Starting phenix.real_space_refine on Sun Jul 21 15:15:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3f_29694/07_2024/8g3f_29694.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3f_29694/07_2024/8g3f_29694.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3f_29694/07_2024/8g3f_29694.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3f_29694/07_2024/8g3f_29694.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3f_29694/07_2024/8g3f_29694.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3f_29694/07_2024/8g3f_29694.cif" } resolution = 3.7 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= 0.001 sd= 0.015 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 2 5.49 5 S 62 5.16 5 C 9385 2.51 5 N 2374 2.21 5 O 2619 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 14442 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 635, 5000 Classifications: {'peptide': 635} Link IDs: {'PTRANS': 10, 'TRANS': 624} Chain breaks: 1 Chain: "B" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1915 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 5, 'TRANS': 238} Chain: "C" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1915 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 5, 'TRANS': 238} Chain: "D" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2738 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 324} Chain: "E" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2738 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 324} Chain: "A" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 116 Unusual residues: {'6OU': 2, 'PLM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'OLA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.56, per 1000 atoms: 0.59 Number of scatterers: 14442 At special positions: 0 Unit cell: (95.048, 113.36, 198.816, 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 62 16.00 P 2 15.00 O 2619 8.00 N 2374 7.00 C 9385 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 - 3.50 Amino acid : False - 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: 5.36 Conformation dependent library (CDL) restraints added in 2.5 seconds 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3374 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 12 sheets defined 61.9% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 2 through 18 Processing helix chain 'A' and resid 19 through 40 removed outlier: 3.640A pdb=" N TYR A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 47 removed outlier: 3.836A pdb=" N ASN A 45 " --> pdb=" O PRO A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 80 removed outlier: 3.621A pdb=" N ILE A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA A 66 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A 80 " --> pdb=" O ASN A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 94 removed outlier: 3.586A pdb=" N ILE A 87 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU A 89 " --> pdb=" O LYS A 85 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY A 94 " --> pdb=" O PHE A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 104 removed outlier: 3.839A pdb=" N ILE A 100 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ARG A 102 " --> pdb=" O HIS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 122 Processing helix chain 'A' and resid 126 through 138 removed outlier: 3.560A pdb=" N LYS A 136 " --> pdb=" O MET A 132 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 176 removed outlier: 4.291A pdb=" N VAL A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN A 155 " --> pdb=" O GLN A 151 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS A 176 " --> pdb=" O TYR A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 222 removed outlier: 4.371A pdb=" N GLY A 205 " --> pdb=" O GLN A 201 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ALA A 206 " --> pdb=" O MET A 202 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU A 221 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 253 removed outlier: 4.302A pdb=" N VAL A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR A 252 " --> pdb=" O THR A 248 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS A 253 " --> pdb=" O PHE A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 265 Processing helix chain 'A' and resid 272 through 282 removed outlier: 3.614A pdb=" N SER A 280 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N SER A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 289 removed outlier: 3.980A pdb=" N SER A 288 " --> pdb=" O PHE A 284 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN A 289 " --> pdb=" O ARG A 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 284 through 289' Processing helix chain 'A' and resid 292 through 325 removed outlier: 3.653A pdb=" N TYR A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR A 315 " --> pdb=" O TYR A 311 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU A 318 " --> pdb=" O TYR A 314 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ALA A 321 " --> pdb=" O SER A 317 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 346 removed outlier: 3.902A pdb=" N GLU A 346 " --> pdb=" O ASN A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 382 Processing helix chain 'A' and resid 409 through 416 removed outlier: 3.776A pdb=" N GLN A 413 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS A 414 " --> pdb=" O ASP A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 472 removed outlier: 3.601A pdb=" N GLN A 467 " --> pdb=" O SER A 463 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 515 through 556 removed outlier: 4.031A pdb=" N ALA A 519 " --> pdb=" O ASP A 515 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLN A 520 " --> pdb=" O THR A 516 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LYS A 521 " --> pdb=" O SER A 517 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS A 549 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLN A 550 " --> pdb=" O LEU A 546 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N MET A 551 " --> pdb=" O TYR A 547 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N GLY A 552 " --> pdb=" O PHE A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 566 removed outlier: 3.544A pdb=" N LYS A 566 " --> pdb=" O THR A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 602 removed outlier: 3.774A pdb=" N LYS A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE A 580 " --> pdb=" O LYS A 576 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N MET A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ILE A 588 " --> pdb=" O TYR A 584 " (cutoff:3.500A) Proline residue: A 589 - end of helix removed outlier: 3.514A pdb=" N GLN A 602 " --> pdb=" O TYR A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 608 removed outlier: 5.486A pdb=" N PHE A 606 " --> pdb=" O SER A 603 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 607 " --> pdb=" O GLY A 604 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE A 608 " --> pdb=" O TRP A 605 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 603 through 608' Processing helix chain 'A' and resid 614 through 633 removed outlier: 3.969A pdb=" N MET A 618 " --> pdb=" O ALA A 614 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N PHE A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY A 631 " --> pdb=" O TYR A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 644 removed outlier: 3.804A pdb=" N LYS A 640 " --> pdb=" O LEU A 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 54 Processing helix chain 'B' and resid 75 through 86 Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 107 through 111 Processing helix chain 'B' and resid 117 through 132 removed outlier: 3.745A pdb=" N GLU B 130 " --> pdb=" O GLU B 126 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 131 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 137 removed outlier: 4.120A pdb=" N ARG B 137 " --> pdb=" O TYR B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 144 removed outlier: 3.603A pdb=" N ILE B 144 " --> pdb=" O PRO B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 158 removed outlier: 3.604A pdb=" N LYS B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 193 Processing helix chain 'B' and resid 203 through 209 removed outlier: 4.091A pdb=" N TYR B 209 " --> pdb=" O VAL B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 246 Processing helix chain 'C' and resid 45 through 55 Processing helix chain 'C' and resid 75 through 86 Processing helix chain 'C' and resid 101 through 108 removed outlier: 3.526A pdb=" N ILE C 106 " --> pdb=" O VAL C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 132 removed outlier: 3.669A pdb=" N ALA C 120 " --> pdb=" O SER C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 157 removed outlier: 3.928A pdb=" N ALA C 157 " --> pdb=" O SER C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 193 Processing helix chain 'C' and resid 203 through 209 removed outlier: 3.998A pdb=" N TYR C 209 " --> pdb=" O VAL C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 246 Processing helix chain 'D' and resid 2 through 9 Processing helix chain 'D' and resid 9 through 29 removed outlier: 3.649A pdb=" N ILE D 13 " --> pdb=" O ARG D 9 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA D 14 " --> pdb=" O ARG D 10 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA D 15 " --> pdb=" O SER D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 61 removed outlier: 3.569A pdb=" N VAL D 38 " --> pdb=" O SER D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 71 removed outlier: 3.612A pdb=" N GLU D 71 " --> pdb=" O LEU D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 139 removed outlier: 4.381A pdb=" N VAL D 90 " --> pdb=" O PHE D 86 " (cutoff:3.500A) Proline residue: D 129 - end of helix Processing helix chain 'D' and resid 142 through 169 Processing helix chain 'D' and resid 170 through 176 removed outlier: 5.178A pdb=" N GLU D 173 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU D 176 " --> pdb=" O GLU D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 194 Processing helix chain 'D' and resid 194 through 202 Processing helix chain 'D' and resid 217 through 235 Processing helix chain 'D' and resid 264 through 271 Proline residue: D 269 - end of helix Processing helix chain 'D' and resid 281 through 285 removed outlier: 3.599A pdb=" N GLN D 285 " --> pdb=" O HIS D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 300 removed outlier: 4.007A pdb=" N ALA D 300 " --> pdb=" O LYS D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 334 removed outlier: 3.986A pdb=" N HIS D 330 " --> pdb=" O ASN D 326 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL D 331 " --> pdb=" O GLN D 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 9 Processing helix chain 'E' and resid 11 through 30 removed outlier: 3.563A pdb=" N ASP E 30 " --> pdb=" O ILE E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 37 removed outlier: 3.592A pdb=" N ASN E 37 " --> pdb=" O SER E 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 34 through 37' Processing helix chain 'E' and resid 38 through 61 removed outlier: 4.090A pdb=" N ARG E 58 " --> pdb=" O TRP E 54 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS E 59 " --> pdb=" O PHE E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 71 removed outlier: 4.075A pdb=" N LYS E 68 " --> pdb=" O TYR E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 79 removed outlier: 4.180A pdb=" N ILE E 79 " --> pdb=" O VAL E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 138 removed outlier: 3.654A pdb=" N ALA E 88 " --> pdb=" O THR E 84 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N MET E 89 " --> pdb=" O PRO E 85 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL E 90 " --> pdb=" O PHE E 86 " (cutoff:3.500A) Proline residue: E 129 - end of helix Processing helix chain 'E' and resid 143 through 170 Processing helix chain 'E' and resid 171 through 175 Processing helix chain 'E' and resid 182 through 194 removed outlier: 4.278A pdb=" N LEU E 186 " --> pdb=" O GLN E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 202 Processing helix chain 'E' and resid 218 through 235 Processing helix chain 'E' and resid 264 through 268 Processing helix chain 'E' and resid 281 through 287 removed outlier: 3.748A pdb=" N ALA E 286 " --> pdb=" O HIS E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 300 removed outlier: 4.551A pdb=" N TYR E 293 " --> pdb=" O GLY E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 327 Processing helix chain 'E' and resid 328 through 333 Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 330 removed outlier: 3.602A pdb=" N LEU A 511 " --> pdb=" O SER A 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 359 through 364 removed outlier: 8.822A pdb=" N VAL A 458 " --> pdb=" O GLN A 384 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ALA A 386 " --> pdb=" O VAL A 458 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA A 457 " --> pdb=" O SER A 406 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL A 404 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ALA A 403 " --> pdb=" O TYR A 437 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLY A 439 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS A 425 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 29 through 30 removed outlier: 5.859A pdb=" N ALA B 6 " --> pdb=" O HIS B 65 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N HIS B 65 " --> pdb=" O ALA B 6 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LYS B 8 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N THR B 63 " --> pdb=" O LYS B 8 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS B 61 " --> pdb=" O ARG B 10 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 12 through 14 Processing sheet with id=AA5, first strand: chain 'B' and resid 88 through 90 removed outlier: 7.457A pdb=" N GLY B 88 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ILE B 165 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N VAL B 200 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ALA B 167 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET B 199 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N PHE B 35 " --> pdb=" O ARG B 212 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N ILE B 214 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N SER B 37 " --> pdb=" O ILE B 214 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 28 through 29 removed outlier: 4.024A pdb=" N GLU C 5 " --> pdb=" O HIS C 65 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N HIS C 65 " --> pdb=" O GLU C 5 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 37 through 39 Processing sheet with id=AA8, first strand: chain 'C' and resid 87 through 88 removed outlier: 6.568A pdb=" N GLY C 88 " --> pdb=" O PHE C 166 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE C 198 " --> pdb=" O ILE C 165 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 179 through 182 Processing sheet with id=AB1, first strand: chain 'D' and resid 205 through 209 removed outlier: 3.611A pdb=" N ILE D 243 " --> pdb=" O ASP D 206 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER D 245 " --> pdb=" O GLN D 208 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 179 through 181 removed outlier: 3.725A pdb=" N GLU E 179 " --> pdb=" O SER E 216 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER E 216 " --> pdb=" O GLU E 179 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 205 through 209 removed outlier: 3.567A pdb=" N GLN E 208 " --> pdb=" O ILE E 243 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER E 245 " --> pdb=" O GLN E 208 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU E 320 " --> pdb=" O LEU E 254 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N HIS E 305 " --> pdb=" O THR E 321 " (cutoff:3.500A) 793 hydrogen bonds defined for protein. 2268 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: 4.10 Time building geometry restraints manager: 5.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2343 1.32 - 1.44: 3765 1.44 - 1.57: 8465 1.57 - 1.69: 22 1.69 - 1.82: 114 Bond restraints: 14709 Sorted by residual: bond pdb=" C10 OLA E 401 " pdb=" C9 OLA E 401 " ideal model delta sigma weight residual 1.332 1.469 -0.137 2.00e-02 2.50e+03 4.71e+01 bond pdb=" C16 6OU A 702 " pdb=" O18 6OU A 702 " ideal model delta sigma weight residual 1.327 1.464 -0.137 2.00e-02 2.50e+03 4.66e+01 bond pdb=" C16 6OU A 703 " pdb=" O18 6OU A 703 " ideal model delta sigma weight residual 1.327 1.462 -0.135 2.00e-02 2.50e+03 4.57e+01 bond pdb=" C31 6OU A 703 " pdb=" O30 6OU A 703 " ideal model delta sigma weight residual 1.331 1.424 -0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" C14 6OU A 702 " pdb=" C15 6OU A 702 " ideal model delta sigma weight residual 1.521 1.609 -0.088 2.00e-02 2.50e+03 1.95e+01 ... (remaining 14704 not shown) Histogram of bond angle deviations from ideal: 98.04 - 108.91: 626 108.91 - 119.78: 12207 119.78 - 130.64: 6887 130.64 - 141.51: 56 141.51 - 152.37: 2 Bond angle restraints: 19778 Sorted by residual: angle pdb=" C40 6OU A 703 " pdb=" C41 6OU A 703 " pdb=" C42 6OU A 703 " ideal model delta sigma weight residual 127.56 152.37 -24.81 3.00e+00 1.11e-01 6.84e+01 angle pdb=" C40 6OU A 702 " pdb=" C41 6OU A 702 " pdb=" C42 6OU A 702 " ideal model delta sigma weight residual 127.56 152.10 -24.54 3.00e+00 1.11e-01 6.69e+01 angle pdb=" O22 6OU A 702 " pdb=" P23 6OU A 702 " pdb=" O26 6OU A 702 " ideal model delta sigma weight residual 93.95 110.79 -16.84 3.00e+00 1.11e-01 3.15e+01 angle pdb=" C39 6OU A 702 " pdb=" C40 6OU A 702 " pdb=" C41 6OU A 702 " ideal model delta sigma weight residual 127.60 111.61 15.99 3.00e+00 1.11e-01 2.84e+01 angle pdb=" O22 6OU A 703 " pdb=" P23 6OU A 703 " pdb=" O26 6OU A 703 " ideal model delta sigma weight residual 93.95 109.65 -15.70 3.00e+00 1.11e-01 2.74e+01 ... (remaining 19773 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.61: 8665 35.61 - 71.21: 215 71.21 - 106.82: 16 106.82 - 142.42: 1 142.42 - 178.03: 4 Dihedral angle restraints: 8901 sinusoidal: 3689 harmonic: 5212 Sorted by residual: dihedral pdb=" CA ILE A 282 " pdb=" C ILE A 282 " pdb=" N MET A 283 " pdb=" CA MET A 283 " ideal model delta harmonic sigma weight residual 180.00 150.27 29.73 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA ARG D 139 " pdb=" C ARG D 139 " pdb=" N MET D 140 " pdb=" CA MET D 140 " ideal model delta harmonic sigma weight residual 180.00 156.90 23.10 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" C19 6OU A 703 " pdb=" C20 6OU A 703 " pdb=" C21 6OU A 703 " pdb=" O22 6OU A 703 " ideal model delta sinusoidal sigma weight residual -59.00 119.03 -178.03 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 8898 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1731 0.048 - 0.097: 402 0.097 - 0.145: 97 0.145 - 0.193: 13 0.193 - 0.241: 3 Chirality restraints: 2246 Sorted by residual: chirality pdb=" C20 6OU A 702 " pdb=" C19 6OU A 702 " pdb=" C21 6OU A 702 " pdb=" O30 6OU A 702 " both_signs ideal model delta sigma weight residual False 2.35 2.59 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA PHE A 174 " pdb=" N PHE A 174 " pdb=" C PHE A 174 " pdb=" CB PHE A 174 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA ILE E 156 " pdb=" N ILE E 156 " pdb=" C ILE E 156 " pdb=" CB ILE E 156 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.42e-01 ... (remaining 2243 not shown) Planarity restraints: 2468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 OLA E 401 " -0.197 2.00e-02 2.50e+03 1.52e-01 2.32e+02 pdb=" C11 OLA E 401 " 0.088 2.00e-02 2.50e+03 pdb=" C8 OLA E 401 " -0.088 2.00e-02 2.50e+03 pdb=" C9 OLA E 401 " 0.197 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 173 " 0.021 2.00e-02 2.50e+03 3.94e-02 1.55e+01 pdb=" C THR A 173 " -0.068 2.00e-02 2.50e+03 pdb=" O THR A 173 " 0.025 2.00e-02 2.50e+03 pdb=" N PHE A 174 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP E 30 " 0.036 5.00e-02 4.00e+02 5.48e-02 4.80e+00 pdb=" N PRO E 31 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO E 31 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 31 " 0.030 5.00e-02 4.00e+02 ... (remaining 2465 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 260 2.70 - 3.25: 14113 3.25 - 3.80: 21907 3.80 - 4.35: 26921 4.35 - 4.90: 44883 Nonbonded interactions: 108084 Sorted by model distance: nonbonded pdb=" OD1 ASP C 168 " pdb=" N GLU C 169 " model vdw 2.148 2.520 nonbonded pdb=" O PHE A 251 " pdb=" OG SER A 255 " model vdw 2.227 2.440 nonbonded pdb=" OG SER A 421 " pdb=" O TYR A 437 " model vdw 2.241 2.440 nonbonded pdb=" ND2 ASN C 7 " pdb=" OD1 ASP C 27 " model vdw 2.250 2.520 nonbonded pdb=" OG1 THR A 451 " pdb=" O MET A 455 " model vdw 2.259 2.440 ... (remaining 108079 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = (chain 'E' and resid 1 through 334) } 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: 2.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 39.020 Find NCS groups from input model: 0.450 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 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 : 0.005 0.137 14709 Z= 0.329 Angle : 0.791 24.814 19778 Z= 0.404 Chirality : 0.044 0.241 2246 Planarity : 0.005 0.152 2468 Dihedral : 16.236 178.030 5527 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 0.90 % Allowed : 0.83 % Favored : 98.27 % 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: 0.23 (0.21), residues: 1779 helix: 1.42 (0.17), residues: 998 sheet: -0.51 (0.43), residues: 159 loop : -1.81 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 153 HIS 0.008 0.001 HIS C 86 PHE 0.019 0.001 PHE A 124 TYR 0.022 0.001 TYR C 222 ARG 0.007 0.000 ARG C 212 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 231 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 THR cc_start: 0.7393 (m) cc_final: 0.7084 (p) REVERT: C 215 PHE cc_start: 0.7535 (m-80) cc_final: 0.7254 (m-80) REVERT: D 157 HIS cc_start: 0.5035 (t-90) cc_final: 0.4750 (t-90) REVERT: E 18 PHE cc_start: 0.6522 (m-80) cc_final: 0.6121 (t80) REVERT: E 23 MET cc_start: 0.7482 (tpp) cc_final: 0.7075 (tpp) REVERT: E 110 LEU cc_start: 0.8446 (tp) cc_final: 0.8176 (tt) REVERT: E 158 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7265 (tt) outliers start: 14 outliers final: 2 residues processed: 237 average time/residue: 0.2614 time to fit residues: 90.4854 Evaluate side-chains 187 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 184 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 159 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 0.6980 chunk 134 optimal weight: 7.9990 chunk 74 optimal weight: 0.0970 chunk 45 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 138 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 GLN ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14709 Z= 0.187 Angle : 0.596 9.869 19778 Z= 0.305 Chirality : 0.042 0.162 2246 Planarity : 0.004 0.075 2468 Dihedral : 11.716 166.607 2023 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.79 % Allowed : 8.96 % Favored : 89.25 % 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: 0.49 (0.21), residues: 1779 helix: 1.62 (0.17), residues: 992 sheet: -0.38 (0.44), residues: 155 loop : -1.65 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 220 HIS 0.011 0.001 HIS C 160 PHE 0.015 0.001 PHE A 529 TYR 0.026 0.002 TYR E 151 ARG 0.009 0.001 ARG E 226 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 200 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 LYS cc_start: 0.7660 (mmmt) cc_final: 0.7449 (mmtp) REVERT: E 18 PHE cc_start: 0.6523 (m-80) cc_final: 0.6184 (t80) REVERT: E 157 HIS cc_start: 0.4913 (t70) cc_final: 0.4469 (t70) outliers start: 28 outliers final: 18 residues processed: 216 average time/residue: 0.2694 time to fit residues: 84.9448 Evaluate side-chains 192 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 174 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain E residue 134 HIS Chi-restraints excluded: chain E residue 227 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 89 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 109 optimal weight: 0.0980 chunk 44 optimal weight: 10.0000 chunk 161 optimal weight: 5.9990 chunk 173 optimal weight: 20.0000 chunk 143 optimal weight: 8.9990 chunk 159 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 129 optimal weight: 6.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.070 14709 Z= 0.563 Angle : 0.844 11.367 19778 Z= 0.437 Chirality : 0.050 0.233 2246 Planarity : 0.005 0.056 2468 Dihedral : 11.720 151.184 2019 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.48 % Favored : 92.47 % Rotamer: Outliers : 3.20 % Allowed : 14.33 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.20), residues: 1779 helix: 0.68 (0.17), residues: 1001 sheet: -0.47 (0.43), residues: 162 loop : -1.95 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP E 122 HIS 0.013 0.002 HIS A 596 PHE 0.029 0.003 PHE A 33 TYR 0.033 0.003 TYR A 561 ARG 0.009 0.001 ARG D 168 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 185 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 PHE cc_start: 0.7263 (OUTLIER) cc_final: 0.6876 (t80) REVERT: A 556 ASP cc_start: 0.7738 (t0) cc_final: 0.7337 (t0) REVERT: C 50 LEU cc_start: 0.3888 (OUTLIER) cc_final: 0.3375 (mm) REVERT: E 18 PHE cc_start: 0.6719 (m-80) cc_final: 0.6222 (t80) outliers start: 50 outliers final: 34 residues processed: 221 average time/residue: 0.2513 time to fit residues: 82.9419 Evaluate side-chains 201 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 165 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 210 CYS Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 210 CYS Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain E residue 134 HIS Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 159 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 161 optimal weight: 9.9990 chunk 171 optimal weight: 30.0000 chunk 84 optimal weight: 0.9980 chunk 153 optimal weight: 0.8980 chunk 46 optimal weight: 7.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14709 Z= 0.203 Angle : 0.612 9.050 19778 Z= 0.314 Chirality : 0.042 0.148 2246 Planarity : 0.003 0.060 2468 Dihedral : 11.245 155.631 2019 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.56 % Allowed : 17.59 % Favored : 79.85 % 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: 0.17 (0.21), residues: 1779 helix: 1.32 (0.17), residues: 991 sheet: -0.33 (0.43), residues: 163 loop : -1.76 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 153 HIS 0.009 0.001 HIS C 160 PHE 0.016 0.001 PHE A 529 TYR 0.025 0.001 TYR E 151 ARG 0.007 0.001 ARG D 226 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 178 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7316 (mp) REVERT: A 556 ASP cc_start: 0.7672 (t0) cc_final: 0.7265 (t0) REVERT: D 153 TRP cc_start: 0.6193 (t-100) cc_final: 0.5664 (t-100) REVERT: E 18 PHE cc_start: 0.6564 (m-80) cc_final: 0.6230 (t80) REVERT: E 140 MET cc_start: 0.3690 (ppp) cc_final: 0.3100 (ppp) outliers start: 40 outliers final: 26 residues processed: 201 average time/residue: 0.2580 time to fit residues: 76.0590 Evaluate side-chains 188 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 161 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 595 PHE Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain E residue 134 HIS Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 142 optimal weight: 8.9990 chunk 97 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 145 optimal weight: 1.9990 chunk 118 optimal weight: 0.0770 chunk 0 optimal weight: 3.9990 chunk 87 optimal weight: 20.0000 chunk 153 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 GLN A 477 GLN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14709 Z= 0.228 Angle : 0.632 13.036 19778 Z= 0.318 Chirality : 0.042 0.155 2246 Planarity : 0.003 0.061 2468 Dihedral : 10.932 151.327 2018 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.56 % Allowed : 19.58 % Favored : 77.86 % 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: 0.26 (0.21), residues: 1779 helix: 1.38 (0.17), residues: 991 sheet: -0.26 (0.43), residues: 163 loop : -1.72 (0.26), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP D 153 HIS 0.013 0.001 HIS D 157 PHE 0.019 0.001 PHE A 529 TYR 0.022 0.001 TYR E 151 ARG 0.007 0.000 ARG D 226 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 178 time to evaluate : 1.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 500 LEU cc_start: 0.8294 (mt) cc_final: 0.8021 (mt) REVERT: A 534 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7334 (mp) REVERT: A 556 ASP cc_start: 0.7634 (t0) cc_final: 0.7204 (t0) REVERT: E 18 PHE cc_start: 0.6614 (m-80) cc_final: 0.6252 (t80) outliers start: 40 outliers final: 28 residues processed: 202 average time/residue: 0.2632 time to fit residues: 78.1391 Evaluate side-chains 195 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 166 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 595 PHE Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 210 CYS Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/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-5388/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-5388/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-5388/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-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.775 > 50: distance: 27 - 191: 13.078 distance: 70 - 153: 34.057 distance: 73 - 150: 26.192 distance: 110 - 118: 24.157 distance: 118 - 119: 14.461 distance: 119 - 120: 10.088 distance: 119 - 122: 30.971 distance: 120 - 121: 20.928 distance: 120 - 127: 23.640 distance: 122 - 123: 37.878 distance: 123 - 124: 24.223 distance: 124 - 125: 46.061 distance: 124 - 126: 35.058 distance: 127 - 128: 10.926 distance: 128 - 129: 34.707 distance: 128 - 131: 28.081 distance: 129 - 130: 41.853 distance: 129 - 134: 20.936 distance: 131 - 132: 25.091 distance: 131 - 133: 51.552 distance: 134 - 135: 28.308 distance: 135 - 136: 23.666 distance: 135 - 138: 25.342 distance: 136 - 137: 20.686 distance: 136 - 143: 36.149 distance: 138 - 139: 25.419 distance: 139 - 140: 20.577 distance: 140 - 141: 25.887 distance: 140 - 142: 15.274 distance: 143 - 144: 11.474 distance: 143 - 149: 6.060 distance: 144 - 145: 40.596 distance: 144 - 147: 24.496 distance: 145 - 146: 28.287 distance: 145 - 150: 36.629 distance: 147 - 148: 35.773 distance: 148 - 149: 26.979 distance: 150 - 151: 16.434 distance: 151 - 152: 24.475 distance: 151 - 154: 40.795 distance: 152 - 153: 9.387 distance: 152 - 158: 16.015 distance: 154 - 155: 7.459 distance: 155 - 156: 5.636 distance: 155 - 157: 41.767 distance: 158 - 159: 8.573 distance: 159 - 160: 30.895 distance: 159 - 162: 32.311 distance: 160 - 161: 9.623 distance: 160 - 167: 14.683 distance: 162 - 163: 18.435 distance: 163 - 164: 7.816 distance: 164 - 165: 16.720 distance: 165 - 166: 17.198 distance: 167 - 168: 16.234 distance: 168 - 169: 17.287 distance: 168 - 171: 16.713 distance: 169 - 170: 33.833 distance: 169 - 179: 7.378 distance: 171 - 172: 7.975 distance: 172 - 173: 5.834 distance: 172 - 174: 4.391 distance: 173 - 175: 10.292 distance: 174 - 176: 21.335 distance: 175 - 177: 5.556 distance: 176 - 177: 12.918 distance: 177 - 178: 12.998 distance: 179 - 180: 9.783 distance: 180 - 181: 12.536 distance: 180 - 183: 19.722 distance: 181 - 182: 26.744 distance: 181 - 188: 25.851 distance: 183 - 184: 46.483 distance: 184 - 185: 30.292 distance: 185 - 186: 42.235 distance: 186 - 187: 42.673 distance: 188 - 189: 16.359 distance: 189 - 190: 28.753 distance: 190 - 191: 28.407 distance: 190 - 192: 26.552 distance: 192 - 193: 32.009 distance: 193 - 194: 21.508 distance: 193 - 196: 23.165 distance: 194 - 195: 34.096 distance: 194 - 200: 27.944 distance: 196 - 197: 26.906 distance: 197 - 198: 16.219 distance: 197 - 199: 27.916