Starting phenix.real_space_refine on Sun Nov 17 07:12:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5s_35992/11_2024/8j5s_35992.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5s_35992/11_2024/8j5s_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5s_35992/11_2024/8j5s_35992.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5s_35992/11_2024/8j5s_35992.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5s_35992/11_2024/8j5s_35992.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5s_35992/11_2024/8j5s_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-5513/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: 8.45, per 1000 atoms: 0.64 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: 3.88 Conformation dependent library (CDL) restraints added in 1.8 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: 1.62 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: 4.18 Time building geometry restraints manager: 4.19 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: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 35.000 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 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:13.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.530 ------------------------------------------------------------------------------- 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 : 0.009 0.162 13527 Z= 0.585 Angle : 0.852 10.380 18441 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 *********************** 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 : 1.434 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: 1.3768 time to fit residues: 262.9932 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 : 1.419 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 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 13527 Z= 0.191 Angle : 0.629 11.666 18441 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 *********************** 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 : 1.490 Fit side-chains REVERT: A 293 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8429 (pt) REVERT: A 589 MET cc_start: 0.6051 (OUTLIER) cc_final: 0.5328 (pmm) REVERT: C 46 TYR cc_start: 0.6886 (OUTLIER) cc_final: 0.5717 (t80) REVERT: C 280 ASP cc_start: 0.7115 (m-30) cc_final: 0.6902 (m-30) REVERT: D 161 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.7875 (tp40) outliers start: 26 outliers final: 5 residues processed: 160 average time/residue: 1.2575 time to fit residues: 221.2541 Evaluate side-chains 140 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 131 time to evaluate : 1.529 ------------------------------------------------------------------------------- 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 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 86 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 129 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 156 optimal weight: 0.0970 chunk 169 optimal weight: 4.9990 chunk 139 optimal weight: 0.3980 chunk 155 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 125 optimal weight: 0.6980 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13527 Z= 0.199 Angle : 0.593 8.334 18441 Z= 0.304 Chirality : 0.043 0.162 2175 Planarity : 0.005 0.064 2379 Dihedral : 6.452 52.542 1983 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.62 % Allowed : 14.79 % Favored : 82.59 % 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: -1.49 (0.20), residues: 1734 helix: 0.17 (0.19), residues: 802 sheet: -2.14 (0.38), residues: 163 loop : -1.97 (0.20), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 172 HIS 0.005 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 *********************** 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 182 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 146 time to evaluate : 1.480 Fit side-chains REVERT: A 293 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8311 (pt) REVERT: A 589 MET cc_start: 0.6101 (OUTLIER) cc_final: 0.5787 (pmm) REVERT: B 283 ARG cc_start: 0.8018 (tpt90) cc_final: 0.7722 (tmt-80) REVERT: C 46 TYR cc_start: 0.6857 (OUTLIER) cc_final: 0.5490 (t80) REVERT: D 161 GLN cc_start: 0.9045 (OUTLIER) cc_final: 0.7847 (tp40) REVERT: D 483 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8449 (pt) REVERT: D 551 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8355 (mp) outliers start: 36 outliers final: 14 residues processed: 171 average time/residue: 1.2727 time to fit residues: 239.5343 Evaluate side-chains 155 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 1.513 ------------------------------------------------------------------------------- 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 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 154 optimal weight: 5.9990 chunk 117 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 157 optimal weight: 0.8980 chunk 166 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 148 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13527 Z= 0.238 Angle : 0.603 13.087 18441 Z= 0.306 Chirality : 0.043 0.155 2175 Planarity : 0.005 0.063 2379 Dihedral : 5.790 54.537 1979 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.84 % Allowed : 16.97 % Favored : 80.19 % 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: -1.44 (0.20), residues: 1734 helix: 0.23 (0.19), residues: 801 sheet: -2.09 (0.38), residues: 165 loop : -1.96 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 172 HIS 0.008 0.001 HIS B 72 PHE 0.010 0.001 PHE B 145 TYR 0.013 0.001 TYR A 340 ARG 0.008 0.000 ARG D 319 *********************** 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 178 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 139 time to evaluate : 1.689 Fit side-chains REVERT: A 293 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8327 (pt) REVERT: A 589 MET cc_start: 0.6160 (OUTLIER) cc_final: 0.5935 (pmm) REVERT: C 46 TYR cc_start: 0.6867 (OUTLIER) cc_final: 0.5481 (t80) REVERT: D 161 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.7892 (tp40) REVERT: D 483 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8502 (pt) REVERT: D 551 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8502 (mp) outliers start: 39 outliers final: 17 residues processed: 169 average time/residue: 1.1999 time to fit residues: 223.8873 Evaluate side-chains 153 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 1.669 ------------------------------------------------------------------------------- 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 472 SER Chi-restraints excluded: chain A residue 589 MET Chi-restraints excluded: chain B residue 10 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 551 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 138 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 68 optimal weight: 0.0980 chunk 141 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 84 optimal weight: 6.9990 chunk 149 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13527 Z= 0.212 Angle : 0.583 10.560 18441 Z= 0.297 Chirality : 0.043 0.168 2175 Planarity : 0.004 0.064 2379 Dihedral : 5.351 58.088 1979 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.42 % Allowed : 17.26 % Favored : 79.32 % 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: -1.31 (0.20), residues: 1734 helix: 0.31 (0.19), residues: 803 sheet: -2.01 (0.38), residues: 165 loop : -1.87 (0.21), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 172 HIS 0.005 0.001 HIS D 568 PHE 0.010 0.001 PHE B 145 TYR 0.013 0.001 TYR A 340 ARG 0.006 0.000 ARG B 283 *********************** 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 187 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 140 time to evaluate : 1.485 Fit side-chains REVERT: A 293 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8316 (pt) REVERT: A 589 MET cc_start: 0.6192 (OUTLIER) cc_final: 0.5978 (pmm) REVERT: B 35 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6706 (tp30) REVERT: C 46 TYR cc_start: 0.6839 (OUTLIER) cc_final: 0.5518 (t80) REVERT: D 161 GLN cc_start: 0.9029 (OUTLIER) cc_final: 0.7884 (tp40) REVERT: D 483 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8523 (pt) outliers start: 47 outliers final: 22 residues processed: 178 average time/residue: 1.1500 time to fit residues: 226.9383 Evaluate side-chains 158 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 1.482 ------------------------------------------------------------------------------- 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 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 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 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 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 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 55 optimal weight: 2.9990 chunk 149 optimal weight: 0.0870 chunk 32 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 138 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 87 optimal weight: 0.4980 chunk 160 optimal weight: 0.8980 overall best weight: 0.8962 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13527 Z= 0.182 Angle : 0.568 9.249 18441 Z= 0.290 Chirality : 0.042 0.156 2175 Planarity : 0.004 0.063 2379 Dihedral : 5.172 58.243 1979 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.06 % Allowed : 18.65 % Favored : 78.30 % 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: -1.10 (0.20), residues: 1734 helix: 0.42 (0.19), residues: 806 sheet: -1.84 (0.39), residues: 163 loop : -1.72 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 172 HIS 0.004 0.001 HIS D 568 PHE 0.009 0.001 PHE B 145 TYR 0.012 0.001 TYR A 340 ARG 0.009 0.000 ARG A 325 *********************** 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 184 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 142 time to evaluate : 1.564 Fit side-chains REVERT: A 293 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8304 (pt) REVERT: C 46 TYR cc_start: 0.6781 (OUTLIER) cc_final: 0.5463 (t80) REVERT: D 161 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.7850 (tp40) outliers start: 42 outliers final: 25 residues processed: 175 average time/residue: 1.1305 time to fit residues: 218.9030 Evaluate side-chains 157 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 1.516 ------------------------------------------------------------------------------- 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 B residue 10 LEU Chi-restraints excluded: chain B residue 72 HIS 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 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 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 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 18 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 165 optimal weight: 0.0070 chunk 103 optimal weight: 5.9990 chunk 101 optimal weight: 0.0770 chunk 76 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 overall best weight: 1.3560 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13527 Z= 0.234 Angle : 0.605 15.240 18441 Z= 0.307 Chirality : 0.043 0.154 2175 Planarity : 0.005 0.063 2379 Dihedral : 5.193 58.925 1979 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.20 % Allowed : 19.66 % Favored : 77.13 % 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: 0.42 (0.19), residues: 813 sheet: -1.79 (0.39), residues: 161 loop : -1.73 (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 0.011 0.001 PHE B 145 TYR 0.012 0.001 TYR A 340 ARG 0.013 0.000 ARG A 68 *********************** 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 180 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 136 time to evaluate : 1.560 Fit side-chains REVERT: A 293 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8361 (pt) REVERT: A 296 ASP cc_start: 0.7941 (p0) cc_final: 0.7648 (p0) REVERT: A 589 MET cc_start: 0.5860 (OUTLIER) cc_final: 0.5176 (pmt) REVERT: B 35 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6780 (tp30) REVERT: C 46 TYR cc_start: 0.6816 (OUTLIER) cc_final: 0.5566 (t80) REVERT: D 161 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.7884 (tp40) outliers start: 44 outliers final: 27 residues processed: 169 average time/residue: 1.1436 time to fit residues: 213.8300 Evaluate side-chains 162 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 1.510 ------------------------------------------------------------------------------- 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 472 SER 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 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 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 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 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 298 GLU 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 99 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 150 optimal weight: 0.3980 chunk 158 optimal weight: 0.8980 chunk 144 optimal weight: 5.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13527 Z= 0.188 Angle : 0.593 14.722 18441 Z= 0.300 Chirality : 0.042 0.187 2175 Planarity : 0.005 0.063 2379 Dihedral : 5.109 58.199 1979 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.62 % Allowed : 20.68 % 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: -0.97 (0.20), residues: 1734 helix: 0.53 (0.19), residues: 811 sheet: -1.74 (0.40), residues: 161 loop : -1.67 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 172 HIS 0.003 0.001 HIS D 568 PHE 0.009 0.001 PHE B 145 TYR 0.011 0.001 TYR A 340 ARG 0.012 0.000 ARG A 148 *********************** 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 171 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 135 time to evaluate : 1.492 Fit side-chains REVERT: A 293 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8315 (pt) REVERT: A 296 ASP cc_start: 0.7918 (p0) cc_final: 0.7619 (p0) REVERT: A 589 MET cc_start: 0.5899 (OUTLIER) cc_final: 0.5275 (pmt) REVERT: B 35 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6734 (tp30) REVERT: B 129 ASP cc_start: 0.7647 (t0) cc_final: 0.7418 (t0) REVERT: C 46 TYR cc_start: 0.6765 (OUTLIER) cc_final: 0.5535 (t80) outliers start: 36 outliers final: 26 residues processed: 164 average time/residue: 1.1575 time to fit residues: 210.7360 Evaluate side-chains 159 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 129 time to evaluate : 1.503 ------------------------------------------------------------------------------- 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 35 GLU Chi-restraints excluded: chain B residue 72 HIS 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 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 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 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 154 optimal weight: 3.9990 chunk 158 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 47 optimal weight: 7.9990 chunk 139 optimal weight: 0.0670 chunk 146 optimal weight: 6.9990 chunk 153 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 163 optimal weight: 1.9990 overall best weight: 0.9120 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13527 Z= 0.189 Angle : 0.589 12.746 18441 Z= 0.300 Chirality : 0.042 0.153 2175 Planarity : 0.004 0.064 2379 Dihedral : 5.048 58.555 1979 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.99 % Allowed : 20.32 % 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: -0.86 (0.20), residues: 1734 helix: 0.61 (0.19), residues: 813 sheet: -1.67 (0.40), residues: 161 loop : -1.62 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 172 HIS 0.003 0.001 HIS D 568 PHE 0.009 0.001 PHE B 145 TYR 0.011 0.001 TYR A 340 ARG 0.011 0.000 ARG A 325 *********************** 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 176 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 135 time to evaluate : 1.452 Fit side-chains REVERT: A 293 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8304 (pt) REVERT: A 296 ASP cc_start: 0.7879 (p0) cc_final: 0.7623 (p0) REVERT: A 589 MET cc_start: 0.5755 (OUTLIER) cc_final: 0.5117 (pmt) REVERT: B 35 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6742 (tp30) REVERT: C 46 TYR cc_start: 0.6713 (OUTLIER) cc_final: 0.5504 (t80) outliers start: 41 outliers final: 26 residues processed: 166 average time/residue: 1.1048 time to fit residues: 203.5306 Evaluate side-chains 163 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 1.485 ------------------------------------------------------------------------------- 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 472 SER Chi-restraints excluded: chain A residue 589 MET Chi-restraints excluded: chain B residue 11 ASN Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 72 HIS 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 129 SER 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 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 99 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 171 optimal weight: 0.8980 chunk 157 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 108 optimal weight: 0.0170 chunk 145 optimal weight: 0.1980 overall best weight: 0.8220 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13527 Z= 0.184 Angle : 0.599 13.877 18441 Z= 0.304 Chirality : 0.042 0.173 2175 Planarity : 0.004 0.064 2379 Dihedral : 5.016 58.358 1979 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.40 % Allowed : 20.98 % Favored : 76.62 % 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: -0.79 (0.20), residues: 1734 helix: 0.66 (0.19), residues: 813 sheet: -1.64 (0.40), residues: 161 loop : -1.58 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 172 HIS 0.003 0.001 HIS D 568 PHE 0.009 0.001 PHE B 145 TYR 0.011 0.001 TYR A 340 ARG 0.010 0.000 ARG A 68 ********************** 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 166 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 133 time to evaluate : 1.549 Fit side-chains REVERT: A 293 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8324 (pt) REVERT: A 589 MET cc_start: 0.5749 (OUTLIER) cc_final: 0.5047 (pmt) REVERT: B 35 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6727 (tp30) REVERT: B 135 LEU cc_start: 0.9023 (mt) cc_final: 0.8793 (mp) REVERT: C 46 TYR cc_start: 0.6715 (OUTLIER) cc_final: 0.5503 (t80) outliers start: 33 outliers final: 26 residues processed: 159 average time/residue: 1.1229 time to fit residues: 198.3162 Evaluate side-chains 159 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 129 time to evaluate : 1.492 ------------------------------------------------------------------------------- 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 11 ASN Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 72 HIS 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 234 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 83 MET 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 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 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 41 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 140 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 = 0.3340 r_free = 0.3340 target = 0.112525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.097176 restraints weight = 19810.548| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.71 r_work: 0.3031 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2913 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13527 Z= 0.278 Angle : 0.637 12.332 18441 Z= 0.324 Chirality : 0.044 0.150 2175 Planarity : 0.005 0.064 2379 Dihedral : 5.228 60.633 1979 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.33 % Allowed : 21.56 % Favored : 76.11 % 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: -0.96 (0.20), residues: 1734 helix: 0.54 (0.19), residues: 817 sheet: -1.66 (0.40), residues: 161 loop : -1.71 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 172 HIS 0.004 0.001 HIS D 568 PHE 0.011 0.001 PHE B 145 TYR 0.012 0.001 TYR A 340 ARG 0.017 0.001 ARG A 325 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4443.36 seconds wall clock time: 80 minutes 24.32 seconds (4824.32 seconds total)