 2.00e-02 2.50e+03 6.55e+01 bond pdb=" N3B ANP D 701 " pdb=" PG ANP D 701 " ideal model delta sigma weight residual 1.795 1.633 0.162 2.00e-02 2.50e+03 6.55e+01 bond pdb=" O3A ANP D 701 " pdb=" PB ANP D 701 " ideal model delta sigma weight residual 1.700 1.602 0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" O3A ANP D 703 " pdb=" PB ANP D 703 " ideal model delta sigma weight residual 1.700 1.602 0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" C HIS D 476 " pdb=" O HIS D 476 " ideal model delta sigma weight residual 1.236 1.295 -0.058 1.25e-02 6.40e+03 2.19e+01 ... (remaining 13522 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 17818 2.08 - 4.15: 526 4.15 - 6.23: 68 6.23 - 8.30: 22 8.30 - 10.38: 7 Bond angle restraints: 18441 Sorted by residual: angle pdb=" N ARG D 85 " pdb=" CA ARG D 85 " pdb=" C ARG D 85 " ideal model delta sigma weight residual 114.62 106.39 8.23 1.14e+00 7.69e-01 5.21e+01 angle pdb=" N VAL D 479 " pdb=" CA VAL D 479 " pdb=" C VAL D 479 " ideal model delta sigma weight residual 111.05 104.26 6.79 1.25e+00 6.40e-01 2.95e+01 angle pdb=" N ARG B 40 " pdb=" CA ARG B 40 " pdb=" C ARG B 40 " ideal model delta sigma weight residual 109.59 101.43 8.16 1.61e+00 3.86e-01 2.57e+01 angle pdb=" C MET A 589 " pdb=" N ARG A 590 " pdb=" CA ARG A 590 " ideal model delta sigma weight residual 122.41 115.60 6.81 1.41e+00 5.03e-01 2.34e+01 angle pdb=" CA TRP A 281 " pdb=" CB TRP A 281 " pdb=" CG TRP A 281 " ideal model delta sigma weight residual 113.60 122.37 -8.77 1.90e+00 2.77e-01 2.13e+01 ... (remaining 18436 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 7080 17.97 - 35.95: 801 35.95 - 53.92: 178 53.92 - 71.90: 36 71.90 - 89.87: 18 Dihedral angle restraints: 8113 sinusoidal: 3140 harmonic: 4973 Sorted by residual: dihedral pdb=" CA ARG B 123 " pdb=" C ARG B 123 " pdb=" N GLN B 124 " pdb=" CA GLN B 124 " ideal model delta harmonic sigma weight residual 180.00 -157.17 -22.83 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA ALA A 150 " pdb=" C ALA A 150 " pdb=" N PRO A 151 " pdb=" CA PRO A 151 " ideal model delta harmonic sigma weight residual 180.00 157.44 22.56 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA ILE A 322 " pdb=" C ILE A 322 " pdb=" N ALA A 323 " pdb=" CA ALA A 323 " ideal model delta harmonic sigma weight residual 180.00 158.07 21.93 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 8110 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1768 0.067 - 0.134: 372 0.134 - 0.201: 29 0.201 - 0.268: 4 0.268 - 0.335: 2 Chirality restraints: 2175 Sorted by residual: chirality pdb=" C3' ANP D 703 " pdb=" C2' ANP D 703 " pdb=" C4' ANP D 703 " pdb=" O3' ANP D 703 " both_signs ideal model delta sigma weight residual False -2.36 -2.69 0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" C3' ANP D 701 " pdb=" C2' ANP D 701 " pdb=" C4' ANP D 701 " pdb=" O3' ANP D 701 " both_signs ideal model delta sigma weight residual False -2.36 -2.69 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CA CYS D 292 " pdb=" N CYS D 292 " pdb=" C CYS D 292 " pdb=" CB CYS D 292 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 2172 not shown) Planarity restraints: 2379 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 43 " -0.585 9.50e-02 1.11e+02 2.62e-01 4.20e+01 pdb=" NE ARG B 43 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG B 43 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG B 43 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 43 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 40 " -0.347 9.50e-02 1.11e+02 1.56e-01 1.48e+01 pdb=" NE ARG B 40 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG B 40 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 40 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 40 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 281 " 0.024 2.00e-02 2.50e+03 1.75e-02 7.64e+00 pdb=" CG TRP A 281 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP A 281 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP A 281 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 281 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 281 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 281 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 281 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 281 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 281 " -0.001 2.00e-02 2.50e+03 ... (remaining 2376 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1603 2.74 - 3.28: 13093 3.28 - 3.82: 21405 3.82 - 4.36: 26803 4.36 - 4.90: 45953 Nonbonded interactions: 108857 Sorted by model distance: nonbonded pdb=" OG SER A 423 " pdb=" OE1 GLU A 428 " model vdw 2.199 3.040 nonbonded pdb=" OD1 ASP A 416 " pdb=" NH2 ARG A 427 " model vdw 2.202 3.120 nonbonded pdb=" OG1 THR A 147 " pdb=" O VAL A 153 " model vdw 2.203 3.040 nonbonded pdb=" NH1 ARG D 375 " pdb=" OD1 ASP D 378 " model vdw 2.214 3.120 nonbonded pdb=" OD1 ASP A 208 " pdb=" OD1 ASP A 209 " model vdw 2.232 3.040 ... (remaining 108852 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.94 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.080 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: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 36.370 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.070 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:11.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 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 : 0.010 0.313 13531 Z= 0.438 Angle : 0.874 12.504 18453 Z= 0.491 Chirality : 0.054 0.335 2175 Planarity : 0.008 0.262 2379 Dihedral : 16.458 89.871 4923 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.36 % Allowed : 0.80 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.19), residues: 1734 helix: -0.61 (0.18), residues: 816 sheet: -2.16 (0.40), residues: 148 loop : -2.45 (0.19), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 281 HIS 0.010 0.002 HIS D 568 PHE 0.028 0.002 PHE C 224 TYR 0.017 0.002 TYR A 340 ARG 0.009 0.001 ARG A 173 Details of bonding type rmsd hydrogen bonds : bond 0.17159 ( 584) hydrogen bonds : angle 6.91426 ( 1716) metal coordination : bond 0.23931 ( 4) metal coordination : angle 7.65712 ( 12) covalent geometry : bond 0.00880 (13527) covalent geometry : angle 0.85183 (18441) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 170 time to evaluate : 1.450 Fit side-chains REVERT: C 273 ASP cc_start: 0.7986 (m-30) cc_final: 0.7786 (m-30) REVERT: C 280 ASP cc_start: 0.7127 (m-30) cc_final: 0.6893 (m-30) outliers start: 5 outliers final: 3 residues processed: 175 average time/residue: 1.2863 time to fit residues: 246.3461 Evaluate side-chains 140 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 137 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 43 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 69 optimal weight: 0.3980 chunk 134 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 156 optimal weight: 0.6980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 GLN B 275 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.116056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.099695 restraints weight = 19428.975| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.95 r_work: 0.3069 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2949 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13531 Z= 0.131 Angle : 0.644 11.881 18453 Z= 0.324 Chirality : 0.044 0.155 2175 Planarity : 0.005 0.064 2379 Dihedral : 8.249 56.478 1989 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.89 % Allowed : 11.14 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.19), residues: 1734 helix: -0.07 (0.19), residues: 804 sheet: -1.94 (0.40), residues: 151 loop : -2.17 (0.20), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 172 HIS 0.006 0.001 HIS D 568 PHE 0.013 0.001 PHE C 256 TYR 0.015 0.001 TYR A 340 ARG 0.007 0.001 ARG A 68 Details of bonding type rmsd hydrogen bonds : bond 0.04583 ( 584) hydrogen bonds : angle 5.27652 ( 1716) metal coordination : bond 0.00491 ( 4) metal coordination : angle 5.40258 ( 12) covalent geometry : bond 0.00289 (13527) covalent geometry : angle 0.62881 (18441) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 1.466 Fit side-chains REVERT: A 238 MET cc_start: 0.8444 (mmm) cc_final: 0.8198 (mmm) REVERT: A 293 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8258 (pt) REVERT: A 589 MET cc_start: 0.6264 (OUTLIER) cc_final: 0.5598 (pmm) REVERT: B 40 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7864 (mpt-90) REVERT: B 279 GLU cc_start: 0.8556 (tt0) cc_final: 0.8325 (tt0) REVERT: C 46 TYR cc_start: 0.6855 (OUTLIER) cc_final: 0.5630 (t80) REVERT: C 280 ASP cc_start: 0.7109 (m-30) cc_final: 0.6807 (m-30) REVERT: D 161 GLN cc_start: 0.9478 (OUTLIER) cc_final: 0.8337 (tp40) outliers start: 26 outliers final: 5 residues processed: 160 average time/residue: 1.1886 time to fit residues: 209.0963 Evaluate side-chains 141 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 589 MET Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain D residue 85 ARG Chi-restraints excluded: chain D residue 161 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 140 optimal weight: 0.0570 chunk 104 optimal weight: 4.9990 chunk 159 optimal weight: 0.9980 chunk 167 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 154 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 111 optimal weight: 0.4980 chunk 160 optimal weight: 0.4980 chunk 36 optimal weight: 6.9990 chunk 169 optimal weight: 4.9990 overall best weight: 1.0100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A 455 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.115744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.099095 restraints weight = 19520.170| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.01 r_work: 0.3061 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2941 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2941 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13531 Z= 0.131 Angle : 0.597 8.151 18453 Z= 0.303 Chirality : 0.043 0.164 2175 Planarity : 0.005 0.064 2379 Dihedral : 6.597 53.985 1987 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.77 % Allowed : 14.35 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.20), residues: 1734 helix: 0.17 (0.19), residues: 803 sheet: -2.12 (0.39), residues: 163 loop : -1.97 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 172 HIS 0.006 0.001 HIS D 568 PHE 0.009 0.001 PHE A 449 TYR 0.014 0.001 TYR A 340 ARG 0.006 0.000 ARG B 283 Details of bonding type rmsd hydrogen bonds : bond 0.04004 ( 584) hydrogen bonds : angle 4.84780 ( 1716) metal coordination : bond 0.00296 ( 4) metal coordination : angle 3.39568 ( 12) covalent geometry : bond 0.00304 (13527) covalent geometry : angle 0.59077 (18441) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 145 time to evaluate : 1.536 Fit side-chains REVERT: A 238 MET cc_start: 0.8490 (mmm) cc_final: 0.8189 (mmm) REVERT: A 293 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8125 (pt) REVERT: A 589 MET cc_start: 0.6321 (OUTLIER) cc_final: 0.6019 (pmm) REVERT: B 40 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7920 (mpt-90) REVERT: B 283 ARG cc_start: 0.8587 (tpt90) cc_final: 0.8300 (tmt-80) REVERT: C 46 TYR cc_start: 0.6864 (OUTLIER) cc_final: 0.5434 (t80) REVERT: C 280 ASP cc_start: 0.7069 (m-30) cc_final: 0.6483 (t0) REVERT: D 161 GLN cc_start: 0.9473 (OUTLIER) cc_final: 0.8311 (tp40) REVERT: D 483 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8177 (pt) REVERT: D 551 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8587 (mp) outliers start: 38 outliers final: 14 residues processed: 172 average time/residue: 1.1422 time to fit residues: 216.1688 Evaluate side-chains 156 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 589 MET Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 85 ARG Chi-restraints excluded: chain D residue 161 GLN Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 557 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 168 optimal weight: 0.7980 chunk 153 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 146 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.115382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.098718 restraints weight = 19459.519| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.01 r_work: 0.3056 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2935 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2935 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13531 Z= 0.129 Angle : 0.595 13.254 18453 Z= 0.298 Chirality : 0.043 0.156 2175 Planarity : 0.004 0.063 2379 Dihedral : 5.860 54.844 1983 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.84 % Allowed : 16.68 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.20), residues: 1734 helix: 0.27 (0.19), residues: 804 sheet: -2.07 (0.38), residues: 165 loop : -1.90 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 172 HIS 0.016 0.001 HIS B 72 PHE 0.010 0.001 PHE B 145 TYR 0.013 0.001 TYR A 340 ARG 0.006 0.000 ARG D 319 Details of bonding type rmsd hydrogen bonds : bond 0.03836 ( 584) hydrogen bonds : angle 4.72402 ( 1716) metal coordination : bond 0.00335 ( 4) metal coordination : angle 3.57303 ( 12) covalent geometry : bond 0.00302 (13527) covalent geometry : angle 0.58835 (18441) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 140 time to evaluate : 1.599 Fit side-chains REVERT: A 238 MET cc_start: 0.8472 (mmm) cc_final: 0.8161 (mmm) REVERT: A 293 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8081 (pt) REVERT: A 589 MET cc_start: 0.6317 (OUTLIER) cc_final: 0.6035 (pmm) REVERT: B 138 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8783 (pp) REVERT: B 279 GLU cc_start: 0.8468 (tt0) cc_final: 0.8267 (tt0) REVERT: C 46 TYR cc_start: 0.6885 (OUTLIER) cc_final: 0.5435 (t80) REVERT: C 280 ASP cc_start: 0.7085 (m-30) cc_final: 0.6441 (t0) REVERT: D 161 GLN cc_start: 0.9463 (OUTLIER) cc_final: 0.8340 (tp40) REVERT: D 483 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8232 (pt) outliers start: 39 outliers final: 16 residues processed: 171 average time/residue: 1.1653 time to fit residues: 219.1753 Evaluate side-chains 151 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 589 MET Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 85 ARG Chi-restraints excluded: chain D residue 161 GLN Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 557 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 142 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 69 optimal weight: 0.0270 chunk 122 optimal weight: 0.2980 chunk 135 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.6042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.117106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.100374 restraints weight = 19563.144| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.02 r_work: 0.3081 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2964 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2964 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13531 Z= 0.103 Angle : 0.556 10.001 18453 Z= 0.279 Chirality : 0.041 0.169 2175 Planarity : 0.004 0.063 2379 Dihedral : 5.092 55.537 1979 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.99 % Allowed : 17.55 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.20), residues: 1734 helix: 0.44 (0.19), residues: 806 sheet: -1.91 (0.39), residues: 163 loop : -1.70 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 172 HIS 0.003 0.001 HIS D 119 PHE 0.009 0.001 PHE B 145 TYR 0.011 0.001 TYR A 340 ARG 0.007 0.000 ARG B 283 Details of bonding type rmsd hydrogen bonds : bond 0.03415 ( 584) hydrogen bonds : angle 4.54980 ( 1716) metal coordination : bond 0.00134 ( 4) metal coordination : angle 3.39700 ( 12) covalent geometry : bond 0.00232 (13527) covalent geometry : angle 0.54928 (18441) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 141 time to evaluate : 1.439 Fit side-chains REVERT: A 293 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8004 (pt) REVERT: A 325 ARG cc_start: 0.7790 (mtm110) cc_final: 0.7459 (ttm-80) REVERT: A 589 MET cc_start: 0.6342 (OUTLIER) cc_final: 0.6085 (pmm) REVERT: B 138 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8687 (pp) REVERT: C 46 TYR cc_start: 0.6786 (OUTLIER) cc_final: 0.5419 (t80) REVERT: D 161 GLN cc_start: 0.9431 (OUTLIER) cc_final: 0.8311 (tp40) outliers start: 41 outliers final: 18 residues processed: 176 average time/residue: 1.1023 time to fit residues: 215.5064 Evaluate side-chains 149 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 589 MET Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 85 ARG Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 161 GLN Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 556 VAL Chi-restraints excluded: chain D residue 557 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 167 optimal weight: 0.5980 chunk 90 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 171 optimal weight: 0.9990 chunk 145 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 160 optimal weight: 0.8980 chunk 118 optimal weight: 0.9980 chunk 7 optimal weight: 0.2980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.116699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.100109 restraints weight = 19751.444| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.00 r_work: 0.3078 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13531 Z= 0.113 Angle : 0.567 8.906 18453 Z= 0.285 Chirality : 0.042 0.151 2175 Planarity : 0.004 0.063 2379 Dihedral : 4.995 56.337 1979 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.91 % Allowed : 18.86 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.20), residues: 1734 helix: 0.53 (0.19), residues: 813 sheet: -1.77 (0.40), residues: 161 loop : -1.64 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 172 HIS 0.003 0.001 HIS D 568 PHE 0.010 0.001 PHE B 145 TYR 0.011 0.001 TYR A 340 ARG 0.006 0.000 ARG B 283 Details of bonding type rmsd hydrogen bonds : bond 0.03440 ( 584) hydrogen bonds : angle 4.50205 ( 1716) metal coordination : bond 0.00188 ( 4) metal coordination : angle 3.66491 ( 12) covalent geometry : bond 0.00258 (13527) covalent geometry : angle 0.55895 (18441) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 137 time to evaluate : 1.363 Fit side-chains REVERT: A 293 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8093 (pt) REVERT: B 138 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8660 (pp) REVERT: C 46 TYR cc_start: 0.6762 (OUTLIER) cc_final: 0.5405 (t80) REVERT: C 168 MET cc_start: 0.7852 (OUTLIER) cc_final: 0.7624 (ttt) REVERT: D 161 GLN cc_start: 0.9421 (OUTLIER) cc_final: 0.8329 (tp40) outliers start: 40 outliers final: 22 residues processed: 167 average time/residue: 1.1269 time to fit residues: 207.7735 Evaluate side-chains 158 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 85 ARG Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 161 GLN Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 556 VAL Chi-restraints excluded: chain D residue 557 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 11 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 154 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 137 optimal weight: 0.3980 chunk 53 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 chunk 136 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.115665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.098899 restraints weight = 19685.902| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.03 r_work: 0.3064 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2942 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2942 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13531 Z= 0.124 Angle : 0.585 14.607 18453 Z= 0.291 Chirality : 0.042 0.163 2175 Planarity : 0.004 0.063 2379 Dihedral : 4.984 57.620 1979 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.28 % Allowed : 19.30 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.20), residues: 1734 helix: 0.59 (0.19), residues: 813 sheet: -1.69 (0.40), residues: 161 loop : -1.62 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 172 HIS 0.004 0.001 HIS D 568 PHE 0.010 0.001 PHE B 145 TYR 0.012 0.001 TYR A 340 ARG 0.010 0.000 ARG A 325 Details of bonding type rmsd hydrogen bonds : bond 0.03586 ( 584) hydrogen bonds : angle 4.48057 ( 1716) metal coordination : bond 0.00300 ( 4) metal coordination : angle 3.75221 ( 12) covalent geometry : bond 0.00291 (13527) covalent geometry : angle 0.57697 (18441) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 134 time to evaluate : 1.473 Fit side-chains REVERT: A 148 ARG cc_start: 0.7558 (mmm160) cc_final: 0.7354 (mmm160) REVERT: A 293 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8111 (pt) REVERT: A 296 ASP cc_start: 0.8473 (p0) cc_final: 0.7716 (p0) REVERT: A 589 MET cc_start: 0.6135 (OUTLIER) cc_final: 0.5598 (pmt) REVERT: B 35 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7484 (tp30) REVERT: B 129 ASP cc_start: 0.7861 (t0) cc_final: 0.7455 (t0) REVERT: B 138 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8654 (pp) REVERT: C 46 TYR cc_start: 0.6793 (OUTLIER) cc_final: 0.5430 (t80) REVERT: C 168 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.7631 (ttt) REVERT: D 133 VAL cc_start: 0.8473 (OUTLIER) cc_final: 0.8162 (t) outliers start: 45 outliers final: 24 residues processed: 167 average time/residue: 1.0919 time to fit residues: 201.9372 Evaluate side-chains 163 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 589 MET Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 85 ARG Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 556 VAL Chi-restraints excluded: chain D residue 557 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 168 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.114928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.098142 restraints weight = 19729.110| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.03 r_work: 0.3053 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2937 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2937 r_free = 0.2937 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2937 r_free = 0.2937 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2937 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13531 Z= 0.134 Angle : 0.598 14.419 18453 Z= 0.297 Chirality : 0.042 0.153 2175 Planarity : 0.004 0.063 2379 Dihedral : 5.045 59.286 1979 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.06 % Allowed : 19.96 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.20), residues: 1734 helix: 0.63 (0.19), residues: 813 sheet: -1.66 (0.40), residues: 161 loop : -1.63 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 172 HIS 0.004 0.001 HIS D 568 PHE 0.010 0.001 PHE B 145 TYR 0.012 0.001 TYR A 340 ARG 0.012 0.000 ARG A 68 Details of bonding type rmsd hydrogen bonds : bond 0.03706 ( 584) hydrogen bonds : angle 4.48886 ( 1716) metal coordination : bond 0.00388 ( 4) metal coordination : angle 4.01647 ( 12) covalent geometry : bond 0.00317 (13527) covalent geometry : angle 0.58977 (18441) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 139 time to evaluate : 1.339 Fit side-chains REVERT: A 148 ARG cc_start: 0.7573 (mmm160) cc_final: 0.7354 (mmm160) REVERT: A 293 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8130 (pt) REVERT: A 589 MET cc_start: 0.6177 (OUTLIER) cc_final: 0.5585 (pmt) REVERT: B 35 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7443 (tp30) REVERT: B 129 ASP cc_start: 0.7931 (t0) cc_final: 0.7597 (t0) REVERT: B 138 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8681 (pp) REVERT: C 46 TYR cc_start: 0.6850 (OUTLIER) cc_final: 0.5457 (t80) REVERT: C 168 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.7621 (ttt) REVERT: C 280 ASP cc_start: 0.7037 (m-30) cc_final: 0.6340 (t0) outliers start: 42 outliers final: 26 residues processed: 171 average time/residue: 1.0431 time to fit residues: 197.7167 Evaluate side-chains 163 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 589 MET Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 85 ARG Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 388 ARG Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 556 VAL Chi-restraints excluded: chain D residue 557 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 34 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 143 optimal weight: 5.9990 chunk 170 optimal weight: 6.9990 chunk 139 optimal weight: 0.0670 chunk 40 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN C 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.112202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.095377 restraints weight = 19709.752| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.02 r_work: 0.3006 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2883 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2883 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 13531 Z= 0.210 Angle : 0.661 12.174 18453 Z= 0.331 Chirality : 0.046 0.164 2175 Planarity : 0.005 0.064 2379 Dihedral : 5.387 60.420 1979 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.69 % Allowed : 20.61 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.20), residues: 1734 helix: 0.46 (0.19), residues: 815 sheet: -1.72 (0.40), residues: 163 loop : -1.81 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 172 HIS 0.004 0.001 HIS B 72 PHE 0.012 0.001 PHE B 145 TYR 0.013 0.001 TYR A 340 ARG 0.012 0.001 ARG A 68 Details of bonding type rmsd hydrogen bonds : bond 0.04490 ( 584) hydrogen bonds : angle 4.66234 ( 1716) metal coordination : bond 0.00893 ( 4) metal coordination : angle 4.44120 ( 12) covalent geometry : bond 0.00504 (13527) covalent geometry : angle 0.65098 (18441) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 129 time to evaluate : 1.457 Fit side-chains REVERT: A 148 ARG cc_start: 0.7619 (mmm160) cc_final: 0.7380 (mmm160) REVERT: A 293 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8353 (pt) REVERT: A 589 MET cc_start: 0.6211 (OUTLIER) cc_final: 0.5470 (pmt) REVERT: B 35 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7546 (tp30) REVERT: B 129 ASP cc_start: 0.7969 (t0) cc_final: 0.7649 (t0) REVERT: C 46 TYR cc_start: 0.7006 (OUTLIER) cc_final: 0.5694 (t80) REVERT: C 168 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7589 (ttt) REVERT: C 280 ASP cc_start: 0.7302 (m-30) cc_final: 0.6570 (t0) REVERT: D 359 TYR cc_start: 0.8634 (m-80) cc_final: 0.8344 (m-80) outliers start: 37 outliers final: 26 residues processed: 158 average time/residue: 1.0504 time to fit residues: 184.7738 Evaluate side-chains 156 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 125 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 589 MET Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 11 ASN Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 85 ARG Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 388 ARG Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 556 VAL Chi-restraints excluded: chain D residue 557 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 11 optimal weight: 8.9990 chunk 153 optimal weight: 3.9990 chunk 139 optimal weight: 0.0870 chunk 95 optimal weight: 0.9980 chunk 134 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN A 305 GLN C 67 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.114925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.098143 restraints weight = 19594.244| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.02 r_work: 0.3056 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2939 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2939 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13531 Z= 0.119 Angle : 0.600 13.596 18453 Z= 0.300 Chirality : 0.042 0.165 2175 Planarity : 0.004 0.064 2379 Dihedral : 5.152 58.092 1979 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.11 % Allowed : 21.41 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.20), residues: 1734 helix: 0.62 (0.19), residues: 815 sheet: -1.65 (0.40), residues: 161 loop : -1.67 (0.21), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 172 HIS 0.003 0.001 HIS D 119 PHE 0.009 0.001 PHE A 342 TYR 0.011 0.001 TYR A 340 ARG 0.012 0.000 ARG A 68 Details of bonding type rmsd hydrogen bonds : bond 0.03582 ( 584) hydrogen bonds : angle 4.49837 ( 1716) metal coordination : bond 0.00264 ( 4) metal coordination : angle 4.15643 ( 12) covalent geometry : bond 0.00275 (13527) covalent geometry : angle 0.59057 (18441) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 1.526 Fit side-chains revert: symmetry clash REVERT: A 293 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8193 (pt) REVERT: A 589 MET cc_start: 0.6025 (OUTLIER) cc_final: 0.5372 (pmt) REVERT: B 129 ASP cc_start: 0.7770 (t0) cc_final: 0.7502 (t0) REVERT: C 46 TYR cc_start: 0.6900 (OUTLIER) cc_final: 0.5590 (t80) REVERT: C 168 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.7543 (ttt) REVERT: C 280 ASP cc_start: 0.7204 (m-30) cc_final: 0.6466 (t0) outliers start: 29 outliers final: 20 residues processed: 154 average time/residue: 1.1297 time to fit residues: 192.6719 Evaluate side-chains 153 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 589 MET Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 85 ARG Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 556 VAL Chi-restraints excluded: chain D residue 557 SER Chi-restraints excluded: chain D residue 574 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 16 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 89 optimal weight: 0.0370 chunk 159 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 87 optimal weight: 0.1980 chunk 129 optimal weight: 0.1980 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 overall best weight: 0.4260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.117155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.100477 restraints weight = 19534.124| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.02 r_work: 0.3094 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2972 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2972 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 13531 Z= 0.102 Angle : 0.581 10.411 18453 Z= 0.289 Chirality : 0.041 0.174 2175 Planarity : 0.004 0.064 2379 Dihedral : 4.883 55.759 1979 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.18 % Allowed : 21.49 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.20), residues: 1734 helix: 0.80 (0.19), residues: 823 sheet: -1.54 (0.41), residues: 161 loop : -1.54 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 172 HIS 0.003 0.001 HIS D 119 PHE 0.009 0.001 PHE B 145 TYR 0.009 0.001 TYR A 340 ARG 0.018 0.000 ARG A 325 Details of bonding type rmsd hydrogen bonds : bond 0.03165 ( 584) hydrogen bonds : angle 4.37874 ( 1716) metal coordination : bond 0.00232 ( 4) metal coordination : angle 3.89338 ( 12) covalent geometry : bond 0.00231 (13527) covalent geometry : angle 0.57233 (18441) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8471.51 seconds wall clock time: 146 minutes 19.37 seconds (8779.37 seconds total)