Starting phenix.real_space_refine (version: dev) on Wed Mar 15 05:33:50 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cq7_30438/03_2023/7cq7_30438_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cq7_30438/03_2023/7cq7_30438.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cq7_30438/03_2023/7cq7_30438.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cq7_30438/03_2023/7cq7_30438.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cq7_30438/03_2023/7cq7_30438_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cq7_30438/03_2023/7cq7_30438_updated.pdb" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.000 sd= 0.005 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 Process input model Symmetric amino acids flipped Residue "A ARG 107": "NH1" <-> "NH2" Residue "A ARG 144": "NH1" <-> "NH2" Residue "B ARG 107": "NH1" <-> "NH2" Residue "B ARG 131": "NH1" <-> "NH2" Residue "B ARG 144": "NH1" <-> "NH2" Residue "C ARG 113": "NH1" <-> "NH2" Residue "C ARG 265": "NH1" <-> "NH2" Residue "C ARG 280": "NH1" <-> "NH2" Residue "C PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 526": "NH1" <-> "NH2" Residue "C ARG 639": "NH1" <-> "NH2" Residue "C ARG 641": "NH1" <-> "NH2" Residue "C ARG 775": "NH1" <-> "NH2" Residue "D ARG 112": "NH1" <-> "NH2" Residue "D ARG 265": "NH1" <-> "NH2" Residue "D ARG 280": "NH1" <-> "NH2" Residue "D ARG 362": "NH1" <-> "NH2" Residue "D ARG 526": "NH1" <-> "NH2" Residue "D ARG 640": "NH1" <-> "NH2" Residue "D ARG 707": "NH1" <-> "NH2" Residue "D ARG 712": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/chem_data/mon_lib" Total number of atoms: 13810 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1630 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1637 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 5194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5194 Classifications: {'peptide': 676} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 28, 'TRANS': 647} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 5236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5236 Classifications: {'peptide': 676} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 28, 'TRANS': 647} Chain breaks: 3 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' CL': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CL': 2, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 7.87, per 1000 atoms: 0.57 Number of scatterers: 13810 At special positions: 0 Unit cell: (136.14, 111.986, 132.846, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 3 17.00 S 92 16.00 P 4 15.00 O 2481 8.00 N 2304 7.00 C 8926 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 115 " distance=2.03 Simple disulfide: pdb=" SG CYS A 112 " - pdb=" SG CYS A 171 " distance=2.03 Simple disulfide: pdb=" SG CYS A 174 " - pdb=" SG CYS A 255 " distance=2.03 Simple disulfide: pdb=" SG CYS A 221 " - pdb=" SG CYS A 275 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 142 " distance=2.04 Simple disulfide: pdb=" SG CYS B 101 " - pdb=" SG CYS B 115 " distance=2.03 Simple disulfide: pdb=" SG CYS B 112 " - pdb=" SG CYS B 171 " distance=2.03 Simple disulfide: pdb=" SG CYS B 174 " - pdb=" SG CYS B 255 " distance=2.04 Simple disulfide: pdb=" SG CYS B 221 " - pdb=" SG CYS B 275 " distance=2.03 Simple disulfide: pdb=" SG CYS C 438 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS D 438 " - pdb=" SG CYS D 454 " distance=2.03 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=5, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG E 1 " - " ASN A 263 " " NAG F 1 " - " ASN B 263 " Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.78 Conformation dependent library (CDL) restraints added in 1.9 seconds 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3312 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 71 helices and 5 sheets defined 55.9% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 82 through 104 removed outlier: 3.783A pdb=" N GLU A 86 " --> pdb=" O PRO A 82 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N LEU A 87 " --> pdb=" O GLU A 83 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU A 97 " --> pdb=" O ASN A 93 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 98 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 114 No H-bonds generated for 'chain 'A' and resid 111 through 114' Processing helix chain 'A' and resid 116 through 128 removed outlier: 3.750A pdb=" N GLN A 120 " --> pdb=" O TYR A 116 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 146 No H-bonds generated for 'chain 'A' and resid 143 through 146' Processing helix chain 'A' and resid 154 through 169 Processing helix chain 'A' and resid 184 through 202 Processing helix chain 'A' and resid 218 through 221 No H-bonds generated for 'chain 'A' and resid 218 through 221' Processing helix chain 'A' and resid 225 through 244 removed outlier: 4.010A pdb=" N GLU A 243 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LEU A 244 " --> pdb=" O LYS A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 270 Processing helix chain 'A' and resid 282 through 293 Processing helix chain 'A' and resid 295 through 305 Processing helix chain 'B' and resid 82 through 104 removed outlier: 4.311A pdb=" N GLU B 86 " --> pdb=" O PRO B 82 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N LEU B 87 " --> pdb=" O GLU B 83 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N PHE B 91 " --> pdb=" O LEU B 87 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA B 96 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N GLU B 97 " --> pdb=" O ASN B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 129 removed outlier: 3.710A pdb=" N ILE B 129 " --> pdb=" O LYS B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 154 through 169 Processing helix chain 'B' and resid 186 through 202 removed outlier: 3.586A pdb=" N ASN B 191 " --> pdb=" O VAL B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 221 No H-bonds generated for 'chain 'B' and resid 218 through 221' Processing helix chain 'B' and resid 225 through 245 removed outlier: 4.223A pdb=" N THR B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 269 removed outlier: 3.540A pdb=" N ALA B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 289 removed outlier: 3.625A pdb=" N VAL B 288 " --> pdb=" O PRO B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 305 Proline residue: B 296 - end of helix removed outlier: 3.610A pdb=" N SER B 303 " --> pdb=" O PHE B 299 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 114 Processing helix chain 'C' and resid 123 through 166 removed outlier: 3.630A pdb=" N VAL C 128 " --> pdb=" O ILE C 124 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG C 157 " --> pdb=" O GLY C 153 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL C 158 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE C 159 " --> pdb=" O LYS C 155 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LYS C 165 " --> pdb=" O GLY C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 195 removed outlier: 4.126A pdb=" N ILE C 193 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N VAL C 194 " --> pdb=" O GLY C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.863A pdb=" N CYS C 211 " --> pdb=" O PRO C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 238 removed outlier: 3.682A pdb=" N ILE C 235 " --> pdb=" O VAL C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 262 removed outlier: 3.694A pdb=" N ILE C 251 " --> pdb=" O GLY C 248 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N HIS C 252 " --> pdb=" O PRO C 249 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE C 257 " --> pdb=" O GLY C 254 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE C 261 " --> pdb=" O ALA C 258 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER C 262 " --> pdb=" O ALA C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 279 No H-bonds generated for 'chain 'C' and resid 277 through 279' Processing helix chain 'C' and resid 283 through 301 removed outlier: 3.837A pdb=" N ASP C 287 " --> pdb=" O THR C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 311 removed outlier: 3.734A pdb=" N VAL C 308 " --> pdb=" O PRO C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 345 Processing helix chain 'C' and resid 372 through 406 Proline residue: C 376 - end of helix removed outlier: 3.726A pdb=" N ILE C 379 " --> pdb=" O PRO C 376 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET C 381 " --> pdb=" O PHE C 378 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL C 383 " --> pdb=" O ALA C 380 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU C 388 " --> pdb=" O GLY C 385 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN C 396 " --> pdb=" O ASN C 393 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ILE C 404 " --> pdb=" O MET C 401 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ARG C 405 " --> pdb=" O PHE C 402 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR C 406 " --> pdb=" O ARG C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 433 removed outlier: 3.805A pdb=" N ALA C 421 " --> pdb=" O ALA C 417 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N VAL C 423 " --> pdb=" O LEU C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 465 Processing helix chain 'C' and resid 470 through 479 Processing helix chain 'C' and resid 487 through 503 removed outlier: 4.084A pdb=" N PHE C 499 " --> pdb=" O LEU C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 530 removed outlier: 3.647A pdb=" N LEU C 527 " --> pdb=" O ALA C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 535 No H-bonds generated for 'chain 'C' and resid 532 through 535' Processing helix chain 'C' and resid 544 through 559 removed outlier: 3.890A pdb=" N LEU C 549 " --> pdb=" O GLY C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 572 Processing helix chain 'C' and resid 577 through 595 removed outlier: 3.804A pdb=" N PHE C 581 " --> pdb=" O THR C 578 " (cutoff:3.500A) Proline residue: C 582 - end of helix removed outlier: 3.592A pdb=" N VAL C 593 " --> pdb=" O ALA C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 609 removed outlier: 4.345A pdb=" N GLN C 609 " --> pdb=" O HIS C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 651 Processing helix chain 'C' and resid 681 through 689 Processing helix chain 'C' and resid 708 through 710 No H-bonds generated for 'chain 'C' and resid 708 through 710' Processing helix chain 'C' and resid 721 through 723 No H-bonds generated for 'chain 'C' and resid 721 through 723' Processing helix chain 'C' and resid 754 through 762 removed outlier: 3.838A pdb=" N LYS C 759 " --> pdb=" O PRO C 755 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 111 Processing helix chain 'D' and resid 122 through 165 removed outlier: 3.843A pdb=" N ASP D 164 " --> pdb=" O LYS D 160 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS D 165 " --> pdb=" O GLY D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 195 removed outlier: 3.673A pdb=" N LEU D 178 " --> pdb=" O PHE D 174 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE D 193 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N VAL D 194 " --> pdb=" O GLY D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 201 No H-bonds generated for 'chain 'D' and resid 199 through 201' Processing helix chain 'D' and resid 206 through 213 Processing helix chain 'D' and resid 224 through 238 Processing helix chain 'D' and resid 249 through 261 Processing helix chain 'D' and resid 282 through 301 Processing helix chain 'D' and resid 304 through 313 Processing helix chain 'D' and resid 321 through 345 Processing helix chain 'D' and resid 372 through 405 removed outlier: 3.582A pdb=" N ILE D 375 " --> pdb=" O ILE D 372 " (cutoff:3.500A) Proline residue: D 376 - end of helix removed outlier: 3.693A pdb=" N GLY D 385 " --> pdb=" O GLY D 382 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU D 388 " --> pdb=" O GLY D 385 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLY D 389 " --> pdb=" O GLY D 386 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN D 393 " --> pdb=" O ALA D 390 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU D 395 " --> pdb=" O PHE D 392 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TRP D 398 " --> pdb=" O LEU D 395 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR D 400 " --> pdb=" O TYR D 397 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N MET D 401 " --> pdb=" O TRP D 398 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE D 404 " --> pdb=" O MET D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 433 removed outlier: 3.644A pdb=" N ALA D 417 " --> pdb=" O GLN D 413 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL D 418 " --> pdb=" O VAL D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 465 No H-bonds generated for 'chain 'D' and resid 462 through 465' Processing helix chain 'D' and resid 470 through 477 Processing helix chain 'D' and resid 487 through 503 removed outlier: 4.601A pdb=" N PHE D 499 " --> pdb=" O LEU D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 535 removed outlier: 3.509A pdb=" N ALA D 523 " --> pdb=" O LEU D 519 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG D 526 " --> pdb=" O ALA D 522 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY D 529 " --> pdb=" O GLY D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 559 removed outlier: 4.367A pdb=" N LEU D 549 " --> pdb=" O GLY D 545 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET D 550 " --> pdb=" O LYS D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 564 through 573 Processing helix chain 'D' and resid 578 through 595 removed outlier: 3.850A pdb=" N PHE D 581 " --> pdb=" O THR D 578 " (cutoff:3.500A) Proline residue: D 582 - end of helix removed outlier: 3.509A pdb=" N MET D 588 " --> pdb=" O LEU D 585 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL D 593 " --> pdb=" O ALA D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 609 removed outlier: 4.100A pdb=" N GLN D 609 " --> pdb=" O HIS D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 651 Processing helix chain 'D' and resid 681 through 684 No H-bonds generated for 'chain 'D' and resid 681 through 684' Processing helix chain 'D' and resid 686 through 689 No H-bonds generated for 'chain 'D' and resid 686 through 689' Processing helix chain 'D' and resid 754 through 761 removed outlier: 3.902A pdb=" N LYS D 759 " --> pdb=" O PRO D 755 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 438 through 440 Processing sheet with id= B, first strand: chain 'C' and resid 660 through 664 Processing sheet with id= C, first strand: chain 'D' and resid 641 through 643 removed outlier: 3.632A pdb=" N GLU D 642 " --> pdb=" O MET D 735 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 661 through 663 removed outlier: 3.714A pdb=" N GLY D 677 " --> pdb=" O VAL D 663 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 747 through 749 removed outlier: 6.169A pdb=" N VAL D 770 " --> pdb=" O VAL D 748 " (cutoff:3.500A) No H-bonds generated for sheet with id= E 624 hydrogen bonds defined for protein. 1671 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: 3.79 Time building geometry restraints manager: 6.16 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: 4350 1.34 - 1.47: 3464 1.47 - 1.59: 6154 1.59 - 1.71: 6 1.71 - 1.83: 140 Bond restraints: 14114 Sorted by residual: bond pdb=" C4 ADP D 901 " pdb=" C5 ADP D 901 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C4 ADP C 901 " pdb=" C5 ADP C 901 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C5 ADP D 901 " pdb=" C6 ADP D 901 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" C5 ADP C 901 " pdb=" C6 ADP C 901 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" CB VAL C 586 " pdb=" CG1 VAL C 586 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.49e+00 ... (remaining 14109 not shown) Histogram of bond angle deviations from ideal: 98.68 - 105.81: 318 105.81 - 112.94: 7623 112.94 - 120.07: 5412 120.07 - 127.20: 5654 127.20 - 134.33: 178 Bond angle restraints: 19185 Sorted by residual: angle pdb=" C THR A 282 " pdb=" N VAL A 283 " pdb=" CA VAL A 283 " ideal model delta sigma weight residual 120.24 125.32 -5.08 6.30e-01 2.52e+00 6.50e+01 angle pdb=" N GLN D 722 " pdb=" CA GLN D 722 " pdb=" C GLN D 722 " ideal model delta sigma weight residual 114.75 105.85 8.90 1.26e+00 6.30e-01 4.99e+01 angle pdb=" C ARG B 271 " pdb=" N THR B 272 " pdb=" CA THR B 272 " ideal model delta sigma weight residual 121.54 131.38 -9.84 1.91e+00 2.74e-01 2.65e+01 angle pdb=" C ARG A 271 " pdb=" N THR A 272 " pdb=" CA THR A 272 " ideal model delta sigma weight residual 121.54 131.06 -9.52 1.91e+00 2.74e-01 2.49e+01 angle pdb=" N ILE D 724 " pdb=" CA ILE D 724 " pdb=" C ILE D 724 " ideal model delta sigma weight residual 110.62 115.92 -5.30 1.14e+00 7.69e-01 2.16e+01 ... (remaining 19180 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.84: 8137 22.84 - 45.68: 174 45.68 - 68.52: 10 68.52 - 91.36: 8 91.36 - 114.20: 1 Dihedral angle restraints: 8330 sinusoidal: 3215 harmonic: 5115 Sorted by residual: dihedral pdb=" CA ASP C 282 " pdb=" C ASP C 282 " pdb=" N THR C 283 " pdb=" CA THR C 283 " ideal model delta harmonic sigma weight residual 180.00 150.26 29.74 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" C5' ADP D 901 " pdb=" O5' ADP D 901 " pdb=" PA ADP D 901 " pdb=" O2A ADP D 901 " ideal model delta sinusoidal sigma weight residual -60.00 -174.20 114.20 1 2.00e+01 2.50e-03 3.38e+01 dihedral pdb=" CA ARG A 107 " pdb=" C ARG A 107 " pdb=" N PRO A 108 " pdb=" CA PRO A 108 " ideal model delta harmonic sigma weight residual 180.00 152.58 27.42 0 5.00e+00 4.00e-02 3.01e+01 ... (remaining 8327 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1658 0.060 - 0.120: 513 0.120 - 0.180: 68 0.180 - 0.240: 11 0.240 - 0.301: 2 Chirality restraints: 2252 Sorted by residual: chirality pdb=" CB ILE D 721 " pdb=" CA ILE D 721 " pdb=" CG1 ILE D 721 " pdb=" CG2 ILE D 721 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CB ILE C 724 " pdb=" CA ILE C 724 " pdb=" CG1 ILE C 724 " pdb=" CG2 ILE C 724 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CB ILE D 275 " pdb=" CA ILE D 275 " pdb=" CG1 ILE D 275 " pdb=" CG2 ILE D 275 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 2249 not shown) Planarity restraints: 2399 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 179 " 0.028 2.00e-02 2.50e+03 2.30e-02 1.32e+01 pdb=" CG TRP C 179 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP C 179 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP C 179 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 179 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 179 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 179 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 179 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 179 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 179 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 783 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.78e+00 pdb=" C THR C 783 " 0.048 2.00e-02 2.50e+03 pdb=" O THR C 783 " -0.018 2.00e-02 2.50e+03 pdb=" N ARG C 784 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET D 349 " 0.013 2.00e-02 2.50e+03 2.56e-02 6.54e+00 pdb=" C MET D 349 " -0.044 2.00e-02 2.50e+03 pdb=" O MET D 349 " 0.016 2.00e-02 2.50e+03 pdb=" N TRP D 350 " 0.015 2.00e-02 2.50e+03 ... (remaining 2396 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 75 2.51 - 3.11: 10253 3.11 - 3.71: 21285 3.71 - 4.30: 29477 4.30 - 4.90: 49539 Nonbonded interactions: 110629 Sorted by model distance: nonbonded pdb=" OD2 ASP D 786 " pdb=" O2' ADP D 901 " model vdw 1.915 2.440 nonbonded pdb=" O MET C 368 " pdb=" OH TYR C 579 " model vdw 2.236 2.440 nonbonded pdb=" CG HIS C 658 " pdb=" N7 ADP C 901 " model vdw 2.251 2.672 nonbonded pdb=" O MET D 368 " pdb=" OH TYR D 579 " model vdw 2.261 2.440 nonbonded pdb=" NH2 ARG D 767 " pdb=" O2B ADP D 901 " model vdw 2.261 2.520 ... (remaining 110624 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' and resid 73 through 306) selection = (chain 'B' and (resid 73 through 130 or resid 142 through 245 or resid 253 throu \ gh 306)) } ncs_group { reference = (chain 'C' and (resid 94 through 115 or (resid 116 and (name N or name CA or nam \ e C or name O or name CB )) or resid 121 through 652 or (resid 653 through 656 a \ nd (name N or name CA or name C or name O or name CB )) or resid 657 through 664 \ or resid 673 through 693 or resid 706 through 789 or (resid 790 and (name N or \ name CA or name C or name O or name CB )) or resid 901 through 902)) selection = (chain 'D' and (resid 94 through 116 or resid 121 through 366 or (resid 367 and \ (name N or name CA or name C or name O or name CB )) or resid 368 through 619 or \ (resid 620 and (name N or name CA or name C or name O or name CB )) or resid 62 \ 1 through 642 or (resid 643 and (name N or name CA or name C or name O or name C \ B )) or resid 644 through 690 or (resid 691 and (name N or name CA or name C or \ name O or name CB )) or resid 692 or (resid 693 and (name N or name CA or name C \ or name O or name CB )) or resid 706 through 707 or (resid 708 and (name N or n \ ame CA or name C or name O or name CB )) or resid 709 through 716 or (resid 717 \ and (name N or name CA or name C or name O or name CB )) or resid 718 or (resid \ 719 and (name N or name CA or name C or name O or name CB )) or resid 720 throug \ h 724 or (resid 725 through 732 and (name N or name CA or name C or name O or na \ me CB )) or resid 733 through 790 or resid 901 through 902)) } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 92 5.16 5 Cl 3 4.86 5 C 8926 2.51 5 N 2304 2.21 5 O 2481 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 1.250 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: 5.840 Check model and map are aligned: 0.200 Process input model: 36.270 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.120 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4205 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 0.109 14114 Z= 0.528 Angle : 1.069 10.899 19185 Z= 0.570 Chirality : 0.056 0.301 2252 Planarity : 0.008 0.063 2397 Dihedral : 10.328 114.200 4982 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer Outliers : 0.07 % 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: -4.47 (0.15), residues: 1734 helix: -2.46 (0.12), residues: 1046 sheet: None (None), residues: 0 loop : -3.68 (0.20), residues: 688 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 468 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 469 average time/residue: 0.2789 time to fit residues: 185.7198 Evaluate side-chains 248 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 1.586 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1246 ------------------------------------------------------------------------------- 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: 0.9980 chunk 131 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 70 optimal weight: 3.9990 chunk 136 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 101 optimal weight: 9.9990 chunk 158 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 GLN A 202 HIS ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 GLN B 173 ASN C 183 ASN C 220 HIS C 468 ASN C 774 ASN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 373 HIS D 725 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4895 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 14114 Z= 0.237 Angle : 0.806 11.626 19185 Z= 0.397 Chirality : 0.045 0.318 2252 Planarity : 0.006 0.045 2397 Dihedral : 6.540 104.401 1912 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer Outliers : 3.42 % 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: -2.75 (0.18), residues: 1734 helix: -0.80 (0.15), residues: 1049 sheet: -4.56 (1.58), residues: 10 loop : -3.47 (0.20), residues: 675 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 294 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 23 residues processed: 326 average time/residue: 0.2622 time to fit residues: 132.5467 Evaluate side-chains 262 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 239 time to evaluate : 1.690 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1456 time to fit residues: 8.6044 ------------------------------------------------------------------------------- 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: 0.0870 chunk 49 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 107 optimal weight: 0.0470 chunk 43 optimal weight: 0.8980 chunk 158 optimal weight: 3.9990 chunk 171 optimal weight: 0.7980 chunk 140 optimal weight: 0.8980 chunk 156 optimal weight: 0.2980 chunk 53 optimal weight: 0.9980 chunk 126 optimal weight: 0.7980 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 GLN ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 683 GLN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 623 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5056 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.075 14114 Z= 0.201 Angle : 0.733 12.639 19185 Z= 0.355 Chirality : 0.044 0.410 2252 Planarity : 0.005 0.039 2397 Dihedral : 5.948 89.187 1912 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer Outliers : 2.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.19), residues: 1734 helix: -0.11 (0.16), residues: 1056 sheet: -4.50 (1.58), residues: 10 loop : -3.25 (0.21), residues: 668 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 257 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 15 residues processed: 280 average time/residue: 0.2159 time to fit residues: 94.2596 Evaluate side-chains 249 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 234 time to evaluate : 1.414 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1234 time to fit residues: 5.6869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 0.4980 chunk 119 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 chunk 75 optimal weight: 0.6980 chunk 106 optimal weight: 4.9990 chunk 158 optimal weight: 0.2980 chunk 168 optimal weight: 7.9990 chunk 150 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 683 GLN D 162 ASN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 623 HIS ** D 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5677 moved from start: 0.6100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.108 14114 Z= 0.278 Angle : 0.751 11.814 19185 Z= 0.372 Chirality : 0.045 0.251 2252 Planarity : 0.005 0.047 2397 Dihedral : 5.464 62.435 1912 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.79 % Favored : 92.16 % Rotamer Outliers : 2.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.20), residues: 1734 helix: 0.18 (0.16), residues: 1060 sheet: -3.23 (3.28), residues: 5 loop : -3.06 (0.21), residues: 669 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 273 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 16 residues processed: 289 average time/residue: 0.2413 time to fit residues: 108.3975 Evaluate side-chains 252 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 236 time to evaluate : 1.573 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1393 time to fit residues: 6.5392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-4893/modules/cctbx_project/iotbx/cli_parser.py", line 865, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-dev-4893/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-dev-4893/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-4893/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-4893/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-4893/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-4893/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-4893/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-4893/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-4893/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-4893/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-4893/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-4893/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: 51.0536 > 50: distance: 48 - 70: 11.521 distance: 52 - 78: 9.841 distance: 57 - 59: 17.969 distance: 59 - 60: 16.069 distance: 60 - 61: 6.324 distance: 60 - 63: 13.414 distance: 61 - 62: 15.800 distance: 61 - 70: 7.047 distance: 62 - 93: 17.753 distance: 63 - 64: 28.831 distance: 64 - 65: 31.457 distance: 65 - 66: 3.159 distance: 67 - 68: 6.442 distance: 67 - 69: 13.292 distance: 71 - 72: 3.931 distance: 71 - 74: 14.349 distance: 72 - 73: 13.000 distance: 72 - 78: 3.493 distance: 73 - 101: 25.984 distance: 74 - 75: 10.163 distance: 75 - 76: 23.128 distance: 75 - 77: 26.391 distance: 78 - 79: 10.672 distance: 79 - 80: 12.629 distance: 79 - 82: 10.695 distance: 80 - 81: 8.188 distance: 80 - 89: 10.570 distance: 81 - 107: 23.333 distance: 83 - 84: 7.785 distance: 84 - 86: 11.643 distance: 85 - 87: 8.273 distance: 86 - 88: 4.544 distance: 87 - 88: 11.124 distance: 89 - 90: 9.949 distance: 90 - 91: 17.324 distance: 91 - 92: 28.374 distance: 91 - 93: 14.872 distance: 92 - 115: 18.848 distance: 93 - 94: 17.328 distance: 94 - 95: 21.268 distance: 94 - 97: 9.941 distance: 95 - 96: 29.558 distance: 95 - 101: 27.737 distance: 96 - 121: 26.872 distance: 97 - 98: 18.612 distance: 97 - 99: 22.363 distance: 98 - 100: 25.945 distance: 101 - 102: 9.286 distance: 102 - 103: 13.354 distance: 102 - 105: 17.318 distance: 103 - 104: 10.594 distance: 103 - 107: 16.750 distance: 104 - 133: 41.771 distance: 105 - 106: 36.032 distance: 107 - 108: 23.899 distance: 108 - 109: 23.786 distance: 108 - 111: 22.910 distance: 109 - 110: 14.204 distance: 109 - 115: 21.852 distance: 111 - 112: 18.027 distance: 112 - 113: 20.439 distance: 112 - 114: 11.763 distance: 115 - 116: 25.798 distance: 116 - 117: 20.267 distance: 116 - 119: 23.158 distance: 117 - 118: 5.772 distance: 117 - 121: 15.065 distance: 119 - 120: 19.005 distance: 121 - 122: 8.824 distance: 122 - 123: 9.575 distance: 122 - 125: 13.652 distance: 123 - 124: 22.009 distance: 123 - 133: 17.231 distance: 125 - 126: 18.890 distance: 126 - 127: 15.203 distance: 126 - 128: 8.584 distance: 127 - 129: 10.387 distance: 128 - 130: 12.369 distance: 129 - 131: 4.557 distance: 130 - 131: 7.960 distance: 131 - 132: 6.580 distance: 133 - 134: 17.021 distance: 134 - 135: 8.480 distance: 134 - 137: 10.447 distance: 135 - 136: 8.203 distance: 135 - 141: 7.812 distance: 138 - 139: 22.225 distance: 138 - 140: 13.916