Starting phenix.real_space_refine on Thu Jun 12 22:52:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6oxl_20220/06_2025/6oxl_20220.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oxl_20220/06_2025/6oxl_20220.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6oxl_20220/06_2025/6oxl_20220.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oxl_20220/06_2025/6oxl_20220.map" model { file = "/net/cci-nas-00/data/ceres_data/6oxl_20220/06_2025/6oxl_20220.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oxl_20220/06_2025/6oxl_20220.cif" } resolution = 3.5 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= 0.173 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 74 5.16 5 C 9236 2.51 5 N 2435 2.21 5 O 2667 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14413 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4629 Classifications: {'peptide': 589} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 21, 'TRANS': 567} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 4} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 4465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4465 Classifications: {'peptide': 564} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 24, 'TRANS': 539} Chain breaks: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "M" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3118 Classifications: {'peptide': 390} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 17, 'TRANS': 372} Chain breaks: 5 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'TPO:plan-1': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 16 Chain: "S" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1190 Classifications: {'peptide': 141} Link IDs: {'TRANS': 140} Chain: "N" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 975 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 117} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 4} Unresolved non-hydrogen planarities: 20 Chain: "n" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 36 Classifications: {'peptide': 7} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'UNK:plan-1': 6} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 8.48, per 1000 atoms: 0.59 Number of scatterers: 14413 At special positions: 0 Unit cell: (100.92, 107.88, 124.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 74 16.00 P 1 15.00 O 2667 8.00 N 2435 7.00 C 9236 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: 3.31 Conformation dependent library (CDL) restraints added in 1.9 seconds 3544 Ramachandran restraints generated. 1772 Oldfield, 0 Emsley, 1772 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3500 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 11 sheets defined 57.9% alpha, 14.5% 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 11 through 22 removed outlier: 3.654A pdb=" N VAL A 15 " --> pdb=" O ARG A 11 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE A 16 " --> pdb=" O GLY A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 45 Processing helix chain 'A' and resid 52 through 68 Processing helix chain 'A' and resid 75 through 84 removed outlier: 3.787A pdb=" N LEU A 82 " --> pdb=" O GLU A 78 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER A 84 " --> pdb=" O VAL A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 101 removed outlier: 3.598A pdb=" N ILE A 93 " --> pdb=" O THR A 89 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A 98 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N SER A 99 " --> pdb=" O TYR A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 121 removed outlier: 3.925A pdb=" N ARG A 110 " --> pdb=" O SER A 106 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 139 removed outlier: 4.011A pdb=" N LEU A 130 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N HIS A 133 " --> pdb=" O GLY A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 148 removed outlier: 4.173A pdb=" N ALA A 146 " --> pdb=" O GLU A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 161 through 179 removed outlier: 3.530A pdb=" N LYS A 165 " --> pdb=" O MET A 161 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLN A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 170 " --> pdb=" O GLN A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 193 removed outlier: 3.693A pdb=" N VAL A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 198 Processing helix chain 'A' and resid 201 through 218 removed outlier: 3.669A pdb=" N THR A 213 " --> pdb=" O SER A 209 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN A 216 " --> pdb=" O THR A 212 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS A 217 " --> pdb=" O THR A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 224 No H-bonds generated for 'chain 'A' and resid 222 through 224' Processing helix chain 'A' and resid 225 through 238 removed outlier: 3.678A pdb=" N SER A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 264 removed outlier: 4.021A pdb=" N LEU A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 268 removed outlier: 3.591A pdb=" N TYR A 268 " --> pdb=" O LEU A 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 265 through 268' Processing helix chain 'A' and resid 273 through 291 removed outlier: 4.047A pdb=" N GLU A 282 " --> pdb=" O GLY A 278 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A 287 " --> pdb=" O CYS A 283 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 304 Processing helix chain 'A' and resid 304 through 321 removed outlier: 3.814A pdb=" N VAL A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER A 315 " --> pdb=" O PHE A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 335 removed outlier: 3.655A pdb=" N LEU A 327 " --> pdb=" O GLU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 340 removed outlier: 3.779A pdb=" N HIS A 340 " --> pdb=" O PHE A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 357 removed outlier: 3.686A pdb=" N ARG A 346 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR A 355 " --> pdb=" O GLU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 367 removed outlier: 3.864A pdb=" N LYS A 367 " --> pdb=" O HIS A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 380 removed outlier: 3.536A pdb=" N VAL A 373 " --> pdb=" O HIS A 369 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE A 374 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU A 380 " --> pdb=" O ALA A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 397 removed outlier: 3.830A pdb=" N ARG A 388 " --> pdb=" O SER A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 400 No H-bonds generated for 'chain 'A' and resid 398 through 400' Processing helix chain 'A' and resid 401 through 414 Processing helix chain 'A' and resid 420 through 435 removed outlier: 3.579A pdb=" N VAL A 425 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU A 426 " --> pdb=" O GLU A 422 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 454 removed outlier: 3.528A pdb=" N TYR A 442 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP A 444 " --> pdb=" O THR A 440 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN A 448 " --> pdb=" O ASP A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 472 removed outlier: 3.500A pdb=" N TRP A 462 " --> pdb=" O SER A 458 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR A 463 " --> pdb=" O GLU A 459 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ARG A 464 " --> pdb=" O GLU A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 487 removed outlier: 4.427A pdb=" N TYR A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE A 484 " --> pdb=" O ALA A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 507 removed outlier: 3.742A pdb=" N VAL A 497 " --> pdb=" O HIS A 493 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS A 498 " --> pdb=" O GLU A 494 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY A 505 " --> pdb=" O GLY A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 511 Processing helix chain 'A' and resid 518 through 529 removed outlier: 3.512A pdb=" N ASN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 552 removed outlier: 3.522A pdb=" N LEU A 542 " --> pdb=" O ARG A 538 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS A 547 " --> pdb=" O SER A 543 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL A 549 " --> pdb=" O TYR A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 564 removed outlier: 3.872A pdb=" N ASP A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL A 562 " --> pdb=" O THR A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 589 removed outlier: 3.571A pdb=" N GLN A 577 " --> pdb=" O ASP A 573 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU A 582 " --> pdb=" O GLN A 578 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N SER A 587 " --> pdb=" O TYR A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 599 Processing helix chain 'B' and resid 13 through 23 removed outlier: 3.587A pdb=" N GLU B 17 " --> pdb=" O GLY B 13 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU B 21 " --> pdb=" O GLU B 17 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN B 23 " --> pdb=" O LYS B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 44 removed outlier: 3.585A pdb=" N ARG B 30 " --> pdb=" O LYS B 26 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS B 36 " --> pdb=" O GLU B 32 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR B 42 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL B 43 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 50 through 55 removed outlier: 3.641A pdb=" N VAL B 55 " --> pdb=" O PHE B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 59 removed outlier: 3.705A pdb=" N GLN B 59 " --> pdb=" O ASN B 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 56 through 59' Processing helix chain 'B' and resid 62 through 79 removed outlier: 3.532A pdb=" N LYS B 66 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU B 68 " --> pdb=" O GLU B 64 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS B 78 " --> pdb=" O MET B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 85 removed outlier: 3.752A pdb=" N ALA B 84 " --> pdb=" O GLN B 80 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE B 85 " --> pdb=" O PRO B 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 80 through 85' Processing helix chain 'B' and resid 87 through 92 Processing helix chain 'B' and resid 100 through 113 removed outlier: 3.546A pdb=" N VAL B 107 " --> pdb=" O ARG B 103 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N CYS B 112 " --> pdb=" O ARG B 108 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE B 113 " --> pdb=" O THR B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 117 No H-bonds generated for 'chain 'B' and resid 115 through 117' Processing helix chain 'B' and resid 118 through 130 removed outlier: 5.118A pdb=" N GLU B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) Proline residue: B 125 - end of helix removed outlier: 3.532A pdb=" N LYS B 128 " --> pdb=" O GLU B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 151 removed outlier: 3.671A pdb=" N THR B 140 " --> pdb=" O TYR B 136 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP B 150 " --> pdb=" O ALA B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 170 removed outlier: 3.764A pdb=" N ASP B 167 " --> pdb=" O ASP B 163 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ALA B 170 " --> pdb=" O ARG B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 187 removed outlier: 4.051A pdb=" N ASN B 179 " --> pdb=" O MET B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 190 No H-bonds generated for 'chain 'B' and resid 188 through 190' Processing helix chain 'B' and resid 202 through 212 Processing helix chain 'B' and resid 217 through 222 Processing helix chain 'B' and resid 222 through 227 Processing helix chain 'B' and resid 235 through 245 removed outlier: 3.631A pdb=" N SER B 239 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ARG B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 249 removed outlier: 4.005A pdb=" N SER B 249 " --> pdb=" O PRO B 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 246 through 249' Processing helix chain 'B' and resid 252 through 264 removed outlier: 4.131A pdb=" N VAL B 256 " --> pdb=" O ASN B 252 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU B 257 " --> pdb=" O SER B 253 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B 263 " --> pdb=" O ALA B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 280 Processing helix chain 'B' and resid 281 through 283 No H-bonds generated for 'chain 'B' and resid 281 through 283' Processing helix chain 'B' and resid 284 through 290 removed outlier: 3.695A pdb=" N LEU B 288 " --> pdb=" O LEU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 313 removed outlier: 3.583A pdb=" N TYR B 300 " --> pdb=" O PRO B 296 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL B 301 " --> pdb=" O GLU B 297 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LEU B 308 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLN B 311 " --> pdb=" O ASN B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 345 removed outlier: 4.119A pdb=" N GLU B 337 " --> pdb=" O TYR B 333 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 363 removed outlier: 3.665A pdb=" N ALA B 356 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU B 357 " --> pdb=" O GLN B 353 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU B 360 " --> pdb=" O ALA B 356 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR B 363 " --> pdb=" O LYS B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 374 removed outlier: 4.116A pdb=" N LYS B 372 " --> pdb=" O ASP B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 382 removed outlier: 3.627A pdb=" N GLY B 378 " --> pdb=" O VAL B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 387 through 399 removed outlier: 3.534A pdb=" N ASP B 397 " --> pdb=" O SER B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 406 through 421 removed outlier: 4.853A pdb=" N VAL B 412 " --> pdb=" O GLN B 408 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG B 415 " --> pdb=" O ILE B 411 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS B 420 " --> pdb=" O ASP B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 427 No H-bonds generated for 'chain 'B' and resid 425 through 427' Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 434 through 436 No H-bonds generated for 'chain 'B' and resid 434 through 436' Processing helix chain 'B' and resid 441 through 454 removed outlier: 3.638A pdb=" N TRP B 450 " --> pdb=" O ALA B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 466 Processing helix chain 'B' and resid 477 through 495 removed outlier: 3.600A pdb=" N VAL B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 507 removed outlier: 3.889A pdb=" N GLN B 505 " --> pdb=" O GLU B 501 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 507 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 531 removed outlier: 3.784A pdb=" N ARG B 522 " --> pdb=" O ASP B 518 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 530 " --> pdb=" O TYR B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 541 removed outlier: 3.752A pdb=" N GLU B 539 " --> pdb=" O VAL B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 564 removed outlier: 3.615A pdb=" N GLU B 562 " --> pdb=" O THR B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 567 No H-bonds generated for 'chain 'B' and resid 565 through 567' Processing helix chain 'B' and resid 569 through 574 removed outlier: 3.854A pdb=" N VAL B 573 " --> pdb=" O SER B 569 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR B 574 " --> pdb=" O LEU B 570 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 569 through 574' Processing helix chain 'B' and resid 577 through 581 Processing helix chain 'M' and resid 27 through 36 removed outlier: 3.520A pdb=" N PHE M 32 " --> pdb=" O ALA M 28 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN M 35 " --> pdb=" O ALA M 31 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 94 removed outlier: 3.766A pdb=" N CYS M 86 " --> pdb=" O LEU M 82 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA M 91 " --> pdb=" O ASP M 87 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 103 removed outlier: 3.540A pdb=" N LYS M 102 " --> pdb=" O GLU M 98 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN M 103 " --> pdb=" O GLU M 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 112 removed outlier: 3.580A pdb=" N TYR M 109 " --> pdb=" O PHE M 105 " (cutoff:3.500A) Processing helix chain 'M' and resid 125 through 130 removed outlier: 4.007A pdb=" N LYS M 130 " --> pdb=" O THR M 126 " (cutoff:3.500A) Processing helix chain 'S' and resid 24 through 36 removed outlier: 3.640A pdb=" N GLN S 29 " --> pdb=" O ASP S 25 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS S 36 " --> pdb=" O ILE S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 78 through 96 removed outlier: 3.576A pdb=" N GLU S 82 " --> pdb=" O LEU S 78 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS S 85 " --> pdb=" O LEU S 81 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL S 90 " --> pdb=" O ASN S 86 " (cutoff:3.500A) Processing helix chain 'S' and resid 99 through 104 removed outlier: 3.500A pdb=" N ASP S 102 " --> pdb=" O CYS S 99 " (cutoff:3.500A) Processing helix chain 'S' and resid 106 through 117 removed outlier: 3.526A pdb=" N TYR S 111 " --> pdb=" O PHE S 107 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR S 112 " --> pdb=" O TYR S 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 127 through 140 removed outlier: 3.666A pdb=" N MET S 137 " --> pdb=" O LYS S 133 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER S 140 " --> pdb=" O LEU S 136 " (cutoff:3.500A) Processing helix chain 'N' and resid 31 through 35 removed outlier: 3.564A pdb=" N GLU N 34 " --> pdb=" O ARG N 31 " (cutoff:3.500A) Processing helix chain 'N' and resid 112 through 138 removed outlier: 3.745A pdb=" N PHE N 118 " --> pdb=" O ASP N 114 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN N 119 " --> pdb=" O ALA N 115 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS N 125 " --> pdb=" O ALA N 121 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE N 126 " --> pdb=" O LEU N 122 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS N 137 " --> pdb=" O CYS N 133 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 248 through 249 Processing sheet with id=AA2, first strand: chain 'M' and resid 14 through 17 removed outlier: 3.567A pdb=" N PHE M 56 " --> pdb=" O ALA M 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 116 through 117 Processing sheet with id=AA4, first strand: chain 'M' and resid 245 through 248 removed outlier: 6.301A pdb=" N GLU M 273 " --> pdb=" O MET M 202 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N MET M 202 " --> pdb=" O GLU M 273 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU M 183 " --> pdb=" O GLY M 429 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TYR M 431 " --> pdb=" O LEU M 183 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N MET M 185 " --> pdb=" O TYR M 431 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N THR M 433 " --> pdb=" O MET M 185 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N PHE M 390 " --> pdb=" O SER M 428 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE M 430 " --> pdb=" O MET M 388 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N MET M 388 " --> pdb=" O ILE M 430 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N GLU M 432 " --> pdb=" O ILE M 386 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE M 386 " --> pdb=" O GLU M 432 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLU M 391 " --> pdb=" O LYS M 319 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N LYS M 319 " --> pdb=" O GLU M 391 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU M 316 " --> pdb=" O ALA M 359 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA M 359 " --> pdb=" O LEU M 316 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLN M 318 " --> pdb=" O ARG M 357 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ARG M 357 " --> pdb=" O GLN M 318 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA M 350 " --> pdb=" O LYS M 345 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 245 through 248 removed outlier: 6.301A pdb=" N GLU M 273 " --> pdb=" O MET M 202 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N MET M 202 " --> pdb=" O GLU M 273 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU M 173 " --> pdb=" O TRP M 421 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 262 through 265 removed outlier: 3.828A pdb=" N LYS M 405 " --> pdb=" O LYS M 213 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR M 403 " --> pdb=" O GLY M 215 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 287 through 296 removed outlier: 3.879A pdb=" N VAL M 296 " --> pdb=" O LYS M 300 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS M 300 " --> pdb=" O VAL M 296 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN M 334 " --> pdb=" O GLU M 369 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLY M 332 " --> pdb=" O GLU M 371 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'S' and resid 14 through 19 removed outlier: 6.483A pdb=" N ILE S 7 " --> pdb=" O ARG S 15 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA S 17 " --> pdb=" O ILE S 5 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE S 5 " --> pdb=" O ALA S 17 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N TRP S 19 " --> pdb=" O ARG S 3 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ARG S 3 " --> pdb=" O TRP S 19 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N CYS S 70 " --> pdb=" O ARG S 3 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE S 5 " --> pdb=" O CYS S 68 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N CYS S 68 " --> pdb=" O ILE S 5 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE S 7 " --> pdb=" O TYR S 66 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TYR S 66 " --> pdb=" O ILE S 7 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 14 through 19 removed outlier: 6.483A pdb=" N ILE S 7 " --> pdb=" O ARG S 15 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA S 17 " --> pdb=" O ILE S 5 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE S 5 " --> pdb=" O ALA S 17 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N TRP S 19 " --> pdb=" O ARG S 3 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ARG S 3 " --> pdb=" O TRP S 19 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N CYS S 70 " --> pdb=" O ARG S 3 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE S 5 " --> pdb=" O CYS S 68 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N CYS S 68 " --> pdb=" O ILE S 5 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE S 7 " --> pdb=" O TYR S 66 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TYR S 66 " --> pdb=" O ILE S 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 118 through 119 Processing sheet with id=AB2, first strand: chain 'N' and resid 67 through 72 removed outlier: 6.763A pdb=" N LEU N 59 " --> pdb=" O PHE N 68 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLN N 70 " --> pdb=" O ILE N 57 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE N 57 " --> pdb=" O GLN N 70 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ALA N 55 " --> pdb=" O PRO N 72 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N TRP N 42 " --> pdb=" O HIS N 17 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N HIS N 17 " --> pdb=" O TRP N 42 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLY N 44 " --> pdb=" O GLU N 15 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N CYS N 11 " --> pdb=" O ILE N 48 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ALA N 50 " --> pdb=" O VAL N 9 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL N 9 " --> pdb=" O ALA N 50 " (cutoff:3.500A) 675 hydrogen bonds defined for protein. 1953 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: 4.51 Time building geometry restraints manager: 3.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4365 1.33 - 1.45: 2041 1.45 - 1.57: 8147 1.57 - 1.69: 3 1.69 - 1.81: 113 Bond restraints: 14669 Sorted by residual: bond pdb=" OG1 TPO M 156 " pdb=" P TPO M 156 " ideal model delta sigma weight residual 1.717 1.629 0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" O1P TPO M 156 " pdb=" P TPO M 156 " ideal model delta sigma weight residual 1.525 1.609 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" O2P TPO M 156 " pdb=" P TPO M 156 " ideal model delta sigma weight residual 1.528 1.612 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C GLU B 544 " pdb=" N LYS B 545 " ideal model delta sigma weight residual 1.329 1.267 0.061 1.60e-02 3.91e+03 1.47e+01 bond pdb=" C THR S 14 " pdb=" N ARG S 15 " ideal model delta sigma weight residual 1.332 1.297 0.034 1.29e-02 6.01e+03 7.10e+00 ... (remaining 14664 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 19385 2.84 - 5.68: 416 5.68 - 8.51: 51 8.51 - 11.35: 8 11.35 - 14.19: 4 Bond angle restraints: 19864 Sorted by residual: angle pdb=" N ALA B 254 " pdb=" CA ALA B 254 " pdb=" C ALA B 254 " ideal model delta sigma weight residual 111.28 119.34 -8.06 1.09e+00 8.42e-01 5.47e+01 angle pdb=" N LEU A 447 " pdb=" CA LEU A 447 " pdb=" C LEU A 447 " ideal model delta sigma weight residual 111.28 106.29 4.99 1.09e+00 8.42e-01 2.10e+01 angle pdb=" C PHE S 52 " pdb=" N ARG S 53 " pdb=" CA ARG S 53 " ideal model delta sigma weight residual 121.54 129.49 -7.95 1.91e+00 2.74e-01 1.73e+01 angle pdb=" C THR B 8 " pdb=" N THR B 9 " pdb=" CA THR B 9 " ideal model delta sigma weight residual 121.54 129.30 -7.76 1.91e+00 2.74e-01 1.65e+01 angle pdb=" CA LEU A 532 " pdb=" CB LEU A 532 " pdb=" CG LEU A 532 " ideal model delta sigma weight residual 116.30 130.49 -14.19 3.50e+00 8.16e-02 1.64e+01 ... (remaining 19859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.34: 8538 15.34 - 30.69: 336 30.69 - 46.03: 78 46.03 - 61.37: 3 61.37 - 76.72: 2 Dihedral angle restraints: 8957 sinusoidal: 3592 harmonic: 5365 Sorted by residual: dihedral pdb=" CA GLN B 154 " pdb=" C GLN B 154 " pdb=" N MET B 155 " pdb=" CA MET B 155 " ideal model delta harmonic sigma weight residual 180.00 150.87 29.13 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA CYS S 70 " pdb=" C CYS S 70 " pdb=" N VAL S 71 " pdb=" CA VAL S 71 " ideal model delta harmonic sigma weight residual 180.00 -153.22 -26.78 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA TRP M 421 " pdb=" C TRP M 421 " pdb=" N VAL M 422 " pdb=" CA VAL M 422 " ideal model delta harmonic sigma weight residual 180.00 156.12 23.88 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 8954 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1667 0.059 - 0.117: 530 0.117 - 0.176: 104 0.176 - 0.234: 11 0.234 - 0.293: 2 Chirality restraints: 2314 Sorted by residual: chirality pdb=" CB ILE M 355 " pdb=" CA ILE M 355 " pdb=" CG1 ILE M 355 " pdb=" CG2 ILE M 355 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA ALA B 254 " pdb=" N ALA B 254 " pdb=" C ALA B 254 " pdb=" CB ALA B 254 " both_signs ideal model delta sigma weight residual False 2.48 2.21 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA ASP M 282 " pdb=" N ASP M 282 " pdb=" C ASP M 282 " pdb=" CB ASP M 282 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 2311 not shown) Planarity restraints: 2522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO N 22 " -0.049 5.00e-02 4.00e+02 7.33e-02 8.60e+00 pdb=" N PRO N 23 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO N 23 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO N 23 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 245 " -0.049 5.00e-02 4.00e+02 7.28e-02 8.48e+00 pdb=" N PRO B 246 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO B 246 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 246 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP M 421 " -0.023 2.00e-02 2.50e+03 1.64e-02 6.72e+00 pdb=" CG TRP M 421 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP M 421 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP M 421 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP M 421 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP M 421 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP M 421 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 421 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 421 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP M 421 " -0.001 2.00e-02 2.50e+03 ... (remaining 2519 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3324 2.77 - 3.30: 12895 3.30 - 3.83: 23047 3.83 - 4.37: 28410 4.37 - 4.90: 47768 Nonbonded interactions: 115444 Sorted by model distance: nonbonded pdb=" OE2 GLU M 179 " pdb=" OH TYR M 277 " model vdw 2.236 3.040 nonbonded pdb=" OE2 GLU A 494 " pdb=" OG1 THR A 537 " model vdw 2.240 3.040 nonbonded pdb=" O PHE M 287 " pdb=" OH TYR M 431 " model vdw 2.255 3.040 nonbonded pdb=" NE2 GLN B 348 " pdb=" OE1 GLN B 386 " model vdw 2.271 3.120 nonbonded pdb=" OH TYR B 328 " pdb=" OD1 ASP N 117 " model vdw 2.273 3.040 ... (remaining 115439 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.760 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: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 33.250 Find NCS groups from input model: 0.190 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: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 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 0.094 14669 Z= 0.413 Angle : 1.086 14.188 19864 Z= 0.611 Chirality : 0.058 0.293 2314 Planarity : 0.007 0.073 2522 Dihedral : 9.339 76.719 5457 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.06 % Allowed : 0.95 % Favored : 98.99 % 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: -5.46 (0.14), residues: 1772 helix: -4.63 (0.06), residues: 965 sheet: -1.75 (0.36), residues: 193 loop : -1.99 (0.21), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.005 TRP M 421 HIS 0.014 0.002 HIS A 320 PHE 0.040 0.004 PHE S 67 TYR 0.036 0.004 TYR B 455 ARG 0.009 0.001 ARG A 579 Details of bonding type rmsd hydrogen bonds : bond 0.29972 ( 651) hydrogen bonds : angle 10.82116 ( 1953) covalent geometry : bond 0.01008 (14669) covalent geometry : angle 1.08622 (19864) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3544 Ramachandran restraints generated. 1772 Oldfield, 0 Emsley, 1772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3544 Ramachandran restraints generated. 1772 Oldfield, 0 Emsley, 1772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 268 time to evaluate : 1.815 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8656 (mmtt) cc_final: 0.8388 (mmmt) REVERT: A 77 MET cc_start: 0.8564 (tpp) cc_final: 0.8305 (tpp) REVERT: A 114 ASN cc_start: 0.8569 (t0) cc_final: 0.8247 (t0) REVERT: A 128 MET cc_start: 0.8408 (mtm) cc_final: 0.8159 (mtp) REVERT: B 205 ASN cc_start: 0.8699 (t0) cc_final: 0.8464 (m-40) REVERT: B 340 ASP cc_start: 0.9121 (t0) cc_final: 0.8690 (t0) REVERT: B 344 ARG cc_start: 0.8522 (mtt90) cc_final: 0.8303 (mtt-85) REVERT: B 384 VAL cc_start: 0.8929 (t) cc_final: 0.8621 (m) REVERT: B 408 GLN cc_start: 0.8502 (mt0) cc_final: 0.8214 (mt0) REVERT: B 565 CYS cc_start: 0.9052 (m) cc_final: 0.8632 (t) REVERT: M 218 ASP cc_start: 0.8217 (m-30) cc_final: 0.7808 (p0) REVERT: M 282 ASP cc_start: 0.8870 (p0) cc_final: 0.8626 (p0) REVERT: M 298 ARG cc_start: 0.8095 (ptp90) cc_final: 0.7587 (mtt180) REVERT: S 1 MET cc_start: 0.8369 (ptm) cc_final: 0.8065 (ptt) REVERT: S 21 MET cc_start: 0.8304 (mtp) cc_final: 0.8079 (mtp) REVERT: N 53 LYS cc_start: 0.8746 (mttt) cc_final: 0.8432 (mmtt) REVERT: N 61 ASP cc_start: 0.8215 (t0) cc_final: 0.7824 (m-30) outliers start: 1 outliers final: 0 residues processed: 269 average time/residue: 0.3207 time to fit residues: 118.5801 Evaluate side-chains 156 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 151 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 85 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 HIS A 76 HIS A 81 ASN A 92 GLN A 200 HIS A 216 GLN A 218 ASN ** A 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 GLN A 550 ASN A 568 GLN B 56 ASN B 75 ASN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 ASN B 203 ASN B 250 HIS B 386 GLN ** M 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 135 GLN ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 134 GLN N 39 GLN N 125 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.128844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.113193 restraints weight = 23533.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.116818 restraints weight = 12808.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.119210 restraints weight = 8201.642| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14669 Z= 0.157 Angle : 0.643 12.640 19864 Z= 0.337 Chirality : 0.043 0.162 2314 Planarity : 0.005 0.065 2522 Dihedral : 5.544 27.848 1956 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.45 % Allowed : 5.86 % Favored : 92.69 % 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: -3.74 (0.17), residues: 1772 helix: -2.94 (0.12), residues: 983 sheet: -1.75 (0.32), residues: 225 loop : -1.35 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP M 353 HIS 0.005 0.001 HIS A 320 PHE 0.017 0.002 PHE M 81 TYR 0.016 0.002 TYR A 412 ARG 0.005 0.000 ARG M 18 Details of bonding type rmsd hydrogen bonds : bond 0.04706 ( 651) hydrogen bonds : angle 5.72051 ( 1953) covalent geometry : bond 0.00357 (14669) covalent geometry : angle 0.64269 (19864) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3544 Ramachandran restraints generated. 1772 Oldfield, 0 Emsley, 1772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3544 Ramachandran restraints generated. 1772 Oldfield, 0 Emsley, 1772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 1.580 Fit side-chains REVERT: A 118 ASN cc_start: 0.7763 (m-40) cc_final: 0.7393 (t0) REVERT: A 128 MET cc_start: 0.8108 (mtm) cc_final: 0.7851 (mtp) REVERT: B 29 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8275 (mppt) REVERT: M 410 LYS cc_start: 0.7065 (mmtt) cc_final: 0.6089 (ptmt) REVERT: N 53 LYS cc_start: 0.8505 (mttt) cc_final: 0.8243 (mmtt) REVERT: N 54 VAL cc_start: 0.8853 (t) cc_final: 0.8504 (p) REVERT: N 56 TYR cc_start: 0.7914 (m-80) cc_final: 0.7636 (m-80) REVERT: N 62 ARG cc_start: 0.6355 (ptp-170) cc_final: 0.6122 (ptp-170) REVERT: N 70 GLN cc_start: 0.8119 (tt0) cc_final: 0.7752 (tt0) REVERT: N 76 PHE cc_start: 0.7402 (t80) cc_final: 0.7182 (t80) REVERT: N 138 GLN cc_start: 0.6995 (mm110) cc_final: 0.6719 (tp40) outliers start: 23 outliers final: 9 residues processed: 188 average time/residue: 0.2892 time to fit residues: 78.6281 Evaluate side-chains 149 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 139 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 CYS Chi-restraints excluded: chain A residue 188 TRP Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain M residue 176 ASP Chi-restraints excluded: chain M residue 328 LEU Chi-restraints excluded: chain M residue 435 CYS Chi-restraints excluded: chain S residue 36 HIS Chi-restraints excluded: chain S residue 68 CYS Chi-restraints excluded: chain S residue 114 VAL Chi-restraints excluded: chain S residue 127 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.281 > 50: distance: 104 - 203: 10.794 distance: 107 - 200: 14.618 distance: 113 - 120: 14.389 distance: 120 - 121: 15.743 distance: 121 - 122: 4.731 distance: 121 - 124: 15.096 distance: 122 - 123: 16.316 distance: 122 - 131: 11.772 distance: 124 - 125: 24.203 distance: 125 - 126: 19.164 distance: 126 - 127: 8.939 distance: 127 - 128: 14.553 distance: 128 - 129: 7.525 distance: 128 - 130: 17.394 distance: 131 - 132: 9.883 distance: 132 - 133: 15.209 distance: 132 - 135: 19.156 distance: 133 - 134: 10.221 distance: 133 - 142: 8.523 distance: 135 - 136: 19.706 distance: 136 - 137: 25.448 distance: 137 - 138: 4.815 distance: 138 - 139: 26.381 distance: 139 - 140: 8.832 distance: 139 - 141: 20.576 distance: 142 - 143: 5.025 distance: 142 - 166: 27.332 distance: 143 - 144: 15.762 distance: 143 - 146: 14.432 distance: 144 - 145: 29.118 distance: 144 - 154: 16.340 distance: 145 - 163: 31.305 distance: 146 - 147: 8.917 distance: 147 - 148: 15.136 distance: 147 - 149: 10.655 distance: 148 - 150: 16.085 distance: 149 - 151: 12.191 distance: 150 - 152: 12.809 distance: 151 - 152: 12.655 distance: 152 - 153: 17.274 distance: 154 - 155: 9.748 distance: 155 - 156: 18.707 distance: 155 - 158: 8.186 distance: 156 - 157: 21.329 distance: 159 - 160: 16.945 distance: 160 - 161: 5.606 distance: 161 - 162: 18.495 distance: 161 - 163: 11.523 distance: 164 - 165: 12.463 distance: 164 - 167: 7.098 distance: 165 - 166: 13.533 distance: 165 - 171: 18.137 distance: 167 - 168: 26.441 distance: 168 - 169: 27.349 distance: 168 - 170: 27.294 distance: 171 - 172: 26.535 distance: 172 - 173: 25.703 distance: 172 - 175: 9.650 distance: 173 - 174: 4.260 distance: 173 - 183: 19.287 distance: 175 - 176: 22.337 distance: 176 - 177: 30.806 distance: 176 - 178: 16.356 distance: 177 - 179: 8.207 distance: 178 - 180: 25.327 distance: 179 - 181: 5.862 distance: 180 - 181: 32.393 distance: 181 - 182: 15.347 distance: 183 - 184: 11.879 distance: 184 - 185: 24.823 distance: 184 - 187: 12.176 distance: 185 - 186: 4.595 distance: 185 - 194: 34.023 distance: 187 - 188: 7.692 distance: 188 - 189: 6.255 distance: 188 - 190: 9.146 distance: 189 - 191: 3.238 distance: 190 - 192: 3.056 distance: 192 - 193: 7.991 distance: 195 - 196: 7.908 distance: 195 - 198: 22.956 distance: 196 - 197: 10.460 distance: 196 - 200: 13.125 distance: 198 - 199: 23.109 distance: 200 - 201: 13.116 distance: 201 - 204: 8.971 distance: 202 - 203: 7.099 distance: 202 - 208: 4.691 distance: 204 - 205: 7.821 distance: 204 - 206: 12.529 distance: 205 - 207: 15.700