Starting phenix.real_space_refine on Fri Mar 15 16:15:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rwc_24714/03_2024/7rwc_24714.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rwc_24714/03_2024/7rwc_24714.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rwc_24714/03_2024/7rwc_24714.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rwc_24714/03_2024/7rwc_24714.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rwc_24714/03_2024/7rwc_24714.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rwc_24714/03_2024/7rwc_24714.pdb" } resolution = 3.8 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= 0.006 sd= 0.117 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: 4 Type Number sf(0) Gaussians S 47 5.16 5 C 7857 2.51 5 N 2070 2.21 5 O 2136 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 460": "OE1" <-> "OE2" Residue "A PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 582": "OE1" <-> "OE2" Residue "B TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 434": "OE1" <-> "OE2" Residue "B GLU 454": "OE1" <-> "OE2" Residue "B GLU 457": "OE1" <-> "OE2" Residue "B PHE 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 98": "OE1" <-> "OE2" Residue "M ASP 176": "OD1" <-> "OD2" Residue "M TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 93": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12110 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4551 Classifications: {'peptide': 613} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 22, 'TRANS': 590} Unresolved non-hydrogen bonds: 290 Unresolved non-hydrogen angles: 347 Unresolved non-hydrogen dihedrals: 236 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 17, 'GLU:plan': 22, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 196 Chain: "B" Number of atoms: 3760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 3760 Classifications: {'peptide': 557} Incomplete info: {'truncation_to_alanine': 201} Link IDs: {'PTRANS': 26, 'TRANS': 530} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 663 Unresolved non-hydrogen angles: 817 Unresolved non-hydrogen dihedrals: 525 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 29, 'TYR:plan': 2, 'ASN:plan1': 21, 'HIS:plan': 2, 'GLU:plan': 35, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 402 Chain: "M" Number of atoms: 2644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 2644 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 137} Link IDs: {'PTRANS': 17, 'TRANS': 375} Chain breaks: 2 Unresolved non-hydrogen bonds: 540 Unresolved non-hydrogen angles: 646 Unresolved non-hydrogen dihedrals: 453 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 20, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 325 Chain: "S" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1115 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'TRANS': 141} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 60 Chain: "P" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 40 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'UNK:plan-1': 8} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 6.73, per 1000 atoms: 0.56 Number of scatterers: 12110 At special positions: 0 Unit cell: (128.76, 115.44, 108.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 47 16.00 O 2136 8.00 N 2070 7.00 C 7857 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: 4.45 Conformation dependent library (CDL) restraints added in 2.4 seconds 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3312 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 10 sheets defined 62.1% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 11 through 22 removed outlier: 3.663A pdb=" N VAL A 15 " --> pdb=" O ARG A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 45 Processing helix chain 'A' and resid 51 through 69 removed outlier: 3.859A pdb=" N GLY A 69 " --> pdb=" O ILE A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 84 removed outlier: 3.749A pdb=" N VAL A 80 " --> pdb=" O HIS A 76 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER A 84 " --> pdb=" O VAL A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 101 Processing helix chain 'A' and resid 105 through 121 removed outlier: 3.509A pdb=" N ALA A 121 " --> pdb=" O LYS A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 139 removed outlier: 4.009A pdb=" N VAL A 138 " --> pdb=" O CYS A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 147 Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 161 through 179 Processing helix chain 'A' and resid 180 through 183 removed outlier: 3.794A pdb=" N VAL A 183 " --> pdb=" O PRO A 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 180 through 183' Processing helix chain 'A' and resid 188 through 197 removed outlier: 4.040A pdb=" N ASN A 197 " --> pdb=" O VAL A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 218 Processing helix chain 'A' and resid 224 through 238 removed outlier: 3.891A pdb=" N LEU A 228 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 267 Processing helix chain 'A' and resid 273 through 293 Processing helix chain 'A' and resid 299 through 321 removed outlier: 3.940A pdb=" N SER A 303 " --> pdb=" O LYS A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 338 Processing helix chain 'A' and resid 342 through 357 removed outlier: 3.742A pdb=" N ARG A 346 " --> pdb=" O GLU A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 369 removed outlier: 4.045A pdb=" N HIS A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 379 Processing helix chain 'A' and resid 384 through 397 Processing helix chain 'A' and resid 401 through 415 removed outlier: 3.770A pdb=" N THR A 415 " --> pdb=" O SER A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 removed outlier: 6.030A pdb=" N SER A 419 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE A 420 " --> pdb=" O ASP A 417 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG A 421 " --> pdb=" O TYR A 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 416 through 421' Processing helix chain 'A' and resid 422 through 435 Processing helix chain 'A' and resid 438 through 453 removed outlier: 3.960A pdb=" N TYR A 442 " --> pdb=" O ASP A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 473 removed outlier: 3.855A pdb=" N ASP A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 488 removed outlier: 3.950A pdb=" N GLN A 488 " --> pdb=" O PHE A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 507 Processing helix chain 'A' and resid 508 through 511 removed outlier: 3.644A pdb=" N ILE A 511 " --> pdb=" O GLY A 508 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 508 through 511' Processing helix chain 'A' and resid 514 through 517 Processing helix chain 'A' and resid 518 through 531 removed outlier: 3.505A pdb=" N GLN A 522 " --> pdb=" O SER A 518 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS A 531 " --> pdb=" O HIS A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 552 removed outlier: 3.982A pdb=" N ASN A 550 " --> pdb=" O ILE A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 563 Processing helix chain 'A' and resid 565 through 570 removed outlier: 3.544A pdb=" N LYS A 570 " --> pdb=" O ASP A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 590 removed outlier: 3.632A pdb=" N ALA A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 599 removed outlier: 3.522A pdb=" N LEU A 599 " --> pdb=" O LEU A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 620 removed outlier: 3.704A pdb=" N ALA A 614 " --> pdb=" O SER A 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 44 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 58 Processing helix chain 'B' and resid 62 through 78 removed outlier: 3.655A pdb=" N TYR B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 86 No H-bonds generated for 'chain 'B' and resid 84 through 86' Processing helix chain 'B' and resid 87 through 95 Processing helix chain 'B' and resid 99 through 113 removed outlier: 3.892A pdb=" N ILE B 113 " --> pdb=" O THR B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 130 removed outlier: 4.651A pdb=" N GLU B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) Proline residue: B 125 - end of helix removed outlier: 3.862A pdb=" N LYS B 128 " --> pdb=" O GLU B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 149 Processing helix chain 'B' and resid 155 through 170 removed outlier: 3.900A pdb=" N GLN B 159 " --> pdb=" O MET B 155 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP B 167 " --> pdb=" O ASP B 163 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA B 170 " --> pdb=" O ARG B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 188 removed outlier: 3.725A pdb=" N VAL B 177 " --> pdb=" O ASN B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 214 removed outlier: 3.549A pdb=" N GLU B 213 " --> pdb=" O THR B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 227 Processing helix chain 'B' and resid 233 through 245 Processing helix chain 'B' and resid 254 through 266 Processing helix chain 'B' and resid 276 through 291 Proline residue: B 286 - end of helix Processing helix chain 'B' and resid 295 through 313 Processing helix chain 'B' and resid 320 through 325 removed outlier: 3.616A pdb=" N VAL B 323 " --> pdb=" O GLU B 320 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE B 325 " --> pdb=" O LYS B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 346 Processing helix chain 'B' and resid 347 through 349 No H-bonds generated for 'chain 'B' and resid 347 through 349' Processing helix chain 'B' and resid 350 through 362 Processing helix chain 'B' and resid 366 through 384 removed outlier: 3.785A pdb=" N GLY B 378 " --> pdb=" O VAL B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 400 Processing helix chain 'B' and resid 403 through 421 removed outlier: 3.515A pdb=" N ARG B 419 " --> pdb=" O ARG B 415 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS B 420 " --> pdb=" O ASP B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 434 removed outlier: 3.960A pdb=" N THR B 431 " --> pdb=" O SER B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 455 Processing helix chain 'B' and resid 461 through 470 removed outlier: 3.525A pdb=" N LEU B 470 " --> pdb=" O LEU B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 495 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 516 through 533 Processing helix chain 'B' and resid 533 through 542 removed outlier: 3.596A pdb=" N LEU B 542 " --> pdb=" O LYS B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 565 removed outlier: 3.768A pdb=" N CYS B 565 " --> pdb=" O ASP B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 575 removed outlier: 4.046A pdb=" N VAL B 573 " --> pdb=" O SER B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 581 Processing helix chain 'M' and resid 25 through 38 removed outlier: 3.530A pdb=" N VAL M 29 " --> pdb=" O GLY M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 94 removed outlier: 3.572A pdb=" N VAL M 78 " --> pdb=" O ASN M 74 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE M 79 " --> pdb=" O ALA M 75 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 104 Processing helix chain 'M' and resid 104 through 115 Processing helix chain 'M' and resid 125 through 131 removed outlier: 3.955A pdb=" N THR M 131 " --> pdb=" O GLY M 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 379 through 383 removed outlier: 3.603A pdb=" N ALA M 382 " --> pdb=" O LYS M 379 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG M 383 " --> pdb=" O LYS M 380 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 379 through 383' Processing helix chain 'M' and resid 414 through 418 Processing helix chain 'S' and resid 24 through 42 removed outlier: 3.902A pdb=" N GLN S 29 " --> pdb=" O ASP S 25 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL S 41 " --> pdb=" O ALA S 37 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG S 42 " --> pdb=" O VAL S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 77 through 96 Processing helix chain 'S' and resid 99 through 106 Processing helix chain 'S' and resid 106 through 118 Processing helix chain 'S' and resid 127 through 137 removed outlier: 3.604A pdb=" N VAL S 131 " --> pdb=" O SER S 127 " (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 19 removed outlier: 3.999A pdb=" N ILE M 16 " --> pdb=" O ILE M 7 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL M 68 " --> pdb=" O GLY M 4 " (cutoff:3.500A) removed outlier: 3.571A 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 removed outlier: 3.793A pdb=" N ASP M 117 " --> pdb=" O TYR M 120 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 172 through 173 removed outlier: 4.268A pdb=" N GLU M 172 " --> pdb=" O TYR M 205 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 176 through 185 removed outlier: 3.653A pdb=" N VAL M 201 " --> pdb=" O ASP M 176 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU M 178 " --> pdb=" O ARG M 199 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER M 193 " --> pdb=" O LEU M 184 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLY M 198 " --> pdb=" O ARG M 276 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ARG M 276 " --> pdb=" O GLY M 198 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL M 200 " --> pdb=" O LEU M 274 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET M 202 " --> pdb=" O PHE M 272 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE M 272 " --> pdb=" O MET M 202 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 264 through 265 removed outlier: 3.930A pdb=" N PHE M 265 " --> pdb=" O CYS M 212 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N CYS M 212 " --> pdb=" O PHE M 265 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 289 through 291 removed outlier: 3.574A pdb=" N VAL M 306 " --> pdb=" O ILE M 290 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL M 303 " --> pdb=" O ALA M 368 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE M 366 " --> pdb=" O VAL M 305 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE M 307 " --> pdb=" O SER M 364 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER M 364 " --> pdb=" O ILE M 307 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN M 334 " --> pdb=" O GLU M 369 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU M 371 " --> pdb=" O GLY M 332 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N GLY M 332 " --> pdb=" O GLU M 371 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 341 through 345 removed outlier: 3.669A pdb=" N LYS M 341 " --> pdb=" O LYS M 354 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ARG M 357 " --> pdb=" O GLN M 318 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N GLN M 318 " --> pdb=" O ARG M 357 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N LYS M 319 " --> pdb=" O GLU M 391 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU M 391 " --> pdb=" O LYS M 319 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'M' and resid 341 through 345 removed outlier: 3.669A pdb=" N LYS M 341 " --> pdb=" O LYS M 354 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ARG M 357 " --> pdb=" O GLN M 318 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N GLN M 318 " --> pdb=" O ARG M 357 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N LYS M 319 " --> pdb=" O GLU M 391 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU M 391 " --> pdb=" O LYS M 319 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR M 431 " --> pdb=" O MET M 388 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 14 through 19 removed outlier: 6.998A pdb=" N THR S 14 " --> pdb=" O ASN S 9 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ASN S 9 " --> pdb=" O THR S 14 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU S 16 " --> pdb=" O ILE S 7 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N CYS S 70 " --> pdb=" O ARG S 3 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE S 5 " --> pdb=" O CYS S 68 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N CYS S 68 " --> pdb=" O ILE S 5 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ILE S 7 " --> pdb=" O TYR S 66 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N TYR S 66 " --> pdb=" O ILE S 7 " (cutoff:3.500A) 765 hydrogen bonds defined for protein. 2232 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: 3.43 Time building geometry restraints manager: 4.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3895 1.34 - 1.45: 1375 1.45 - 1.57: 6994 1.57 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 12334 Sorted by residual: bond pdb=" CA THR A 238 " pdb=" CB THR A 238 " ideal model delta sigma weight residual 1.524 1.547 -0.023 1.62e-02 3.81e+03 2.00e+00 bond pdb=" CB VAL A 483 " pdb=" CG1 VAL A 483 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.69e+00 bond pdb=" CA MET A 10 " pdb=" C MET A 10 " ideal model delta sigma weight residual 1.520 1.534 -0.014 1.20e-02 6.94e+03 1.27e+00 bond pdb=" N ILE M 430 " pdb=" CA ILE M 430 " ideal model delta sigma weight residual 1.474 1.457 0.017 1.57e-02 4.06e+03 1.17e+00 bond pdb=" CB GLU S 82 " pdb=" CG GLU S 82 " ideal model delta sigma weight residual 1.520 1.488 0.032 3.00e-02 1.11e+03 1.11e+00 ... (remaining 12329 not shown) Histogram of bond angle deviations from ideal: 99.48 - 106.39: 290 106.39 - 113.29: 7066 113.29 - 120.20: 4159 120.20 - 127.10: 5289 127.10 - 134.00: 104 Bond angle restraints: 16908 Sorted by residual: angle pdb=" N VAL B 506 " pdb=" CA VAL B 506 " pdb=" C VAL B 506 " ideal model delta sigma weight residual 113.53 108.45 5.08 9.80e-01 1.04e+00 2.69e+01 angle pdb=" N LEU A 201 " pdb=" CA LEU A 201 " pdb=" C LEU A 201 " ideal model delta sigma weight residual 114.75 109.12 5.63 1.26e+00 6.30e-01 2.00e+01 angle pdb=" N GLU B 501 " pdb=" CA GLU B 501 " pdb=" C GLU B 501 " ideal model delta sigma weight residual 114.16 108.36 5.80 1.48e+00 4.57e-01 1.54e+01 angle pdb=" CA GLN A 199 " pdb=" C GLN A 199 " pdb=" O GLN A 199 " ideal model delta sigma weight residual 121.67 117.91 3.76 1.26e+00 6.30e-01 8.91e+00 angle pdb=" N SER A 384 " pdb=" CA SER A 384 " pdb=" C SER A 384 " ideal model delta sigma weight residual 113.88 110.43 3.45 1.23e+00 6.61e-01 7.86e+00 ... (remaining 16903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 6755 17.52 - 35.03: 491 35.03 - 52.55: 81 52.55 - 70.07: 6 70.07 - 87.58: 10 Dihedral angle restraints: 7343 sinusoidal: 2267 harmonic: 5076 Sorted by residual: dihedral pdb=" CA SER A 458 " pdb=" C SER A 458 " pdb=" N GLU A 459 " pdb=" CA GLU A 459 " ideal model delta harmonic sigma weight residual 180.00 157.89 22.11 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA GLU A 460 " pdb=" C GLU A 460 " pdb=" N VAL A 461 " pdb=" CA VAL A 461 " ideal model delta harmonic sigma weight residual 180.00 162.63 17.37 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ASN M 74 " pdb=" C ASN M 74 " pdb=" N ALA M 75 " pdb=" CA ALA M 75 " ideal model delta harmonic sigma weight residual -180.00 -162.64 -17.36 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 7340 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1461 0.038 - 0.075: 511 0.075 - 0.113: 134 0.113 - 0.151: 25 0.151 - 0.188: 3 Chirality restraints: 2134 Sorted by residual: chirality pdb=" CG LEU A 201 " pdb=" CB LEU A 201 " pdb=" CD1 LEU A 201 " pdb=" CD2 LEU A 201 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.87e-01 chirality pdb=" CB THR A 238 " pdb=" CA THR A 238 " pdb=" OG1 THR A 238 " pdb=" CG2 THR A 238 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.19e-01 chirality pdb=" CA ILE S 58 " pdb=" N ILE S 58 " pdb=" C ILE S 58 " pdb=" CB ILE S 58 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.04e-01 ... (remaining 2131 not shown) Planarity restraints: 2134 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 268 " 0.061 5.00e-02 4.00e+02 9.20e-02 1.35e+01 pdb=" N PRO A 269 " -0.159 5.00e-02 4.00e+02 pdb=" CA PRO A 269 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 269 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 269 " -0.027 5.00e-02 4.00e+02 4.05e-02 2.63e+00 pdb=" N PRO A 270 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 270 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 270 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 22 " 0.007 2.00e-02 2.50e+03 1.46e-02 2.13e+00 pdb=" C ASN A 22 " -0.025 2.00e-02 2.50e+03 pdb=" O ASN A 22 " 0.010 2.00e-02 2.50e+03 pdb=" N CYS A 23 " 0.008 2.00e-02 2.50e+03 ... (remaining 2131 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 417 2.72 - 3.27: 12578 3.27 - 3.81: 19597 3.81 - 4.36: 21547 4.36 - 4.90: 38183 Nonbonded interactions: 92322 Sorted by model distance: nonbonded pdb=" O LEU B 507 " pdb=" OG1 THR B 511 " model vdw 2.175 2.440 nonbonded pdb=" OG SER M 97 " pdb=" OD1 ASN M 100 " model vdw 2.239 2.440 nonbonded pdb=" OH TYR S 62 " pdb=" ND1 HIS S 85 " model vdw 2.264 2.520 nonbonded pdb=" O PHE M 287 " pdb=" OH TYR M 431 " model vdw 2.265 2.440 nonbonded pdb=" OD1 ASP A 321 " pdb=" OG SER A 359 " model vdw 2.299 2.440 ... (remaining 92317 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.230 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 33.380 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 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 : 0.004 0.043 12334 Z= 0.242 Angle : 0.605 7.802 16908 Z= 0.334 Chirality : 0.041 0.188 2134 Planarity : 0.004 0.092 2134 Dihedral : 12.871 87.582 4031 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.55 % Favored : 94.39 % Rotamer: Outliers : 0.09 % Allowed : 0.28 % Favored : 99.63 % 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: 0.33 (0.21), residues: 1693 helix: 1.43 (0.17), residues: 966 sheet: -0.16 (0.44), residues: 156 loop : -1.82 (0.24), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 462 HIS 0.011 0.001 HIS A 76 PHE 0.015 0.001 PHE A 66 TYR 0.017 0.001 TYR A 463 ARG 0.004 0.000 ARG B 520 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 173 time to evaluate : 1.299 Fit side-chains revert: symmetry clash REVERT: A 62 LEU cc_start: 0.7544 (tp) cc_final: 0.6923 (tp) REVERT: A 552 PHE cc_start: 0.7651 (m-80) cc_final: 0.7168 (m-10) REVERT: B 379 ARG cc_start: 0.7620 (ttm170) cc_final: 0.7406 (ttp-170) REVERT: M 187 PRO cc_start: 0.7193 (Cg_exo) cc_final: 0.6852 (Cg_endo) outliers start: 1 outliers final: 1 residues processed: 174 average time/residue: 0.2128 time to fit residues: 55.3739 Evaluate side-chains 138 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 137 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 142 optimal weight: 0.5980 chunk 128 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 68 optimal weight: 0.4980 chunk 132 optimal weight: 6.9990 chunk 51 optimal weight: 0.1980 chunk 80 optimal weight: 0.5980 chunk 98 optimal weight: 0.8980 chunk 153 optimal weight: 0.0980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS A 200 HIS A 387 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12334 Z= 0.184 Angle : 0.521 7.553 16908 Z= 0.275 Chirality : 0.041 0.190 2134 Planarity : 0.004 0.071 2134 Dihedral : 3.911 24.928 1818 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.67 % Allowed : 9.62 % Favored : 88.71 % 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: 0.44 (0.21), residues: 1693 helix: 1.49 (0.17), residues: 980 sheet: -0.06 (0.46), residues: 152 loop : -1.81 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 462 HIS 0.004 0.001 HIS A 76 PHE 0.014 0.001 PHE M 93 TYR 0.013 0.001 TYR A 463 ARG 0.004 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 157 time to evaluate : 1.345 Fit side-chains revert: symmetry clash REVERT: M 162 ARG cc_start: 0.3590 (ptt180) cc_final: 0.2875 (mpp80) REVERT: M 187 PRO cc_start: 0.7229 (Cg_exo) cc_final: 0.6825 (Cg_endo) REVERT: M 216 MET cc_start: 0.6123 (ppp) cc_final: 0.5782 (ppp) outliers start: 18 outliers final: 8 residues processed: 165 average time/residue: 0.1990 time to fit residues: 50.2932 Evaluate side-chains 153 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 145 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 550 ASN Chi-restraints excluded: chain B residue 342 MET Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain M residue 316 LEU Chi-restraints excluded: chain S residue 127 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 127 optimal weight: 0.6980 chunk 104 optimal weight: 5.9990 chunk 42 optimal weight: 0.5980 chunk 153 optimal weight: 10.0000 chunk 166 optimal weight: 0.5980 chunk 136 optimal weight: 8.9990 chunk 152 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 349 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12334 Z= 0.236 Angle : 0.518 6.774 16908 Z= 0.274 Chirality : 0.041 0.215 2134 Planarity : 0.004 0.063 2134 Dihedral : 3.881 26.522 1818 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.13 % Allowed : 11.93 % Favored : 85.94 % 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: 0.40 (0.21), residues: 1693 helix: 1.46 (0.17), residues: 977 sheet: -0.16 (0.46), residues: 152 loop : -1.81 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 462 HIS 0.005 0.001 HIS S 85 PHE 0.015 0.001 PHE A 66 TYR 0.013 0.001 TYR A 418 ARG 0.003 0.000 ARG S 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 154 time to evaluate : 1.432 Fit side-chains revert: symmetry clash REVERT: B 208 LEU cc_start: 0.6350 (OUTLIER) cc_final: 0.6020 (tp) REVERT: M 77 MET cc_start: 0.7901 (ttp) cc_final: 0.7389 (ttp) REVERT: M 162 ARG cc_start: 0.3802 (ptt180) cc_final: 0.2990 (mpp80) REVERT: M 187 PRO cc_start: 0.7268 (Cg_exo) cc_final: 0.6847 (Cg_endo) REVERT: M 216 MET cc_start: 0.6000 (ppp) cc_final: 0.5519 (ppp) outliers start: 23 outliers final: 16 residues processed: 166 average time/residue: 0.1933 time to fit residues: 49.6569 Evaluate side-chains 160 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 143 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 550 ASN Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 342 MET Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 305 VAL Chi-restraints excluded: chain M residue 316 LEU Chi-restraints excluded: chain M residue 320 ILE Chi-restraints excluded: chain M residue 349 ASN Chi-restraints excluded: chain S residue 127 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 151 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 154 optimal weight: 0.6980 chunk 163 optimal weight: 0.5980 chunk 80 optimal weight: 0.5980 chunk 146 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 349 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12334 Z= 0.244 Angle : 0.520 6.714 16908 Z= 0.274 Chirality : 0.041 0.233 2134 Planarity : 0.004 0.060 2134 Dihedral : 3.879 27.876 1818 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.24 % Allowed : 13.69 % Favored : 83.07 % 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: 0.40 (0.21), residues: 1693 helix: 1.48 (0.17), residues: 977 sheet: -0.25 (0.45), residues: 152 loop : -1.81 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 462 HIS 0.005 0.001 HIS B 566 PHE 0.013 0.001 PHE M 93 TYR 0.015 0.001 TYR A 418 ARG 0.004 0.000 ARG S 3 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 151 time to evaluate : 1.171 Fit side-chains revert: symmetry clash REVERT: B 208 LEU cc_start: 0.6337 (OUTLIER) cc_final: 0.6041 (tp) REVERT: B 562 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8062 (tm-30) REVERT: M 1 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.7184 (mtm) REVERT: M 162 ARG cc_start: 0.4064 (ptt180) cc_final: 0.3296 (mpp80) REVERT: M 216 MET cc_start: 0.5960 (ppp) cc_final: 0.5482 (ppp) outliers start: 35 outliers final: 24 residues processed: 174 average time/residue: 0.1993 time to fit residues: 53.3677 Evaluate side-chains 169 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 143 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 550 ASN Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 342 MET Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain M residue 303 VAL Chi-restraints excluded: chain M residue 316 LEU Chi-restraints excluded: chain M residue 320 ILE Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain S residue 127 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 136 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 139 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 146 optimal weight: 8.9990 chunk 41 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 349 ASN S 48 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 12334 Z= 0.372 Angle : 0.606 8.674 16908 Z= 0.317 Chirality : 0.044 0.223 2134 Planarity : 0.004 0.060 2134 Dihedral : 4.101 19.602 1816 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 4.26 % Allowed : 15.73 % Favored : 80.02 % 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: 0.07 (0.21), residues: 1693 helix: 1.18 (0.17), residues: 985 sheet: -0.42 (0.44), residues: 155 loop : -1.90 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 527 HIS 0.007 0.001 HIS S 85 PHE 0.016 0.002 PHE A 66 TYR 0.017 0.002 TYR A 418 ARG 0.006 0.001 ARG B 522 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 147 time to evaluate : 1.051 Fit side-chains REVERT: A 577 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.6859 (tt0) REVERT: B 562 GLU cc_start: 0.8861 (tm-30) cc_final: 0.8058 (tm-30) REVERT: M 162 ARG cc_start: 0.3847 (ptt180) cc_final: 0.3076 (mpp80) REVERT: M 216 MET cc_start: 0.5768 (ppp) cc_final: 0.5330 (ppp) REVERT: S 3 ARG cc_start: 0.8137 (tpp-160) cc_final: 0.7798 (tpp-160) outliers start: 46 outliers final: 33 residues processed: 181 average time/residue: 0.1985 time to fit residues: 54.7846 Evaluate side-chains 178 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 144 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 550 ASN Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 342 MET Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 303 VAL Chi-restraints excluded: chain M residue 305 VAL Chi-restraints excluded: chain M residue 316 LEU Chi-restraints excluded: chain M residue 320 ILE Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain S residue 127 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 54 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 163 optimal weight: 0.6980 chunk 135 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 157 optimal weight: 0.0060 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12334 Z= 0.205 Angle : 0.510 6.678 16908 Z= 0.270 Chirality : 0.041 0.229 2134 Planarity : 0.004 0.059 2134 Dihedral : 3.934 20.322 1816 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.02 % Favored : 94.92 % Rotamer: Outliers : 3.79 % Allowed : 18.04 % Favored : 78.17 % 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: 0.28 (0.21), residues: 1693 helix: 1.40 (0.17), residues: 982 sheet: -0.37 (0.45), residues: 152 loop : -1.90 (0.25), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 462 HIS 0.004 0.001 HIS M 57 PHE 0.013 0.001 PHE M 93 TYR 0.014 0.001 TYR A 418 ARG 0.006 0.000 ARG B 313 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 148 time to evaluate : 1.204 Fit side-chains REVERT: A 577 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.6763 (tt0) REVERT: B 208 LEU cc_start: 0.6193 (OUTLIER) cc_final: 0.5916 (tp) REVERT: B 562 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8156 (tm-30) REVERT: M 77 MET cc_start: 0.7751 (ttp) cc_final: 0.7049 (ttp) REVERT: M 216 MET cc_start: 0.5696 (ppp) cc_final: 0.5243 (ppp) outliers start: 41 outliers final: 28 residues processed: 180 average time/residue: 0.1999 time to fit residues: 54.8857 Evaluate side-chains 173 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 143 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 550 ASN Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 342 MET Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 303 VAL Chi-restraints excluded: chain M residue 316 LEU Chi-restraints excluded: chain M residue 320 ILE Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain S residue 127 SER Chi-restraints excluded: chain S residue 135 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.155 > 50: distance: 26 - 44: 35.150 distance: 32 - 52: 26.990 distance: 40 - 44: 33.721 distance: 44 - 45: 24.185 distance: 45 - 46: 54.097 distance: 45 - 48: 47.937 distance: 46 - 52: 21.741 distance: 48 - 49: 55.950 distance: 49 - 50: 40.784 distance: 52 - 53: 21.155 distance: 53 - 54: 57.704 distance: 53 - 56: 58.313 distance: 54 - 55: 43.636 distance: 54 - 57: 41.582 distance: 57 - 58: 47.976 distance: 58 - 59: 12.460 distance: 58 - 61: 28.273 distance: 59 - 60: 40.665 distance: 61 - 62: 40.613 distance: 63 - 64: 39.835 distance: 64 - 67: 38.746 distance: 65 - 66: 40.374 distance: 65 - 68: 10.315 distance: 68 - 69: 32.883 distance: 69 - 70: 30.964 distance: 70 - 71: 4.081 distance: 70 - 73: 6.977 distance: 73 - 74: 39.913 distance: 74 - 75: 23.475 distance: 74 - 77: 10.636 distance: 75 - 76: 53.553 distance: 75 - 81: 47.193 distance: 76 - 103: 49.165 distance: 77 - 78: 8.635 distance: 81 - 82: 42.066 distance: 82 - 83: 56.029 distance: 82 - 85: 33.225 distance: 83 - 84: 56.949 distance: 83 - 89: 57.192 distance: 84 - 110: 35.406 distance: 85 - 86: 10.346 distance: 85 - 87: 51.285 distance: 86 - 88: 5.277 distance: 89 - 90: 55.197 distance: 90 - 91: 55.748 distance: 91 - 92: 56.144 distance: 91 - 94: 69.859 distance: 92 - 118: 36.504 distance: 94 - 95: 56.252 distance: 95 - 96: 41.320 distance: 95 - 98: 40.450 distance: 96 - 97: 38.810 distance: 96 - 103: 68.254 distance: 97 - 122: 36.140 distance: 98 - 99: 34.279 distance: 99 - 100: 32.471 distance: 103 - 104: 49.998 distance: 104 - 105: 54.601 distance: 104 - 107: 14.389 distance: 105 - 106: 26.978 distance: 105 - 110: 24.988 distance: 106 - 128: 23.667 distance: 107 - 108: 31.822 distance: 107 - 109: 30.634