Starting phenix.real_space_refine on Sun Dec 10 04:40:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bxu_30238/12_2023/7bxu_30238.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bxu_30238/12_2023/7bxu_30238.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/7bxu_30238/12_2023/7bxu_30238.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bxu_30238/12_2023/7bxu_30238.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bxu_30238/12_2023/7bxu_30238.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bxu_30238/12_2023/7bxu_30238.pdb" } 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= 0.007 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 84 5.16 5 C 8704 2.51 5 N 2242 2.21 5 O 2414 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 110": "NH1" <-> "NH2" Residue "A GLU 103": "OE1" <-> "OE2" Residue "A GLU 313": "OE1" <-> "OE2" Residue "A ARG 561": "NH1" <-> "NH2" Residue "A ARG 639": "NH1" <-> "NH2" Residue "A ARG 640": "NH1" <-> "NH2" Residue "A ARG 641": "NH1" <-> "NH2" Residue "A ARG 674": "NH1" <-> "NH2" Residue "A ARG 717": "NH1" <-> "NH2" Residue "A PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 761": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 767": "NH1" <-> "NH2" Residue "A ARG 775": "NH1" <-> "NH2" Residue "A ARG 789": "NH1" <-> "NH2" Residue "D ARG 110": "NH1" <-> "NH2" Residue "B GLU 103": "OE1" <-> "OE2" Residue "B GLU 313": "OE1" <-> "OE2" Residue "B ARG 561": "NH1" <-> "NH2" Residue "B ARG 639": "NH1" <-> "NH2" Residue "B ARG 640": "NH1" <-> "NH2" Residue "B ARG 641": "NH1" <-> "NH2" Residue "B ARG 674": "NH1" <-> "NH2" Residue "B ARG 717": "NH1" <-> "NH2" Residue "B PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 761": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 767": "NH1" <-> "NH2" Residue "B ARG 775": "NH1" <-> "NH2" Residue "B ARG 789": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 13444 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1552 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 9, 'TRANS': 193} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "A" Number of atoms: 5072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 5072 Classifications: {'peptide': 673} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 29, 'TRANS': 643} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 224 Unresolved non-hydrogen dihedrals: 154 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 112 Chain: "D" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1552 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 9, 'TRANS': 193} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "B" Number of atoms: 5072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 5072 Classifications: {'peptide': 673} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 29, 'TRANS': 643} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 224 Unresolved non-hydrogen dihedrals: 154 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 112 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "D" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 7.74, per 1000 atoms: 0.58 Number of scatterers: 13444 At special positions: 0 Unit cell: (104.76, 98.28, 140.4, 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 84 16.00 O 2414 8.00 N 2242 7.00 C 8704 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS C 101 " - pdb=" SG CYS C 115 " distance=2.05 Simple disulfide: pdb=" SG CYS C 112 " - pdb=" SG CYS C 171 " distance=1.54 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 101 " - pdb=" SG CYS D 115 " distance=2.05 Simple disulfide: pdb=" SG CYS D 112 " - pdb=" SG CYS D 171 " distance=1.54 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 Links applied NAG-ASN " NAG C 401 " - " ASN C 93 " " NAG C 402 " - " ASN C 263 " " NAG C 403 " - " ASN C 163 " " NAG C 404 " - " ASN C 184 " " NAG C 405 " - " ASN C 194 " " NAG C 406 " - " ASN C 216 " " NAG C 407 " - " ASN C 128 " " NAG D 401 " - " ASN D 93 " " NAG D 402 " - " ASN D 263 " " NAG D 403 " - " ASN D 163 " " NAG D 404 " - " ASN D 184 " " NAG D 405 " - " ASN D 194 " " NAG D 406 " - " ASN D 216 " " NAG D 407 " - " ASN D 128 " Time building additional restraints: 5.38 Conformation dependent library (CDL) restraints added in 2.7 seconds 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3284 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 6 sheets defined 61.1% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'C' and resid 84 through 105 removed outlier: 3.635A pdb=" N GLU C 97 " --> pdb=" O ASN C 93 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER C 105 " --> pdb=" O CYS C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 116 through 131 removed outlier: 4.050A pdb=" N GLN C 120 " --> pdb=" O TYR C 116 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN C 121 " --> pdb=" O PRO C 117 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL C 122 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL C 123 " --> pdb=" O PHE C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 148 Processing helix chain 'C' and resid 153 through 170 Processing helix chain 'C' and resid 184 through 203 removed outlier: 3.991A pdb=" N PHE C 200 " --> pdb=" O THR C 196 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU C 201 " --> pdb=" O LEU C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 223 removed outlier: 4.157A pdb=" N LYS C 222 " --> pdb=" O GLU C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 242 removed outlier: 4.458A pdb=" N THR C 230 " --> pdb=" O GLU C 226 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU C 231 " --> pdb=" O ALA C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 271 removed outlier: 3.562A pdb=" N THR C 265 " --> pdb=" O ALA C 261 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER C 270 " --> pdb=" O ARG C 266 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG C 271 " --> pdb=" O LYS C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 293 removed outlier: 4.339A pdb=" N SER C 289 " --> pdb=" O VAL C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 305 removed outlier: 3.898A pdb=" N LEU C 301 " --> pdb=" O VAL C 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 115 removed outlier: 3.658A pdb=" N ARG A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 163 removed outlier: 3.934A pdb=" N VAL A 128 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLY A 134 " --> pdb=" O CYS A 130 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL A 140 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 147 " --> pdb=" O PHE A 143 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE A 159 " --> pdb=" O LYS A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 196 removed outlier: 3.941A pdb=" N LEU A 178 " --> pdb=" O PHE A 174 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL A 187 " --> pdb=" O ASN A 183 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 234 through 239 Processing helix chain 'A' and resid 249 through 257 removed outlier: 3.948A pdb=" N ILE A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 262 removed outlier: 3.780A pdb=" N ILE A 261 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 257 through 262' Processing helix chain 'A' and resid 284 through 294 removed outlier: 3.783A pdb=" N ALA A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 303 through 315 removed outlier: 3.552A pdb=" N GLY A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 308 " --> pdb=" O PRO A 304 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 335 removed outlier: 3.637A pdb=" N THR A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE A 329 " --> pdb=" O TRP A 325 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A 333 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N SER A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N THR A 335 " --> pdb=" O SER A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 347 removed outlier: 3.675A pdb=" N ILE A 344 " --> pdb=" O PHE A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 373 No H-bonds generated for 'chain 'A' and resid 371 through 373' Processing helix chain 'A' and resid 374 through 388 removed outlier: 3.593A pdb=" N ILE A 379 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL A 384 " --> pdb=" O ALA A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 407 removed outlier: 3.968A pdb=" N ALA A 394 " --> pdb=" O ALA A 390 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 395 " --> pdb=" O VAL A 391 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASN A 396 " --> pdb=" O PHE A 392 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N TYR A 397 " --> pdb=" O ASN A 393 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE A 402 " --> pdb=" O TRP A 398 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE A 407 " --> pdb=" O ARG A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 434 removed outlier: 3.772A pdb=" N GLN A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL A 414 " --> pdb=" O PRO A 410 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE A 415 " --> pdb=" O CYS A 411 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA A 428 " --> pdb=" O THR A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 480 Processing helix chain 'A' and resid 488 through 505 removed outlier: 3.727A pdb=" N VAL A 496 " --> pdb=" O LEU A 492 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N PHE A 499 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR A 505 " --> pdb=" O ALA A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 532 removed outlier: 4.563A pdb=" N ILE A 520 " --> pdb=" O PRO A 516 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 532 " --> pdb=" O PHE A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 560 removed outlier: 4.222A pdb=" N TYR A 547 " --> pdb=" O ASP A 543 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 549 " --> pdb=" O GLY A 545 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA A 552 " --> pdb=" O ALA A 548 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA A 554 " --> pdb=" O MET A 550 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 556 " --> pdb=" O ALA A 552 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY A 557 " --> pdb=" O ALA A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 573 removed outlier: 3.783A pdb=" N VAL A 568 " --> pdb=" O LEU A 564 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE A 569 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A 573 " --> pdb=" O ILE A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 593 removed outlier: 3.881A pdb=" N ILE A 583 " --> pdb=" O TYR A 579 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR A 589 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS A 591 " --> pdb=" O LEU A 587 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 592 " --> pdb=" O MET A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 597 Processing helix chain 'A' and resid 600 through 608 removed outlier: 3.535A pdb=" N MET A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N HIS A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE A 606 " --> pdb=" O TYR A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 652 Processing helix chain 'A' and resid 681 through 690 Processing helix chain 'A' and resid 708 through 713 removed outlier: 3.959A pdb=" N ARG A 712 " --> pdb=" O LEU A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 724 Processing helix chain 'A' and resid 753 through 764 removed outlier: 3.550A pdb=" N LEU A 764 " --> pdb=" O LEU A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 789 removed outlier: 3.755A pdb=" N LEU A 787 " --> pdb=" O THR A 783 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG A 789 " --> pdb=" O LYS A 785 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 105 removed outlier: 3.635A pdb=" N GLU D 97 " --> pdb=" O ASN D 93 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER D 105 " --> pdb=" O CYS D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 115 Processing helix chain 'D' and resid 116 through 131 removed outlier: 4.049A pdb=" N GLN D 120 " --> pdb=" O TYR D 116 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN D 121 " --> pdb=" O PRO D 117 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL D 123 " --> pdb=" O PHE D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 148 Processing helix chain 'D' and resid 153 through 170 Processing helix chain 'D' and resid 184 through 203 removed outlier: 3.992A pdb=" N PHE D 200 " --> pdb=" O THR D 196 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLU D 201 " --> pdb=" O LEU D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 223 removed outlier: 4.158A pdb=" N LYS D 222 " --> pdb=" O GLU D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 242 removed outlier: 4.458A pdb=" N THR D 230 " --> pdb=" O GLU D 226 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU D 231 " --> pdb=" O ALA D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 271 removed outlier: 3.562A pdb=" N THR D 265 " --> pdb=" O ALA D 261 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER D 270 " --> pdb=" O ARG D 266 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG D 271 " --> pdb=" O LYS D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 293 removed outlier: 4.338A pdb=" N SER D 289 " --> pdb=" O VAL D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 305 removed outlier: 3.898A pdb=" N LEU D 301 " --> pdb=" O VAL D 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 115 removed outlier: 3.658A pdb=" N ARG B 112 " --> pdb=" O LEU B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 163 removed outlier: 3.934A pdb=" N VAL B 128 " --> pdb=" O ILE B 124 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE B 129 " --> pdb=" O LYS B 125 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLY B 134 " --> pdb=" O CYS B 130 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE B 135 " --> pdb=" O ALA B 131 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR B 137 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL B 140 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP B 145 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 147 " --> pdb=" O PHE B 143 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU B 149 " --> pdb=" O ASP B 145 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN B 150 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL B 158 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE B 159 " --> pdb=" O LYS B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 196 removed outlier: 3.941A pdb=" N LEU B 178 " --> pdb=" O PHE B 174 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL B 187 " --> pdb=" O ASN B 183 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL B 189 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL B 194 " --> pdb=" O GLY B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 234 through 239 Processing helix chain 'B' and resid 249 through 257 removed outlier: 3.949A pdb=" N ILE B 257 " --> pdb=" O SER B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 262 removed outlier: 3.780A pdb=" N ILE B 261 " --> pdb=" O ILE B 257 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER B 262 " --> pdb=" O ALA B 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 257 through 262' Processing helix chain 'B' and resid 284 through 294 removed outlier: 3.783A pdb=" N ALA B 291 " --> pdb=" O ASP B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 302 Processing helix chain 'B' and resid 303 through 315 removed outlier: 3.552A pdb=" N GLY B 307 " --> pdb=" O ALA B 303 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL B 308 " --> pdb=" O PRO B 304 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU B 309 " --> pdb=" O VAL B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 335 removed outlier: 3.636A pdb=" N THR B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE B 329 " --> pdb=" O TRP B 325 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE B 333 " --> pdb=" O PHE B 329 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N SER B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 347 removed outlier: 3.675A pdb=" N ILE B 344 " --> pdb=" O PHE B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 374 through 388 removed outlier: 3.592A pdb=" N ILE B 379 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N VAL B 384 " --> pdb=" O ALA B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 407 removed outlier: 3.968A pdb=" N ALA B 394 " --> pdb=" O ALA B 390 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 395 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASN B 396 " --> pdb=" O PHE B 392 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N TYR B 397 " --> pdb=" O ASN B 393 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE B 402 " --> pdb=" O TRP B 398 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE B 407 " --> pdb=" O ARG B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 434 removed outlier: 3.771A pdb=" N GLN B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL B 414 " --> pdb=" O PRO B 410 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE B 415 " --> pdb=" O CYS B 411 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA B 428 " --> pdb=" O THR B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 480 Processing helix chain 'B' and resid 488 through 505 removed outlier: 3.726A pdb=" N VAL B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N PHE B 499 " --> pdb=" O LEU B 495 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR B 505 " --> pdb=" O ALA B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 532 removed outlier: 4.563A pdb=" N ILE B 520 " --> pdb=" O PRO B 516 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER B 531 " --> pdb=" O LEU B 527 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU B 532 " --> pdb=" O PHE B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 560 removed outlier: 4.222A pdb=" N TYR B 547 " --> pdb=" O ASP B 543 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU B 549 " --> pdb=" O GLY B 545 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA B 552 " --> pdb=" O ALA B 548 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA B 554 " --> pdb=" O MET B 550 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU B 556 " --> pdb=" O ALA B 552 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY B 557 " --> pdb=" O ALA B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 573 removed outlier: 3.783A pdb=" N VAL B 568 " --> pdb=" O LEU B 564 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE B 569 " --> pdb=" O SER B 565 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA B 573 " --> pdb=" O ILE B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 593 removed outlier: 3.880A pdb=" N ILE B 583 " --> pdb=" O TYR B 579 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR B 589 " --> pdb=" O LEU B 585 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS B 591 " --> pdb=" O LEU B 587 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE B 592 " --> pdb=" O MET B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 597 Processing helix chain 'B' and resid 600 through 608 removed outlier: 3.535A pdb=" N MET B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N HIS B 605 " --> pdb=" O LEU B 601 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE B 606 " --> pdb=" O TYR B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 652 Processing helix chain 'B' and resid 681 through 690 Processing helix chain 'B' and resid 708 through 713 removed outlier: 3.960A pdb=" N ARG B 712 " --> pdb=" O LEU B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 724 Processing helix chain 'B' and resid 753 through 764 removed outlier: 3.549A pdb=" N LEU B 764 " --> pdb=" O LEU B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 789 removed outlier: 3.755A pdb=" N LEU B 787 " --> pdb=" O THR B 783 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG B 789 " --> pdb=" O LYS B 785 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 438 through 440 Processing sheet with id=AA2, first strand: chain 'A' and resid 660 through 662 Processing sheet with id=AA3, first strand: chain 'A' and resid 747 through 749 removed outlier: 3.831A pdb=" N GLY A 780 " --> pdb=" O VAL A 771 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 438 through 440 Processing sheet with id=AA5, first strand: chain 'B' and resid 660 through 662 Processing sheet with id=AA6, first strand: chain 'B' and resid 747 through 749 removed outlier: 3.831A pdb=" N GLY B 780 " --> pdb=" O VAL B 771 " (cutoff:3.500A) 594 hydrogen bonds defined for protein. 1752 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: 3.55 Time building geometry restraints manager: 5.83 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: 4161 1.34 - 1.46: 3322 1.46 - 1.58: 6119 1.58 - 1.71: 0 1.71 - 1.83: 128 Bond restraints: 13730 Sorted by residual: bond pdb=" CA GLU B 313 " pdb=" C GLU B 313 " ideal model delta sigma weight residual 1.524 1.495 0.029 1.27e-02 6.20e+03 5.15e+00 bond pdb=" CA GLU A 313 " pdb=" C GLU A 313 " ideal model delta sigma weight residual 1.524 1.495 0.028 1.27e-02 6.20e+03 5.01e+00 bond pdb=" CA ALA D 106 " pdb=" C ALA D 106 " ideal model delta sigma weight residual 1.533 1.523 0.010 5.60e-03 3.19e+04 3.50e+00 bond pdb=" CA ALA C 106 " pdb=" C ALA C 106 " ideal model delta sigma weight residual 1.533 1.523 0.010 5.60e-03 3.19e+04 3.42e+00 bond pdb=" CA ASP D 257 " pdb=" C ASP D 257 " ideal model delta sigma weight residual 1.524 1.547 -0.024 1.29e-02 6.01e+03 3.39e+00 ... (remaining 13725 not shown) Histogram of bond angle deviations from ideal: 98.25 - 105.52: 310 105.52 - 112.79: 7255 112.79 - 120.06: 5458 120.06 - 127.34: 5527 127.34 - 134.61: 128 Bond angle restraints: 18678 Sorted by residual: angle pdb=" N ARG A 762 " pdb=" CA ARG A 762 " pdb=" C ARG A 762 " ideal model delta sigma weight residual 111.36 118.98 -7.62 1.09e+00 8.42e-01 4.89e+01 angle pdb=" N ARG B 762 " pdb=" CA ARG B 762 " pdb=" C ARG B 762 " ideal model delta sigma weight residual 111.36 118.93 -7.57 1.09e+00 8.42e-01 4.83e+01 angle pdb=" N PRO A 355 " pdb=" CA PRO A 355 " pdb=" CB PRO A 355 " ideal model delta sigma weight residual 103.51 109.92 -6.41 9.60e-01 1.09e+00 4.46e+01 angle pdb=" N PRO B 355 " pdb=" CA PRO B 355 " pdb=" CB PRO B 355 " ideal model delta sigma weight residual 103.51 109.92 -6.41 9.60e-01 1.09e+00 4.45e+01 angle pdb=" N PRO B 672 " pdb=" CA PRO B 672 " pdb=" CB PRO B 672 " ideal model delta sigma weight residual 103.00 110.30 -7.30 1.10e+00 8.26e-01 4.41e+01 ... (remaining 18673 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 7750 17.83 - 35.67: 434 35.67 - 53.50: 58 53.50 - 71.33: 12 71.33 - 89.16: 8 Dihedral angle restraints: 8262 sinusoidal: 3196 harmonic: 5066 Sorted by residual: dihedral pdb=" CB CYS C 112 " pdb=" SG CYS C 112 " pdb=" SG CYS C 171 " pdb=" CB CYS C 171 " ideal model delta sinusoidal sigma weight residual -86.00 -175.16 89.16 1 1.00e+01 1.00e-02 9.46e+01 dihedral pdb=" CB CYS D 112 " pdb=" SG CYS D 112 " pdb=" SG CYS D 171 " pdb=" CB CYS D 171 " ideal model delta sinusoidal sigma weight residual -86.00 -175.11 89.11 1 1.00e+01 1.00e-02 9.45e+01 dihedral pdb=" CB CYS D 84 " pdb=" SG CYS D 84 " pdb=" SG CYS D 142 " pdb=" CB CYS D 142 " ideal model delta sinusoidal sigma weight residual -86.00 -161.81 75.81 1 1.00e+01 1.00e-02 7.25e+01 ... (remaining 8259 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1811 0.077 - 0.154: 361 0.154 - 0.232: 58 0.232 - 0.309: 17 0.309 - 0.386: 7 Chirality restraints: 2254 Sorted by residual: chirality pdb=" CA VAL A 221 " pdb=" N VAL A 221 " pdb=" C VAL A 221 " pdb=" CB VAL A 221 " both_signs ideal model delta sigma weight residual False 2.44 2.06 0.39 2.00e-01 2.50e+01 3.73e+00 chirality pdb=" CA VAL B 221 " pdb=" N VAL B 221 " pdb=" C VAL B 221 " pdb=" CB VAL B 221 " both_signs ideal model delta sigma weight residual False 2.44 2.06 0.39 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" CA ARG A 762 " pdb=" N ARG A 762 " pdb=" C ARG A 762 " pdb=" CB ARG A 762 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.09e+00 ... (remaining 2251 not shown) Planarity restraints: 2340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 401 " -0.044 2.00e-02 2.50e+03 3.65e-02 1.66e+01 pdb=" C7 NAG C 401 " 0.011 2.00e-02 2.50e+03 pdb=" C8 NAG C 401 " -0.033 2.00e-02 2.50e+03 pdb=" N2 NAG C 401 " 0.058 2.00e-02 2.50e+03 pdb=" O7 NAG C 401 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 404 " 0.044 2.00e-02 2.50e+03 3.64e-02 1.65e+01 pdb=" C7 NAG C 404 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG C 404 " 0.033 2.00e-02 2.50e+03 pdb=" N2 NAG C 404 " -0.058 2.00e-02 2.50e+03 pdb=" O7 NAG C 404 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 402 " 0.044 2.00e-02 2.50e+03 3.64e-02 1.65e+01 pdb=" C7 NAG D 402 " -0.011 2.00e-02 2.50e+03 pdb=" C8 NAG D 402 " 0.033 2.00e-02 2.50e+03 pdb=" N2 NAG D 402 " -0.058 2.00e-02 2.50e+03 pdb=" O7 NAG D 402 " -0.008 2.00e-02 2.50e+03 ... (remaining 2337 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 3584 2.79 - 3.32: 12390 3.32 - 3.85: 20377 3.85 - 4.37: 22351 4.37 - 4.90: 40193 Nonbonded interactions: 98895 Sorted by model distance: nonbonded pdb=" O ASN C 173 " pdb=" OG SER C 183 " model vdw 2.267 2.440 nonbonded pdb=" O ASN D 173 " pdb=" OG SER D 183 " model vdw 2.267 2.440 nonbonded pdb=" O4 NAG D 402 " pdb=" O6 NAG D 402 " model vdw 2.302 2.440 nonbonded pdb=" O4 NAG C 402 " pdb=" O6 NAG C 402 " model vdw 2.303 2.440 nonbonded pdb=" NH2 ARG B 640 " pdb=" OE1 GLN B 676 " model vdw 2.364 2.520 ... (remaining 98890 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 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 0.450 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: 2.500 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 38.570 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 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 : 0.008 0.069 13730 Z= 0.529 Angle : 1.170 11.542 18678 Z= 0.662 Chirality : 0.069 0.386 2254 Planarity : 0.009 0.072 2326 Dihedral : 11.207 75.404 4960 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 0.43 % Allowed : 6.81 % Favored : 92.75 % Cbeta Deviations : 0.12 % 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: -4.33 (0.16), residues: 1708 helix: -2.63 (0.13), residues: 1004 sheet: None (None), residues: 0 loop : -3.12 (0.20), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.003 TRP B 179 HIS 0.005 0.001 HIS A 658 PHE 0.047 0.003 PHE A 478 TYR 0.019 0.003 TYR A 156 ARG 0.007 0.001 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 259 time to evaluate : 1.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 265 average time/residue: 0.2643 time to fit residues: 101.0674 Evaluate side-chains 198 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 194 time to evaluate : 1.502 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1196 time to fit residues: 2.9177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 0.8980 chunk 131 optimal weight: 0.8980 chunk 73 optimal weight: 0.2980 chunk 45 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 136 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 101 optimal weight: 0.0970 chunk 158 optimal weight: 0.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 167 GLN C 191 ASN A 252 HIS A 460 ASN A 576 ASN A 623 HIS A 657 ASN A 666 HIS ** A 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 GLN D 191 ASN D 195 HIS B 252 HIS B 460 ASN B 576 ASN B 623 HIS B 657 ASN ** B 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13730 Z= 0.164 Angle : 0.628 7.701 18678 Z= 0.326 Chirality : 0.041 0.175 2254 Planarity : 0.006 0.049 2326 Dihedral : 5.520 33.785 2150 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 1.16 % Allowed : 12.83 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.18), residues: 1708 helix: -1.41 (0.15), residues: 1026 sheet: -3.75 (0.93), residues: 20 loop : -2.93 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 179 HIS 0.012 0.001 HIS A 623 PHE 0.028 0.001 PHE C 119 TYR 0.010 0.001 TYR B 397 ARG 0.003 0.000 ARG A 628 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 221 time to evaluate : 1.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 231 average time/residue: 0.2724 time to fit residues: 90.5857 Evaluate side-chains 193 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 185 time to evaluate : 1.528 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1197 time to fit residues: 3.9268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 0.0270 chunk 49 optimal weight: 1.9990 chunk 131 optimal weight: 0.0370 chunk 107 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 158 optimal weight: 0.8980 chunk 171 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 126 optimal weight: 0.4980 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 ASN C 242 ASN ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 GLN ** A 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 GLN D 203 ASN ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 GLN ** B 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13730 Z= 0.142 Angle : 0.563 6.900 18678 Z= 0.288 Chirality : 0.040 0.169 2254 Planarity : 0.005 0.043 2326 Dihedral : 4.682 19.790 2150 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 1.09 % Allowed : 15.43 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.19), residues: 1708 helix: -0.64 (0.16), residues: 1030 sheet: -3.55 (1.01), residues: 20 loop : -2.77 (0.22), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 524 HIS 0.004 0.001 HIS C 195 PHE 0.032 0.001 PHE D 119 TYR 0.011 0.001 TYR A 397 ARG 0.003 0.000 ARG B 762 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 205 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 5 residues processed: 218 average time/residue: 0.2452 time to fit residues: 79.5853 Evaluate side-chains 188 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 183 time to evaluate : 1.969 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1749 time to fit residues: 4.2251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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: 65.6913 > 50: distance: 87 - 93: 30.656 distance: 93 - 94: 34.160 distance: 94 - 95: 51.281 distance: 94 - 97: 7.996 distance: 95 - 96: 23.051 distance: 95 - 101: 53.833 distance: 97 - 98: 25.465 distance: 98 - 99: 21.988 distance: 98 - 100: 26.484 distance: 101 - 102: 20.558 distance: 102 - 103: 31.841 distance: 102 - 105: 55.476 distance: 103 - 107: 17.411 distance: 105 - 106: 39.701 distance: 107 - 108: 49.229 distance: 108 - 109: 38.163 distance: 108 - 111: 34.493 distance: 109 - 110: 15.672 distance: 109 - 112: 21.646 distance: 112 - 113: 18.770 distance: 113 - 114: 14.098 distance: 113 - 116: 16.166 distance: 114 - 123: 12.667 distance: 116 - 117: 5.635 distance: 117 - 118: 9.131 distance: 117 - 119: 23.340 distance: 118 - 120: 19.090 distance: 119 - 121: 32.733 distance: 120 - 122: 11.660 distance: 121 - 122: 26.752 distance: 123 - 124: 41.867 distance: 124 - 125: 14.912 distance: 124 - 127: 48.285 distance: 125 - 126: 50.235 distance: 125 - 131: 17.072 distance: 127 - 128: 25.503 distance: 128 - 129: 42.198 distance: 129 - 130: 4.429 distance: 131 - 132: 8.152 distance: 132 - 133: 20.294 distance: 132 - 135: 13.165 distance: 133 - 134: 43.794 distance: 133 - 139: 51.319 distance: 136 - 137: 38.550 distance: 136 - 138: 16.647 distance: 139 - 140: 36.926 distance: 139 - 145: 57.228 distance: 140 - 141: 28.887 distance: 140 - 143: 43.680 distance: 141 - 142: 5.359 distance: 141 - 146: 47.900 distance: 143 - 144: 40.157 distance: 144 - 145: 56.564 distance: 146 - 147: 26.937 distance: 147 - 148: 31.024 distance: 147 - 150: 22.243 distance: 148 - 149: 42.729 distance: 148 - 152: 11.608 distance: 150 - 151: 42.464 distance: 152 - 153: 45.156 distance: 152 - 158: 19.819 distance: 153 - 154: 43.538 distance: 154 - 155: 25.519 distance: 154 - 159: 49.195 distance: 156 - 157: 57.119 distance: 157 - 158: 36.736 distance: 159 - 160: 22.259 distance: 160 - 161: 47.343 distance: 160 - 163: 41.924 distance: 161 - 162: 41.751 distance: 161 - 171: 30.288 distance: 163 - 164: 36.579 distance: 164 - 165: 31.208 distance: 164 - 166: 20.593 distance: 165 - 167: 18.554 distance: 166 - 168: 6.917 distance: 167 - 169: 45.283 distance: 168 - 169: 36.373 distance: 169 - 170: 28.148