Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 14:19:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cfs_30346/04_2023/7cfs_30346.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cfs_30346/04_2023/7cfs_30346.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cfs_30346/04_2023/7cfs_30346.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cfs_30346/04_2023/7cfs_30346.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cfs_30346/04_2023/7cfs_30346.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cfs_30346/04_2023/7cfs_30346.pdb" } resolution = 3.56 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 81 5.16 5 Na 1 4.78 5 C 6402 2.51 5 N 1631 2.21 5 O 1859 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 219": "OE1" <-> "OE2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A GLU 375": "OE1" <-> "OE2" Residue "B GLU 219": "OE1" <-> "OE2" Residue "B GLU 254": "OE1" <-> "OE2" Residue "B GLU 315": "OE1" <-> "OE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B GLU 375": "OE1" <-> "OE2" Residue "C GLU 219": "OE1" <-> "OE2" Residue "C GLU 254": "OE1" <-> "OE2" Residue "C GLU 315": "OE1" <-> "OE2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C GLU 375": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 9974 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3249 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 407} Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 217 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 2, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 112 Chain: "B" Number of atoms: 3267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3267 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 407} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 2, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 89 Chain: "C" Number of atoms: 3268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3268 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 407} Unresolved non-hydrogen bonds: 156 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 83 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' NA': 1, 'NAG': 2, 'Y01': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'NAG': 2, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'NAG': 2, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.85, per 1000 atoms: 0.59 Number of scatterers: 9974 At special positions: 0 Unit cell: (97.344, 96.33, 129.792, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 81 16.00 Na 1 11.00 O 1859 8.00 N 1631 7.00 C 6402 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 290 " - pdb=" SG CYS A 367 " distance=2.03 Simple disulfide: pdb=" SG CYS A 310 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 314 " - pdb=" SG CYS A 361 " distance=2.33 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 345 " distance=2.03 Simple disulfide: pdb=" SG CYS A 325 " - pdb=" SG CYS A 337 " distance=2.03 Simple disulfide: pdb=" SG CYS B 93 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS B 290 " - pdb=" SG CYS B 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 310 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 314 " - pdb=" SG CYS B 361 " distance=2.33 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 345 " distance=2.03 Simple disulfide: pdb=" SG CYS B 325 " - pdb=" SG CYS B 337 " distance=2.03 Simple disulfide: pdb=" SG CYS C 93 " - pdb=" SG CYS C 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 172 " - pdb=" SG CYS C 179 " distance=2.03 Simple disulfide: pdb=" SG CYS C 290 " - pdb=" SG CYS C 367 " distance=2.02 Simple disulfide: pdb=" SG CYS C 310 " - pdb=" SG CYS C 363 " distance=2.03 Simple disulfide: pdb=" SG CYS C 314 " - pdb=" SG CYS C 361 " distance=2.33 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 345 " distance=2.03 Simple disulfide: pdb=" SG CYS C 325 " - pdb=" SG CYS C 337 " 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=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 395 " " NAG A 602 " - " ASN A 368 " " NAG B 601 " - " ASN B 395 " " NAG B 602 " - " ASN B 368 " " NAG C 601 " - " ASN C 395 " " NAG C 602 " - " ASN C 368 " Time building additional restraints: 4.00 Conformation dependent library (CDL) restraints added in 1.5 seconds 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2400 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 15 sheets defined 35.2% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 45 through 61 removed outlier: 4.264A pdb=" N LEU A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N CYS A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 71 removed outlier: 3.511A pdb=" N HIS A 70 " --> pdb=" O TYR A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 103 removed outlier: 3.830A pdb=" N VAL A 103 " --> pdb=" O PHE A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 111 removed outlier: 3.543A pdb=" N HIS A 110 " --> pdb=" O ASN A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 140 removed outlier: 3.581A pdb=" N ILE A 137 " --> pdb=" O LYS A 133 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU A 138 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 162 removed outlier: 3.706A pdb=" N ARG A 160 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 169 Processing helix chain 'A' and resid 180 through 184 removed outlier: 3.583A pdb=" N ASP A 183 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A 184 " --> pdb=" O ALA A 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 180 through 184' Processing helix chain 'A' and resid 225 through 229 removed outlier: 3.810A pdb=" N TYR A 229 " --> pdb=" O GLN A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 262 Processing helix chain 'A' and resid 310 through 323 removed outlier: 3.559A pdb=" N TYR A 318 " --> pdb=" O CYS A 314 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU A 319 " --> pdb=" O GLU A 315 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.784A pdb=" N LYS A 343 " --> pdb=" O PRO A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 352 removed outlier: 3.548A pdb=" N PHE A 352 " --> pdb=" O PRO A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 394 removed outlier: 3.620A pdb=" N ALA A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 404 removed outlier: 3.513A pdb=" N GLY A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU A 403 " --> pdb=" O GLN A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 443 removed outlier: 4.012A pdb=" N GLY A 433 " --> pdb=" O ALA A 429 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET A 439 " --> pdb=" O ILE A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 462 removed outlier: 3.822A pdb=" N LEU A 451 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR A 458 " --> pdb=" O PHE A 454 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS A 462 " --> pdb=" O TYR A 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 61 removed outlier: 4.263A pdb=" N LEU B 51 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N CYS B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 71 removed outlier: 3.509A pdb=" N HIS B 70 " --> pdb=" O TYR B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 103 removed outlier: 3.830A pdb=" N VAL B 103 " --> pdb=" O PHE B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 111 removed outlier: 3.542A pdb=" N HIS B 110 " --> pdb=" O ASN B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 140 removed outlier: 3.582A pdb=" N ILE B 137 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU B 138 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP B 140 " --> pdb=" O GLU B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 162 removed outlier: 3.707A pdb=" N ARG B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 169 Processing helix chain 'B' and resid 180 through 184 removed outlier: 3.582A pdb=" N ASP B 183 " --> pdb=" O SER B 180 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE B 184 " --> pdb=" O ALA B 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 180 through 184' Processing helix chain 'B' and resid 225 through 229 removed outlier: 3.810A pdb=" N TYR B 229 " --> pdb=" O GLN B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 262 Processing helix chain 'B' and resid 310 through 323 removed outlier: 3.559A pdb=" N TYR B 318 " --> pdb=" O CYS B 314 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU B 319 " --> pdb=" O GLU B 315 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.784A pdb=" N LYS B 343 " --> pdb=" O PRO B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 352 removed outlier: 3.548A pdb=" N PHE B 352 " --> pdb=" O PRO B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 394 removed outlier: 3.620A pdb=" N ALA B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 404 removed outlier: 3.513A pdb=" N GLY B 402 " --> pdb=" O GLU B 398 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU B 403 " --> pdb=" O GLN B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 443 removed outlier: 4.012A pdb=" N GLY B 433 " --> pdb=" O ALA B 429 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN B 438 " --> pdb=" O ASP B 434 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N MET B 439 " --> pdb=" O ILE B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 462 removed outlier: 3.822A pdb=" N LEU B 451 " --> pdb=" O ILE B 447 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR B 458 " --> pdb=" O PHE B 454 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS B 462 " --> pdb=" O TYR B 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 61 removed outlier: 4.263A pdb=" N LEU C 51 " --> pdb=" O ALA C 47 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N CYS C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 71 removed outlier: 3.510A pdb=" N HIS C 70 " --> pdb=" O TYR C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 103 removed outlier: 3.830A pdb=" N VAL C 103 " --> pdb=" O PHE C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 111 removed outlier: 3.543A pdb=" N HIS C 110 " --> pdb=" O ASN C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 140 removed outlier: 3.581A pdb=" N ILE C 137 " --> pdb=" O LYS C 133 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU C 138 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP C 140 " --> pdb=" O GLU C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 162 removed outlier: 3.707A pdb=" N ARG C 160 " --> pdb=" O GLU C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 169 Processing helix chain 'C' and resid 180 through 184 removed outlier: 3.583A pdb=" N ASP C 183 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE C 184 " --> pdb=" O ALA C 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 180 through 184' Processing helix chain 'C' and resid 225 through 229 removed outlier: 3.811A pdb=" N TYR C 229 " --> pdb=" O GLN C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 262 Processing helix chain 'C' and resid 310 through 323 removed outlier: 3.560A pdb=" N TYR C 318 " --> pdb=" O CYS C 314 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU C 319 " --> pdb=" O GLU C 315 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.783A pdb=" N LYS C 343 " --> pdb=" O PRO C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 352 removed outlier: 3.547A pdb=" N PHE C 352 " --> pdb=" O PRO C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 394 removed outlier: 3.620A pdb=" N ALA C 391 " --> pdb=" O ALA C 387 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 404 removed outlier: 3.513A pdb=" N GLY C 402 " --> pdb=" O GLU C 398 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU C 403 " --> pdb=" O GLN C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 443 removed outlier: 4.013A pdb=" N GLY C 433 " --> pdb=" O ALA C 429 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN C 438 " --> pdb=" O ASP C 434 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N MET C 439 " --> pdb=" O ILE C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 462 removed outlier: 3.822A pdb=" N LEU C 451 " --> pdb=" O ILE C 447 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR C 458 " --> pdb=" O PHE C 454 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS C 462 " --> pdb=" O TYR C 458 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 81 removed outlier: 10.264A pdb=" N PHE A 269 " --> pdb=" O LEU A 408 " (cutoff:3.500A) removed outlier: 10.837A pdb=" N ILE A 410 " --> pdb=" O PHE A 269 " (cutoff:3.500A) removed outlier: 10.376A pdb=" N THR A 271 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 10.747A pdb=" N PHE A 412 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 9.267A pdb=" N VAL A 273 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 9.727A pdb=" N VAL A 414 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N CYS A 275 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ASN A 416 " --> pdb=" O CYS A 275 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLU A 277 " --> pdb=" O ASN A 416 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA A 274 " --> pdb=" O GLU A 375 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN A 276 " --> pdb=" O GLY A 373 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN A 278 " --> pdb=" O ARG A 371 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 221 through 223 removed outlier: 10.264A pdb=" N PHE A 269 " --> pdb=" O LEU A 408 " (cutoff:3.500A) removed outlier: 10.837A pdb=" N ILE A 410 " --> pdb=" O PHE A 269 " (cutoff:3.500A) removed outlier: 10.376A pdb=" N THR A 271 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 10.747A pdb=" N PHE A 412 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 9.267A pdb=" N VAL A 273 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 9.727A pdb=" N VAL A 414 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N CYS A 275 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ASN A 416 " --> pdb=" O CYS A 275 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLU A 277 " --> pdb=" O ASN A 416 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA4, first strand: chain 'A' and resid 185 through 189 removed outlier: 7.261A pdb=" N LYS A 193 " --> pdb=" O ASN A 94 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ASN A 94 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS A 250 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 173 through 174 Processing sheet with id=AA6, first strand: chain 'B' and resid 73 through 81 removed outlier: 10.264A pdb=" N PHE B 269 " --> pdb=" O LEU B 408 " (cutoff:3.500A) removed outlier: 10.838A pdb=" N ILE B 410 " --> pdb=" O PHE B 269 " (cutoff:3.500A) removed outlier: 10.376A pdb=" N THR B 271 " --> pdb=" O ILE B 410 " (cutoff:3.500A) removed outlier: 10.747A pdb=" N PHE B 412 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 9.267A pdb=" N VAL B 273 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 9.726A pdb=" N VAL B 414 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N CYS B 275 " --> pdb=" O VAL B 414 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ASN B 416 " --> pdb=" O CYS B 275 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLU B 277 " --> pdb=" O ASN B 416 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA B 274 " --> pdb=" O GLU B 375 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN B 276 " --> pdb=" O GLY B 373 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN B 278 " --> pdb=" O ARG B 371 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 221 through 223 removed outlier: 10.264A pdb=" N PHE B 269 " --> pdb=" O LEU B 408 " (cutoff:3.500A) removed outlier: 10.838A pdb=" N ILE B 410 " --> pdb=" O PHE B 269 " (cutoff:3.500A) removed outlier: 10.376A pdb=" N THR B 271 " --> pdb=" O ILE B 410 " (cutoff:3.500A) removed outlier: 10.747A pdb=" N PHE B 412 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 9.267A pdb=" N VAL B 273 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 9.726A pdb=" N VAL B 414 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N CYS B 275 " --> pdb=" O VAL B 414 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ASN B 416 " --> pdb=" O CYS B 275 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLU B 277 " --> pdb=" O ASN B 416 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AA9, first strand: chain 'B' and resid 185 through 189 removed outlier: 7.262A pdb=" N LYS B 193 " --> pdb=" O ASN B 94 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ASN B 94 " --> pdb=" O LYS B 193 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS B 250 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 173 through 174 Processing sheet with id=AB2, first strand: chain 'C' and resid 73 through 81 removed outlier: 10.264A pdb=" N PHE C 269 " --> pdb=" O LEU C 408 " (cutoff:3.500A) removed outlier: 10.838A pdb=" N ILE C 410 " --> pdb=" O PHE C 269 " (cutoff:3.500A) removed outlier: 10.376A pdb=" N THR C 271 " --> pdb=" O ILE C 410 " (cutoff:3.500A) removed outlier: 10.747A pdb=" N PHE C 412 " --> pdb=" O THR C 271 " (cutoff:3.500A) removed outlier: 9.268A pdb=" N VAL C 273 " --> pdb=" O PHE C 412 " (cutoff:3.500A) removed outlier: 9.726A pdb=" N VAL C 414 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N CYS C 275 " --> pdb=" O VAL C 414 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ASN C 416 " --> pdb=" O CYS C 275 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLU C 277 " --> pdb=" O ASN C 416 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA C 274 " --> pdb=" O GLU C 375 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN C 276 " --> pdb=" O GLY C 373 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN C 278 " --> pdb=" O ARG C 371 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 221 through 223 removed outlier: 10.264A pdb=" N PHE C 269 " --> pdb=" O LEU C 408 " (cutoff:3.500A) removed outlier: 10.838A pdb=" N ILE C 410 " --> pdb=" O PHE C 269 " (cutoff:3.500A) removed outlier: 10.376A pdb=" N THR C 271 " --> pdb=" O ILE C 410 " (cutoff:3.500A) removed outlier: 10.747A pdb=" N PHE C 412 " --> pdb=" O THR C 271 " (cutoff:3.500A) removed outlier: 9.268A pdb=" N VAL C 273 " --> pdb=" O PHE C 412 " (cutoff:3.500A) removed outlier: 9.726A pdb=" N VAL C 414 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N CYS C 275 " --> pdb=" O VAL C 414 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ASN C 416 " --> pdb=" O CYS C 275 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLU C 277 " --> pdb=" O ASN C 416 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 85 through 86 Processing sheet with id=AB5, first strand: chain 'C' and resid 185 through 189 removed outlier: 7.262A pdb=" N LYS C 193 " --> pdb=" O ASN C 94 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ASN C 94 " --> pdb=" O LYS C 193 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N HIS C 250 " --> pdb=" O ALA C 89 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 173 through 174 303 hydrogen bonds defined for protein. 810 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: 2.66 Time building geometry restraints manager: 4.33 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: 3154 1.34 - 1.45: 1745 1.45 - 1.57: 5202 1.57 - 1.69: 0 1.69 - 1.81: 108 Bond restraints: 10209 Sorted by residual: bond pdb=" CAI Y01 B 603 " pdb=" CAK Y01 B 603 " ideal model delta sigma weight residual 1.492 1.386 0.106 2.00e-02 2.50e+03 2.80e+01 bond pdb=" CAI Y01 C 603 " pdb=" CAK Y01 C 603 " ideal model delta sigma weight residual 1.492 1.386 0.106 2.00e-02 2.50e+03 2.79e+01 bond pdb=" CAI Y01 A 603 " pdb=" CAK Y01 A 603 " ideal model delta sigma weight residual 1.492 1.387 0.105 2.00e-02 2.50e+03 2.78e+01 bond pdb=" CAI Y01 C 603 " pdb=" CAZ Y01 C 603 " ideal model delta sigma weight residual 1.332 1.380 -0.048 2.00e-02 2.50e+03 5.79e+00 bond pdb=" CAI Y01 A 603 " pdb=" CAZ Y01 A 603 " ideal model delta sigma weight residual 1.332 1.380 -0.048 2.00e-02 2.50e+03 5.78e+00 ... (remaining 10204 not shown) Histogram of bond angle deviations from ideal: 96.80 - 104.23: 175 104.23 - 111.65: 4341 111.65 - 119.08: 3783 119.08 - 126.51: 5464 126.51 - 133.94: 119 Bond angle restraints: 13882 Sorted by residual: angle pdb=" N ILE A 381 " pdb=" CA ILE A 381 " pdb=" C ILE A 381 " ideal model delta sigma weight residual 108.88 117.02 -8.14 2.16e+00 2.14e-01 1.42e+01 angle pdb=" N ILE C 381 " pdb=" CA ILE C 381 " pdb=" C ILE C 381 " ideal model delta sigma weight residual 108.88 116.98 -8.10 2.16e+00 2.14e-01 1.41e+01 angle pdb=" N ILE B 381 " pdb=" CA ILE B 381 " pdb=" C ILE B 381 " ideal model delta sigma weight residual 108.88 116.97 -8.09 2.16e+00 2.14e-01 1.40e+01 angle pdb=" CA ILE C 381 " pdb=" C ILE C 381 " pdb=" N PRO C 382 " ideal model delta sigma weight residual 118.88 124.19 -5.31 1.54e+00 4.22e-01 1.19e+01 angle pdb=" CA ILE B 381 " pdb=" C ILE B 381 " pdb=" N PRO B 382 " ideal model delta sigma weight residual 118.88 124.17 -5.29 1.54e+00 4.22e-01 1.18e+01 ... (remaining 13877 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.89: 5216 16.89 - 33.78: 632 33.78 - 50.68: 135 50.68 - 67.57: 39 67.57 - 84.46: 21 Dihedral angle restraints: 6043 sinusoidal: 2307 harmonic: 3736 Sorted by residual: dihedral pdb=" CB CYS C 323 " pdb=" SG CYS C 323 " pdb=" SG CYS C 345 " pdb=" CB CYS C 345 " ideal model delta sinusoidal sigma weight residual -86.00 -170.46 84.46 1 1.00e+01 1.00e-02 8.67e+01 dihedral pdb=" CB CYS B 323 " pdb=" SG CYS B 323 " pdb=" SG CYS B 345 " pdb=" CB CYS B 345 " ideal model delta sinusoidal sigma weight residual -86.00 -170.45 84.45 1 1.00e+01 1.00e-02 8.67e+01 dihedral pdb=" CB CYS A 323 " pdb=" SG CYS A 323 " pdb=" SG CYS A 345 " pdb=" CB CYS A 345 " ideal model delta sinusoidal sigma weight residual -86.00 -170.45 84.45 1 1.00e+01 1.00e-02 8.67e+01 ... (remaining 6040 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1248 0.067 - 0.135: 270 0.135 - 0.202: 33 0.202 - 0.270: 0 0.270 - 0.337: 6 Chirality restraints: 1557 Sorted by residual: chirality pdb=" CBG Y01 C 603 " pdb=" CAQ Y01 C 603 " pdb=" CBD Y01 C 603 " pdb=" CBI Y01 C 603 " both_signs ideal model delta sigma weight residual False -2.33 -2.67 0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CBG Y01 B 603 " pdb=" CAQ Y01 B 603 " pdb=" CBD Y01 B 603 " pdb=" CBI Y01 B 603 " both_signs ideal model delta sigma weight residual False -2.33 -2.67 0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CBG Y01 A 603 " pdb=" CAQ Y01 A 603 " pdb=" CBD Y01 A 603 " pdb=" CBI Y01 A 603 " both_signs ideal model delta sigma weight residual False -2.33 -2.66 0.33 2.00e-01 2.50e+01 2.77e+00 ... (remaining 1554 not shown) Planarity restraints: 1795 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 338 " -0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO B 339 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 339 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 339 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 338 " 0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO A 339 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 339 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 339 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 338 " -0.031 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO C 339 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 339 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 339 " -0.026 5.00e-02 4.00e+02 ... (remaining 1792 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 25 2.45 - 3.06: 5484 3.06 - 3.67: 14301 3.67 - 4.29: 20002 4.29 - 4.90: 33905 Nonbonded interactions: 73717 Sorted by model distance: nonbonded pdb=" CE1 HIS C 73 " pdb=" OE1 GLN C 422 " model vdw 1.835 3.260 nonbonded pdb=" ND1 HIS C 73 " pdb=" OE1 GLN C 422 " model vdw 1.971 2.520 nonbonded pdb=" CD2 HIS A 73 " pdb=" OE1 GLN A 422 " model vdw 1.990 3.260 nonbonded pdb=" CD2 HIS B 73 " pdb=" OE1 GLN B 422 " model vdw 2.116 3.260 nonbonded pdb=" OD1 ASP A 434 " pdb="NA NA A 604 " model vdw 2.251 2.470 ... (remaining 73712 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 40 through 87 or (resid 88 through 89 and (name N or name \ CA or name C or name O or name CB )) or resid 90 through 198 or (resid 199 and ( \ name N or name CA or name C or name O or name CB )) or resid 200 through 290 or \ (resid 291 through 300 and (name N or name CA or name C or name O or name CB )) \ or resid 301 through 452 or (resid 453 through 455 and (name N or name CA or nam \ e C or name O or name CB )) or resid 456 through 464 or (resid 465 and (name N o \ r name CA or name C or name O or name CB )) or resid 601 through 603)) selection = (chain 'B' and (resid 40 through 42 or (resid 43 through 44 and (name N or name \ CA or name C or name O or name CB )) or resid 45 through 146 or (resid 147 throu \ gh 148 and (name N or name CA or name C or name O or name CB )) or resid 149 thr \ ough 181 or (resid 182 and (name N or name CA or name C or name O or name CB )) \ or resid 183 through 290 or (resid 291 through 300 and (name N or name CA or nam \ e C or name O or name CB )) or resid 301 through 314 or (resid 315 and (name N o \ r name CA or name C or name O or name CB )) or resid 316 through 363 or (resid 3 \ 64 and (name N or name CA or name C or name O or name CB )) or resid 365 through \ 452 or (resid 453 through 455 and (name N or name CA or name C or name O or nam \ e CB )) or resid 456 through 465 or resid 601 through 603)) selection = (chain 'C' and (resid 40 through 87 or (resid 88 through 89 and (name N or name \ CA or name C or name O or name CB )) or resid 90 through 146 or (resid 147 throu \ gh 148 and (name N or name CA or name C or name O or name CB )) or resid 149 thr \ ough 181 or (resid 182 and (name N or name CA or name C or name O or name CB )) \ or resid 183 through 198 or (resid 199 and (name N or name CA or name C or name \ O or name CB )) or resid 200 through 234 or (resid 235 and (name N or name CA or \ name C or name O or name CB )) or resid 236 through 314 or (resid 315 and (name \ N or name CA or name C or name O or name CB )) or resid 316 through 363 or (res \ id 364 and (name N or name CA or name C or name O or name CB )) or resid 365 thr \ ough 457 or (resid 458 through 459 and (name N or name CA or name C or name O or \ name CB )) or resid 460 through 465 or resid 601 through 603)) } 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: 0.750 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: 0.000 Extract box with map and model: 2.620 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 28.340 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 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 0.106 10209 Z= 0.495 Angle : 0.936 9.704 13882 Z= 0.481 Chirality : 0.058 0.337 1557 Planarity : 0.005 0.047 1789 Dihedral : 15.945 84.427 3580 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.35 (0.18), residues: 1272 helix: -4.61 (0.10), residues: 342 sheet: -3.63 (0.23), residues: 300 loop : -2.77 (0.21), residues: 630 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 182 time to evaluate : 1.354 Fit side-chains outliers start: 6 outliers final: 0 residues processed: 188 average time/residue: 0.3252 time to fit residues: 82.8884 Evaluate side-chains 127 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.272 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.5980 chunk 95 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 32 optimal weight: 9.9990 chunk 64 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 114 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS A 276 GLN ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 HIS B 276 GLN B 438 GLN C 66 GLN C 276 GLN C 329 HIS ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 10209 Z= 0.155 Angle : 0.559 7.735 13882 Z= 0.283 Chirality : 0.040 0.129 1557 Planarity : 0.004 0.037 1789 Dihedral : 6.537 58.536 1421 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer Outliers : 1.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -4.06 (0.20), residues: 1272 helix: -2.81 (0.19), residues: 390 sheet: -3.40 (0.25), residues: 279 loop : -2.08 (0.23), residues: 603 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 165 time to evaluate : 1.219 Fit side-chains outliers start: 18 outliers final: 11 residues processed: 182 average time/residue: 0.1895 time to fit residues: 50.6096 Evaluate side-chains 141 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 130 time to evaluate : 1.287 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1221 time to fit residues: 3.9225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 252 GLN A 438 GLN B 66 GLN C 72 HIS C 438 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 10209 Z= 0.304 Angle : 0.609 10.729 13882 Z= 0.304 Chirality : 0.042 0.131 1557 Planarity : 0.003 0.032 1789 Dihedral : 6.371 58.380 1421 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 2.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -3.25 (0.22), residues: 1272 helix: -1.64 (0.25), residues: 372 sheet: -3.12 (0.25), residues: 303 loop : -1.80 (0.25), residues: 597 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 137 time to evaluate : 1.298 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 8 residues processed: 148 average time/residue: 0.1710 time to fit residues: 39.4108 Evaluate side-chains 132 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 124 time to evaluate : 1.394 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1382 time to fit residues: 3.3484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 chunk 59 optimal weight: 0.0040 chunk 12 optimal weight: 7.9990 chunk 54 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 115 optimal weight: 0.5980 chunk 121 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 109 optimal weight: 0.1980 chunk 32 optimal weight: 5.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN B 438 GLN C 252 GLN C 276 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 10209 Z= 0.137 Angle : 0.532 14.091 13882 Z= 0.259 Chirality : 0.040 0.132 1557 Planarity : 0.003 0.036 1789 Dihedral : 5.788 59.997 1421 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer Outliers : 1.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -2.51 (0.24), residues: 1272 helix: -0.99 (0.27), residues: 390 sheet: -2.90 (0.28), residues: 279 loop : -1.33 (0.26), residues: 603 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 158 time to evaluate : 1.155 Fit side-chains outliers start: 19 outliers final: 9 residues processed: 169 average time/residue: 0.1677 time to fit residues: 44.0680 Evaluate side-chains 142 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 133 time to evaluate : 1.208 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0951 time to fit residues: 3.1997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 50 optimal weight: 30.0000 chunk 103 optimal weight: 7.9990 chunk 84 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 30 optimal weight: 0.1980 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 438 GLN B 72 HIS C 276 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 10209 Z= 0.306 Angle : 0.621 15.401 13882 Z= 0.304 Chirality : 0.042 0.130 1557 Planarity : 0.003 0.043 1789 Dihedral : 5.839 59.642 1421 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer Outliers : 2.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -2.33 (0.24), residues: 1272 helix: -0.70 (0.27), residues: 390 sheet: -2.91 (0.28), residues: 279 loop : -1.27 (0.27), residues: 603 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 134 time to evaluate : 1.281 Fit side-chains outliers start: 23 outliers final: 14 residues processed: 148 average time/residue: 0.1646 time to fit residues: 38.3297 Evaluate side-chains 143 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 129 time to evaluate : 1.288 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1313 time to fit residues: 4.6509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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-1.21rc1-4938/modules/cctbx_project/iotbx/cli_parser.py", line 870, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/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: 69.4971 > 50: distance: 100 - 210: 30.545 distance: 111 - 197: 25.573 distance: 124 - 174: 30.825 distance: 154 - 159: 33.293 distance: 159 - 160: 32.934 distance: 160 - 161: 30.062 distance: 160 - 163: 29.545 distance: 161 - 162: 42.963 distance: 161 - 167: 23.747 distance: 163 - 164: 29.208 distance: 164 - 165: 48.563 distance: 164 - 166: 28.370 distance: 167 - 168: 13.327 distance: 168 - 169: 35.617 distance: 168 - 171: 12.857 distance: 169 - 170: 8.994 distance: 169 - 174: 5.695 distance: 171 - 172: 28.732 distance: 171 - 173: 34.062 distance: 174 - 175: 69.497 distance: 175 - 176: 42.189 distance: 175 - 178: 66.234 distance: 176 - 177: 14.926 distance: 176 - 185: 41.711 distance: 179 - 180: 18.514 distance: 180 - 181: 35.154 distance: 181 - 182: 3.425 distance: 182 - 183: 22.959 distance: 182 - 184: 17.875 distance: 185 - 186: 31.561 distance: 186 - 187: 50.838 distance: 186 - 189: 38.927 distance: 187 - 188: 42.016 distance: 187 - 197: 39.649 distance: 189 - 190: 18.698 distance: 190 - 191: 16.833 distance: 190 - 192: 6.481 distance: 191 - 193: 26.001 distance: 192 - 194: 35.014 distance: 193 - 195: 26.755 distance: 194 - 195: 24.545 distance: 195 - 196: 17.837 distance: 197 - 198: 41.879 distance: 198 - 199: 21.997 distance: 199 - 200: 29.379 distance: 199 - 201: 10.669 distance: 201 - 202: 36.217 distance: 202 - 203: 35.456 distance: 202 - 205: 36.073 distance: 203 - 210: 5.205 distance: 205 - 206: 10.577 distance: 206 - 207: 18.079 distance: 207 - 208: 35.321 distance: 208 - 209: 22.018 distance: 210 - 211: 7.220 distance: 211 - 212: 6.192 distance: 211 - 214: 27.796 distance: 212 - 213: 40.105 distance: 212 - 219: 36.492 distance: 214 - 215: 8.164 distance: 215 - 216: 21.567 distance: 216 - 217: 11.158 distance: 216 - 218: 42.640 distance: 219 - 220: 40.758 distance: 220 - 221: 26.531 distance: 220 - 223: 38.901 distance: 221 - 222: 23.029 distance: 221 - 227: 28.964 distance: 223 - 224: 47.702 distance: 224 - 225: 10.739 distance: 224 - 226: 17.080 distance: 227 - 228: 43.658 distance: 228 - 229: 17.354 distance: 228 - 231: 21.097 distance: 229 - 230: 12.826 distance: 229 - 233: 17.117 distance: 231 - 232: 21.611 distance: 233 - 234: 11.979 distance: 234 - 235: 12.411 distance: 234 - 237: 33.247 distance: 235 - 236: 32.103 distance: 235 - 241: 23.404 distance: 237 - 238: 15.870 distance: 238 - 239: 17.769 distance: 239 - 240: 25.065