Starting phenix.real_space_refine on Sat Dec 9 03:48:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fii_31598/12_2023/7fii_31598.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fii_31598/12_2023/7fii_31598.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fii_31598/12_2023/7fii_31598.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fii_31598/12_2023/7fii_31598.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fii_31598/12_2023/7fii_31598.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fii_31598/12_2023/7fii_31598.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1206 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 5458 2.51 5 N 1616 2.21 5 O 1643 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 311": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 8765 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2131 Classifications: {'peptide': 359} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 222} Link IDs: {'PTRANS': 8, 'TRANS': 350} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 828 Unresolved non-hydrogen angles: 1041 Unresolved non-hydrogen dihedrals: 675 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'GLN:plan1': 16, 'ASP:plan': 25, 'TYR:plan': 9, 'ASN:plan1': 14, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 8, 'GLU:plan': 19, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 511 Chain: "B" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2060 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 166} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 553 Unresolved non-hydrogen angles: 699 Unresolved non-hydrogen dihedrals: 429 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 12, 'ASP:plan': 26, 'ASN%COO:plan1': 1, 'PHE:plan': 4, 'GLU:plan': 8, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 335 Chain: "G" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 307 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 66 Chain: "R" Number of atoms: 3262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 3262 Classifications: {'peptide': 570} Incomplete info: {'backbone_only': 10, 'truncation_to_alanine': 371} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 541} Chain breaks: 1 Unresolved chain link angles: 22 Unresolved non-hydrogen bonds: 1295 Unresolved non-hydrogen angles: 1658 Unresolved non-hydrogen dihedrals: 1055 Unresolved non-hydrogen chiralities: 148 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 5, 'TYR:plan': 14, 'ASN:plan1': 27, 'TRP:plan': 1, 'ASP:plan': 14, 'PHE:plan': 21, 'GLU:plan': 24, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 613 Chain: "X" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 450 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 6, 'TRANS': 81} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 314 Unresolved non-hydrogen dihedrals: 210 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 4, 'ASP:plan': 1, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 133 Chain: "Y" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 555 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 12, 'TRANS': 97} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 285 Unresolved non-hydrogen angles: 369 Unresolved non-hydrogen dihedrals: 226 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 134 Time building chain proxies: 5.70, per 1000 atoms: 0.65 Number of scatterers: 8765 At special positions: 0 Unit cell: (88.893, 95.319, 184.212, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1643 8.00 N 1616 7.00 C 5458 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS R 439 " - pdb=" SG CYS R 514 " distance=2.03 Simple disulfide: pdb=" SG CYS X 7 " - pdb=" SG CYS X 31 " distance=2.03 Simple disulfide: pdb=" SG CYS X 10 " - pdb=" SG CYS X 60 " distance=2.03 Simple disulfide: pdb=" SG CYS X 28 " - pdb=" SG CYS X 82 " distance=2.03 Simple disulfide: pdb=" SG CYS X 32 " - pdb=" SG CYS X 84 " distance=2.03 Simple disulfide: pdb=" SG CYS X 59 " - pdb=" SG CYS X 87 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 9 " - pdb=" SG CYS Y 57 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 23 " - pdb=" SG CYS Y 72 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 26 " - pdb=" SG CYS Y 110 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 34 " - pdb=" SG CYS Y 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 38 " - pdb=" SG CYS Y 90 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 93 " - pdb=" SG CYS Y 100 " 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 Time building additional restraints: 3.77 Conformation dependent library (CDL) restraints added in 2.2 seconds 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2864 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 19 sheets defined 36.1% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.515A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 45 through 55 removed outlier: 3.539A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 91 Processing helix chain 'A' and resid 99 through 113 Processing helix chain 'A' and resid 120 through 133 removed outlier: 3.627A pdb=" N ASP A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 143 Processing helix chain 'A' and resid 151 through 163 removed outlier: 4.728A pdb=" N ASP A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N ARG A 161 " --> pdb=" O ASN A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 179 Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.231A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 218 removed outlier: 3.722A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASP A 217 " --> pdb=" O CYS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 260 through 270 removed outlier: 3.798A pdb=" N ALA A 270 " --> pdb=" O GLU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 279 Processing helix chain 'A' and resid 280 through 283 removed outlier: 3.509A pdb=" N ALA A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 298 through 317 Processing helix chain 'A' and resid 337 through 358 removed outlier: 3.610A pdb=" N GLN A 357 " --> pdb=" O MET A 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.842A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 46 removed outlier: 3.511A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LYS G 46 " --> pdb=" O GLU G 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 265 Processing helix chain 'R' and resid 275 through 280 removed outlier: 3.569A pdb=" N CYS R 279 " --> pdb=" O TYR R 275 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N CYS R 280 " --> pdb=" O PRO R 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 275 through 280' Processing helix chain 'R' and resid 361 through 386 removed outlier: 4.312A pdb=" N TRP R 367 " --> pdb=" O ARG R 363 " (cutoff:3.500A) Processing helix chain 'R' and resid 392 through 422 Processing helix chain 'R' and resid 425 through 436 removed outlier: 4.628A pdb=" N ILE R 431 " --> pdb=" O TYR R 427 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ASP R 432 " --> pdb=" O ASN R 428 " (cutoff:3.500A) Processing helix chain 'R' and resid 436 through 470 removed outlier: 3.956A pdb=" N SER R 440 " --> pdb=" O GLY R 436 " (cutoff:3.500A) Processing helix chain 'R' and resid 479 through 504 removed outlier: 3.977A pdb=" N LEU R 485 " --> pdb=" O ARG R 481 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE R 486 " --> pdb=" O HIS R 482 " (cutoff:3.500A) Proline residue: R 501 - end of helix removed outlier: 3.511A pdb=" N GLY R 504 " --> pdb=" O LEU R 500 " (cutoff:3.500A) Processing helix chain 'R' and resid 521 through 554 Processing helix chain 'R' and resid 560 through 594 removed outlier: 3.974A pdb=" N ASP R 578 " --> pdb=" O LEU R 574 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N CYS R 581 " --> pdb=" O THR R 577 " (cutoff:3.500A) Proline residue: R 584 - end of helix Processing helix chain 'R' and resid 600 through 611 removed outlier: 3.703A pdb=" N VAL R 606 " --> pdb=" O THR R 602 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU R 607 " --> pdb=" O ASN R 603 " (cutoff:3.500A) Processing helix chain 'R' and resid 613 through 624 Proline residue: R 620 - end of helix Processing helix chain 'R' and resid 627 through 642 Processing helix chain 'X' and resid 40 through 46 Processing helix chain 'X' and resid 71 through 73 No H-bonds generated for 'chain 'X' and resid 71 through 73' Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 34 removed outlier: 6.544A pdb=" N HIS A 34 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N PHE A 199 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N MET A 198 " --> pdb=" O THR A 187 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR A 187 " --> pdb=" O MET A 198 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP A 200 " --> pdb=" O PHE A 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 34 removed outlier: 6.544A pdb=" N HIS A 34 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N PHE A 199 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N GLY A 40 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU A 39 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N ASP A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N VAL A 254 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N HIS A 329 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LEU A 256 " --> pdb=" O HIS A 329 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.934A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU B 51 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 62 removed outlier: 3.945A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 103 removed outlier: 3.581A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYS B 114 " --> pdb=" O SER B 122 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 150 removed outlier: 4.257A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG B 150 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL B 158 " --> pdb=" O ARG B 150 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.857A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 4.181A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.578A pdb=" N ALA B 287 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN B 295 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL B 296 " --> pdb=" O GLY B 306 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 53 through 54 removed outlier: 6.104A pdb=" N LEU R 54 " --> pdb=" O GLU R 79 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N PHE R 151 " --> pdb=" O THR R 178 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N LYS R 180 " --> pdb=" O PHE R 151 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU R 153 " --> pdb=" O LYS R 180 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N VAL R 177 " --> pdb=" O SER R 201 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N GLU R 203 " --> pdb=" O VAL R 177 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N LEU R 179 " --> pdb=" O GLU R 203 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR R 226 " --> pdb=" O THR R 200 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU R 248 " --> pdb=" O THR R 272 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA R 344 " --> pdb=" O ALA R 271 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 63 through 64 removed outlier: 3.930A pdb=" N ILE R 64 " --> pdb=" O ARG R 88 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE R 89 " --> pdb=" O TYR R 113 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'R' and resid 94 through 95 removed outlier: 6.090A pdb=" N PHE R 94 " --> pdb=" O ILE R 120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'R' and resid 195 through 197 Processing sheet with id=AB5, first strand: chain 'X' and resid 11 through 14 removed outlier: 3.737A pdb=" N MET X 29 " --> pdb=" O THR X 11 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLY X 30 " --> pdb=" O THR Y 40 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N THR Y 40 " --> pdb=" O GLY X 30 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'X' and resid 35 through 37 removed outlier: 3.638A pdb=" N ARG X 35 " --> pdb=" O GLU X 56 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'X' and resid 60 through 62 Processing sheet with id=AB8, first strand: chain 'X' and resid 65 through 69 removed outlier: 3.523A pdb=" N VAL X 76 " --> pdb=" O VAL X 68 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'Y' and resid 10 through 18 removed outlier: 3.567A pdb=" N ALA Y 35 " --> pdb=" O ARG Y 10 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Y' and resid 56 through 68 removed outlier: 5.980A pdb=" N CYS Y 57 " --> pdb=" O CYS Y 90 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N CYS Y 90 " --> pdb=" O CYS Y 57 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N TYR Y 59 " --> pdb=" O CYS Y 88 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N CYS Y 88 " --> pdb=" O TYR Y 59 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ASP Y 61 " --> pdb=" O LEU Y 86 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU Y 86 " --> pdb=" O ASP Y 61 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE Y 67 " --> pdb=" O VAL Y 80 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL Y 80 " --> pdb=" O ILE Y 67 " (cutoff:3.500A) 482 hydrogen bonds defined for protein. 1410 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: 2.88 Time building geometry restraints manager: 4.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3168 1.35 - 1.46: 2018 1.46 - 1.58: 3621 1.58 - 1.70: 0 1.70 - 1.81: 59 Bond restraints: 8866 Sorted by residual: bond pdb=" N GLU R 32 " pdb=" CA GLU R 32 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.08e+00 bond pdb=" N CYS A 3 " pdb=" CA CYS A 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 bond pdb=" N GLU B 3 " pdb=" CA GLU B 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 bond pdb=" N GLN X 5 " pdb=" CA GLN X 5 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.99e+00 bond pdb=" N LYS Y 2 " pdb=" CA LYS Y 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 ... (remaining 8861 not shown) Histogram of bond angle deviations from ideal: 100.74 - 107.38: 164 107.38 - 114.03: 4982 114.03 - 120.68: 3664 120.68 - 127.33: 3389 127.33 - 133.98: 51 Bond angle restraints: 12250 Sorted by residual: angle pdb=" N CYS R 581 " pdb=" CA CYS R 581 " pdb=" C CYS R 581 " ideal model delta sigma weight residual 114.62 111.41 3.21 1.14e+00 7.69e-01 7.91e+00 angle pdb=" C THR R 580 " pdb=" N CYS R 581 " pdb=" CA CYS R 581 " ideal model delta sigma weight residual 121.63 126.70 -5.07 1.91e+00 2.74e-01 7.05e+00 angle pdb=" CA ILE B 93 " pdb=" C ILE B 93 " pdb=" O ILE B 93 " ideal model delta sigma weight residual 120.88 119.65 1.23 6.80e-01 2.16e+00 3.26e+00 angle pdb=" CA ASP A 94 " pdb=" C ASP A 94 " pdb=" N PHE A 95 " ideal model delta sigma weight residual 114.76 116.78 -2.02 1.14e+00 7.69e-01 3.15e+00 angle pdb=" CA ILE B 93 " pdb=" C ILE B 93 " pdb=" N PRO B 94 " ideal model delta sigma weight residual 118.12 119.55 -1.43 8.10e-01 1.52e+00 3.11e+00 ... (remaining 12245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 4918 16.52 - 33.04: 160 33.04 - 49.55: 34 49.55 - 66.07: 4 66.07 - 82.59: 2 Dihedral angle restraints: 5118 sinusoidal: 716 harmonic: 4402 Sorted by residual: dihedral pdb=" CB CYS X 28 " pdb=" SG CYS X 28 " pdb=" SG CYS X 82 " pdb=" CB CYS X 82 " ideal model delta sinusoidal sigma weight residual 93.00 174.74 -81.74 1 1.00e+01 1.00e-02 8.22e+01 dihedral pdb=" CB CYS Y 38 " pdb=" SG CYS Y 38 " pdb=" SG CYS Y 90 " pdb=" CB CYS Y 90 " ideal model delta sinusoidal sigma weight residual 93.00 28.21 64.79 1 1.00e+01 1.00e-02 5.51e+01 dihedral pdb=" CB CYS R 439 " pdb=" SG CYS R 439 " pdb=" SG CYS R 514 " pdb=" CB CYS R 514 " ideal model delta sinusoidal sigma weight residual -86.00 -126.86 40.86 1 1.00e+01 1.00e-02 2.34e+01 ... (remaining 5115 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 936 0.026 - 0.052: 409 0.052 - 0.077: 108 0.077 - 0.103: 54 0.103 - 0.129: 65 Chirality restraints: 1572 Sorted by residual: chirality pdb=" CA ILE R 64 " pdb=" N ILE R 64 " pdb=" C ILE R 64 " pdb=" CB ILE R 64 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 chirality pdb=" CA ILE R 155 " pdb=" N ILE R 155 " pdb=" C ILE R 155 " pdb=" CB ILE R 155 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.96e-01 chirality pdb=" CA ILE R 80 " pdb=" N ILE R 80 " pdb=" C ILE R 80 " pdb=" CB ILE R 80 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.91e-01 ... (remaining 1569 not shown) Planarity restraints: 1659 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL R 596 " -0.022 5.00e-02 4.00e+02 3.42e-02 1.87e+00 pdb=" N PRO R 597 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO R 597 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO R 597 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE R 515 " -0.013 5.00e-02 4.00e+02 1.95e-02 6.08e-01 pdb=" N PRO R 516 " 0.034 5.00e-02 4.00e+02 pdb=" CA PRO R 516 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO R 516 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR R 612 " -0.009 5.00e-02 4.00e+02 1.39e-02 3.09e-01 pdb=" N PRO R 613 " 0.024 5.00e-02 4.00e+02 pdb=" CA PRO R 613 " -0.007 5.00e-02 4.00e+02 pdb=" CD PRO R 613 " -0.008 5.00e-02 4.00e+02 ... (remaining 1656 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 37 2.64 - 3.20: 7981 3.20 - 3.77: 12863 3.77 - 4.33: 14620 4.33 - 4.90: 25551 Nonbonded interactions: 61052 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" O THR B 165 " model vdw 2.073 2.440 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.138 2.440 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.361 2.440 nonbonded pdb=" OE1 GLN A 213 " pdb=" NH1 ARG B 314 " model vdw 2.388 2.520 nonbonded pdb=" O THR A 181 " pdb=" ND2 ASN B 119 " model vdw 2.409 2.520 ... (remaining 61047 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.46 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.020 Extract box with map and model: 4.000 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 28.530 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 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 : 0.002 0.033 8866 Z= 0.110 Angle : 0.360 5.073 12250 Z= 0.219 Chirality : 0.039 0.129 1572 Planarity : 0.001 0.034 1659 Dihedral : 8.974 82.588 2218 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: 3.08 (0.24), residues: 1508 helix: 3.93 (0.24), residues: 508 sheet: 1.69 (0.39), residues: 208 loop : 0.97 (0.24), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP R 465 HIS 0.002 0.000 HIS A 324 PHE 0.005 0.000 PHE B 235 TYR 0.008 0.001 TYR B 105 ARG 0.009 0.001 ARG A 31 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.070 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.1452 time to fit residues: 23.1367 Evaluate side-chains 74 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 1.056 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 38 optimal weight: 40.0000 chunk 76 optimal weight: 50.0000 chunk 60 optimal weight: 9.9990 chunk 116 optimal weight: 8.9990 chunk 45 optimal weight: 8.9990 chunk 71 optimal weight: 20.0000 chunk 86 optimal weight: 6.9990 chunk 135 optimal weight: 50.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN R 429 HIS R 466 HIS R 535 ASN R 615 ASN R 619 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 8866 Z= 0.506 Angle : 0.708 9.177 12250 Z= 0.408 Chirality : 0.046 0.221 1572 Planarity : 0.004 0.056 1659 Dihedral : 4.552 28.675 1553 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.12 % Allowed : 12.64 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: 1.14 (0.22), residues: 1508 helix: 1.96 (0.23), residues: 518 sheet: -0.06 (0.31), residues: 275 loop : 0.31 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.004 TRP B 82 HIS 0.019 0.004 HIS B 54 PHE 0.043 0.003 PHE R 611 TYR 0.033 0.003 TYR R 527 ARG 0.006 0.001 ARG A 31 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 79 time to evaluate : 0.947 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 83 average time/residue: 0.1352 time to fit residues: 18.5793 Evaluate side-chains 64 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 61 time to evaluate : 1.135 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0938 time to fit residues: 1.8522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 75 optimal weight: 0.0870 chunk 41 optimal weight: 0.6980 chunk 112 optimal weight: 0.6980 chunk 92 optimal weight: 30.0000 chunk 37 optimal weight: 6.9990 chunk 135 optimal weight: 0.0970 chunk 146 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 134 optimal weight: 30.0000 chunk 46 optimal weight: 4.9990 chunk 108 optimal weight: 0.3980 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS B 311 HIS R 615 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8866 Z= 0.110 Angle : 0.409 7.746 12250 Z= 0.227 Chirality : 0.040 0.135 1572 Planarity : 0.002 0.026 1659 Dihedral : 3.197 19.131 1553 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: 1.86 (0.23), residues: 1508 helix: 2.80 (0.23), residues: 519 sheet: 0.21 (0.32), residues: 260 loop : 0.58 (0.25), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.002 0.001 HIS B 183 PHE 0.011 0.001 PHE A 189 TYR 0.013 0.001 TYR R 527 ARG 0.002 0.001 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 1.072 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1581 time to fit residues: 25.7394 Evaluate side-chains 71 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 1.049 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 133 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 70 optimal weight: 9.9990 chunk 15 optimal weight: 50.0000 chunk 64 optimal weight: 8.9990 chunk 91 optimal weight: 50.0000 chunk 136 optimal weight: 40.0000 chunk 144 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 128 optimal weight: 8.9990 chunk 38 optimal weight: 40.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.4595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 8866 Z= 0.445 Angle : 0.616 8.042 12250 Z= 0.352 Chirality : 0.045 0.166 1572 Planarity : 0.004 0.038 1659 Dihedral : 4.465 27.235 1553 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.28 % Allowed : 8.43 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.22), residues: 1508 helix: 1.79 (0.23), residues: 525 sheet: -0.60 (0.32), residues: 265 loop : 0.03 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP R 491 HIS 0.011 0.002 HIS B 183 PHE 0.033 0.003 PHE A 240 TYR 0.024 0.003 TYR B 105 ARG 0.005 0.001 ARG A 31 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 72 time to evaluate : 1.112 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 73 average time/residue: 0.1394 time to fit residues: 17.1284 Evaluate side-chains 57 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 1.071 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0788 time to fit residues: 1.4651 ------------------------------------------------------------------------------- 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-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.6405 > 50: distance: 10 - 68: 4.425 distance: 28 - 30: 9.279 distance: 30 - 31: 10.538 distance: 31 - 32: 4.785 distance: 32 - 33: 4.682 distance: 32 - 34: 3.428 distance: 34 - 35: 5.727 distance: 35 - 36: 4.884 distance: 36 - 37: 7.280 distance: 36 - 38: 8.118 distance: 38 - 39: 8.374 distance: 39 - 40: 3.970 distance: 40 - 41: 5.318 distance: 40 - 42: 10.049 distance: 42 - 43: 13.611 distance: 43 - 44: 8.503 distance: 44 - 45: 14.379 distance: 44 - 46: 6.931 distance: 46 - 47: 24.714 distance: 47 - 48: 26.673 distance: 47 - 50: 20.397 distance: 48 - 49: 17.551 distance: 48 - 51: 7.249 distance: 51 - 52: 15.889 distance: 52 - 53: 11.160 distance: 53 - 54: 21.312 distance: 53 - 55: 20.346 distance: 55 - 56: 11.503 distance: 56 - 57: 12.862 distance: 56 - 59: 25.838 distance: 57 - 58: 17.712 distance: 57 - 60: 12.863 distance: 60 - 61: 9.009 distance: 61 - 62: 8.243 distance: 61 - 64: 6.101 distance: 62 - 63: 6.959 distance: 62 - 65: 6.827 distance: 65 - 66: 9.109 distance: 66 - 69: 13.000 distance: 67 - 70: 5.570 distance: 70 - 71: 10.320 distance: 71 - 72: 5.167 distance: 71 - 74: 15.207 distance: 72 - 73: 7.821 distance: 72 - 75: 5.635