Starting phenix.real_space_refine on Tue Dec 12 18:35:50 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e4t_30987/12_2023/7e4t_30987.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e4t_30987/12_2023/7e4t_30987.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e4t_30987/12_2023/7e4t_30987.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e4t_30987/12_2023/7e4t_30987.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e4t_30987/12_2023/7e4t_30987.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e4t_30987/12_2023/7e4t_30987.pdb" } resolution = 3.0 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= 0.176 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: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 4 6.06 5 P 8 5.49 5 S 116 5.16 5 C 14632 2.51 5 N 3564 2.21 5 O 3948 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 17": "NH1" <-> "NH2" Residue "A ARG 71": "NH1" <-> "NH2" Residue "A ARG 165": "NH1" <-> "NH2" Residue "A ARG 175": "NH1" <-> "NH2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "A ARG 196": "NH1" <-> "NH2" Residue "A GLU 214": "OE1" <-> "OE2" Residue "A ARG 222": "NH1" <-> "NH2" Residue "A ARG 263": "NH1" <-> "NH2" Residue "A GLU 266": "OE1" <-> "OE2" Residue "A ARG 323": "NH1" <-> "NH2" Residue "A ARG 512": "NH1" <-> "NH2" Residue "B ARG 17": "NH1" <-> "NH2" Residue "B ARG 71": "NH1" <-> "NH2" Residue "B ARG 165": "NH1" <-> "NH2" Residue "B ARG 175": "NH1" <-> "NH2" Residue "B ARG 191": "NH1" <-> "NH2" Residue "B ARG 196": "NH1" <-> "NH2" Residue "B GLU 214": "OE1" <-> "OE2" Residue "B ARG 222": "NH1" <-> "NH2" Residue "B ARG 263": "NH1" <-> "NH2" Residue "B GLU 266": "OE1" <-> "OE2" Residue "B ARG 323": "NH1" <-> "NH2" Residue "B ARG 512": "NH1" <-> "NH2" Residue "C ARG 17": "NH1" <-> "NH2" Residue "C ARG 71": "NH1" <-> "NH2" Residue "C ARG 165": "NH1" <-> "NH2" Residue "C ARG 175": "NH1" <-> "NH2" Residue "C ARG 191": "NH1" <-> "NH2" Residue "C ARG 196": "NH1" <-> "NH2" Residue "C GLU 214": "OE1" <-> "OE2" Residue "C ARG 222": "NH1" <-> "NH2" Residue "C ARG 263": "NH1" <-> "NH2" Residue "C GLU 266": "OE1" <-> "OE2" Residue "C ARG 323": "NH1" <-> "NH2" Residue "C ARG 512": "NH1" <-> "NH2" Residue "D ARG 17": "NH1" <-> "NH2" Residue "D ARG 71": "NH1" <-> "NH2" Residue "D ARG 165": "NH1" <-> "NH2" Residue "D ARG 175": "NH1" <-> "NH2" Residue "D ARG 191": "NH1" <-> "NH2" Residue "D ARG 196": "NH1" <-> "NH2" Residue "D GLU 214": "OE1" <-> "OE2" Residue "D ARG 222": "NH1" <-> "NH2" Residue "D ARG 263": "NH1" <-> "NH2" Residue "D GLU 266": "OE1" <-> "OE2" Residue "D ARG 323": "NH1" <-> "NH2" Residue "D ARG 512": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 22276 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 5412 Classifications: {'peptide': 664} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 639} Chain breaks: 5 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 5412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 5412 Classifications: {'peptide': 664} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 639} Chain breaks: 5 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 5412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 5412 Classifications: {'peptide': 664} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 639} Chain breaks: 5 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "D" Number of atoms: 5412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 5412 Classifications: {'peptide': 664} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 639} Chain breaks: 5 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "A" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 157 Unusual residues: {' CA': 1, ' ZN': 1, 'POV': 1, 'PTY': 1, 'Y01': 1, 'YZY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 22 Chain: "B" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 157 Unusual residues: {' CA': 1, ' ZN': 1, 'POV': 1, 'PTY': 1, 'Y01': 1, 'YZY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 22 Chain: "C" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 157 Unusual residues: {' CA': 1, ' ZN': 1, 'POV': 1, 'PTY': 1, 'Y01': 1, 'YZY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 22 Chain: "D" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 157 Unusual residues: {' CA': 1, ' ZN': 1, 'POV': 1, 'PTY': 1, 'Y01': 1, 'YZY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 22 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1148 SG CYS A 176 14.234 43.015 61.526 1.00172.12 S ATOM 1162 SG CYS A 178 13.069 40.045 59.271 1.00194.88 S ATOM 1184 SG CYS A 181 16.749 40.871 59.364 1.00197.66 S ATOM 6560 SG CYS B 176 69.847 14.233 61.520 1.00172.12 S ATOM 6574 SG CYS B 178 72.817 13.068 59.264 1.00194.88 S ATOM 6596 SG CYS B 181 71.991 16.748 59.358 1.00197.66 S ATOM 11972 SG CYS C 176 98.629 69.846 61.512 1.00172.12 S ATOM 11986 SG CYS C 178 99.793 72.816 59.256 1.00194.88 S ATOM 12008 SG CYS C 181 96.113 71.990 59.350 1.00197.66 S ATOM 17384 SG CYS D 176 43.016 98.628 61.518 1.00172.12 S ATOM 17398 SG CYS D 178 40.046 99.793 59.263 1.00194.88 S ATOM 17420 SG CYS D 181 40.871 96.112 59.357 1.00197.66 S Time building chain proxies: 12.00, per 1000 atoms: 0.54 Number of scatterers: 22276 At special positions: 0 Unit cell: (113.905, 113.905, 136.895, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Ca 4 19.99 S 116 16.00 P 8 15.00 O 3948 8.00 N 3564 7.00 C 14632 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 553 " - pdb=" SG CYS A 558 " distance=2.03 Simple disulfide: pdb=" SG CYS B 553 " - pdb=" SG CYS B 558 " distance=2.03 Simple disulfide: pdb=" SG CYS C 553 " - pdb=" SG CYS C 558 " distance=2.03 Simple disulfide: pdb=" SG CYS D 553 " - pdb=" SG CYS D 558 " 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: 9.68 Conformation dependent library (CDL) restraints added in 4.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 804 " pdb="ZN ZN A 804 " - pdb=" ND1 HIS A 172 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 176 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 178 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 181 " pdb=" ZN B 804 " pdb="ZN ZN B 804 " - pdb=" ND1 HIS B 172 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 176 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 178 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 181 " pdb=" ZN C 804 " pdb="ZN ZN C 804 " - pdb=" ND1 HIS C 172 " pdb="ZN ZN C 804 " - pdb=" SG CYS C 176 " pdb="ZN ZN C 804 " - pdb=" SG CYS C 178 " pdb="ZN ZN C 804 " - pdb=" SG CYS C 181 " pdb=" ZN D 804 " pdb="ZN ZN D 804 " - pdb=" ND1 HIS D 172 " pdb="ZN ZN D 804 " - pdb=" SG CYS D 176 " pdb="ZN ZN D 804 " - pdb=" SG CYS D 178 " pdb="ZN ZN D 804 " - pdb=" SG CYS D 181 " Number of angles added : 12 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5120 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 4 sheets defined 77.3% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'A' and resid 30 through 43 Processing helix chain 'A' and resid 44 through 59 removed outlier: 3.693A pdb=" N ILE A 57 " --> pdb=" O GLN A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 82 through 92 Processing helix chain 'A' and resid 98 through 106 Processing helix chain 'A' and resid 108 through 118 Processing helix chain 'A' and resid 144 through 153 Processing helix chain 'A' and resid 154 through 164 removed outlier: 3.810A pdb=" N LYS A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 188 Processing helix chain 'A' and resid 188 through 204 removed outlier: 3.504A pdb=" N SER A 193 " --> pdb=" O SER A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 211 Processing helix chain 'A' and resid 215 through 234 Processing helix chain 'A' and resid 237 through 258 removed outlier: 3.889A pdb=" N TYR A 241 " --> pdb=" O PHE A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 270 Processing helix chain 'A' and resid 287 through 296 Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 304 through 316 Processing helix chain 'A' and resid 326 through 340 Processing helix chain 'A' and resid 340 through 351 Processing helix chain 'A' and resid 362 through 385 removed outlier: 3.913A pdb=" N SER A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 426 Proline residue: A 409 - end of helix Processing helix chain 'A' and resid 427 through 432 Processing helix chain 'A' and resid 435 through 460 Processing helix chain 'A' and resid 465 through 469 Processing helix chain 'A' and resid 473 through 492 Processing helix chain 'A' and resid 493 through 500 removed outlier: 3.782A pdb=" N THR A 498 " --> pdb=" O SER A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 540 removed outlier: 4.102A pdb=" N LEU A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASP A 516 " --> pdb=" O ARG A 512 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE A 522 " --> pdb=" O LEU A 518 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE A 523 " --> pdb=" O LYS A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 543 No H-bonds generated for 'chain 'A' and resid 541 through 543' Processing helix chain 'A' and resid 567 through 580 removed outlier: 3.695A pdb=" N VAL A 579 " --> pdb=" O LEU A 575 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE A 580 " --> pdb=" O PHE A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 588 removed outlier: 3.636A pdb=" N VAL A 587 " --> pdb=" O ASN A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 613 Processing helix chain 'A' and resid 614 through 633 removed outlier: 3.812A pdb=" N ASN A 618 " --> pdb=" O VAL A 614 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN A 629 " --> pdb=" O ASN A 625 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 630 " --> pdb=" O ASN A 626 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 631 " --> pdb=" O SER A 627 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASP A 633 " --> pdb=" O GLN A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 650 removed outlier: 3.700A pdb=" N TYR A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 731 Processing helix chain 'A' and resid 740 through 761 Processing helix chain 'B' and resid 30 through 43 Processing helix chain 'B' and resid 44 through 59 removed outlier: 3.693A pdb=" N ILE B 57 " --> pdb=" O GLN B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'B' and resid 98 through 106 Processing helix chain 'B' and resid 108 through 118 Processing helix chain 'B' and resid 144 through 153 Processing helix chain 'B' and resid 154 through 164 removed outlier: 3.810A pdb=" N LYS B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 188 Processing helix chain 'B' and resid 188 through 204 removed outlier: 3.503A pdb=" N SER B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 211 Processing helix chain 'B' and resid 215 through 234 Processing helix chain 'B' and resid 237 through 258 removed outlier: 3.889A pdb=" N TYR B 241 " --> pdb=" O PHE B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 270 Processing helix chain 'B' and resid 287 through 296 Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 304 through 316 Processing helix chain 'B' and resid 326 through 340 Processing helix chain 'B' and resid 340 through 351 Processing helix chain 'B' and resid 362 through 385 removed outlier: 3.913A pdb=" N SER B 385 " --> pdb=" O LEU B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 426 Proline residue: B 409 - end of helix Processing helix chain 'B' and resid 427 through 432 Processing helix chain 'B' and resid 435 through 460 Processing helix chain 'B' and resid 465 through 469 Processing helix chain 'B' and resid 473 through 492 Processing helix chain 'B' and resid 493 through 500 removed outlier: 3.782A pdb=" N THR B 498 " --> pdb=" O SER B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 540 removed outlier: 4.101A pdb=" N LEU B 515 " --> pdb=" O GLY B 511 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASP B 516 " --> pdb=" O ARG B 512 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE B 522 " --> pdb=" O LEU B 518 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ILE B 523 " --> pdb=" O LYS B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 543 No H-bonds generated for 'chain 'B' and resid 541 through 543' Processing helix chain 'B' and resid 567 through 580 removed outlier: 3.695A pdb=" N VAL B 579 " --> pdb=" O LEU B 575 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE B 580 " --> pdb=" O PHE B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 588 removed outlier: 3.636A pdb=" N VAL B 587 " --> pdb=" O ASN B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 613 Processing helix chain 'B' and resid 614 through 633 removed outlier: 3.813A pdb=" N ASN B 618 " --> pdb=" O VAL B 614 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN B 629 " --> pdb=" O ASN B 625 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B 630 " --> pdb=" O ASN B 626 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE B 631 " --> pdb=" O SER B 627 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASP B 633 " --> pdb=" O GLN B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 650 removed outlier: 3.700A pdb=" N TYR B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 731 Processing helix chain 'B' and resid 740 through 761 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 44 through 59 removed outlier: 3.693A pdb=" N ILE C 57 " --> pdb=" O GLN C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 82 through 92 Processing helix chain 'C' and resid 98 through 106 Processing helix chain 'C' and resid 108 through 118 Processing helix chain 'C' and resid 144 through 153 Processing helix chain 'C' and resid 154 through 164 removed outlier: 3.810A pdb=" N LYS C 164 " --> pdb=" O LEU C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 188 Processing helix chain 'C' and resid 188 through 204 removed outlier: 3.504A pdb=" N SER C 193 " --> pdb=" O SER C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 211 Processing helix chain 'C' and resid 215 through 234 Processing helix chain 'C' and resid 237 through 258 removed outlier: 3.889A pdb=" N TYR C 241 " --> pdb=" O PHE C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 270 Processing helix chain 'C' and resid 287 through 296 Processing helix chain 'C' and resid 298 through 303 Processing helix chain 'C' and resid 304 through 316 Processing helix chain 'C' and resid 326 through 340 Processing helix chain 'C' and resid 340 through 351 Processing helix chain 'C' and resid 362 through 385 removed outlier: 3.912A pdb=" N SER C 385 " --> pdb=" O LEU C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 426 Proline residue: C 409 - end of helix Processing helix chain 'C' and resid 427 through 432 Processing helix chain 'C' and resid 435 through 460 Processing helix chain 'C' and resid 465 through 469 Processing helix chain 'C' and resid 473 through 492 Processing helix chain 'C' and resid 493 through 500 removed outlier: 3.782A pdb=" N THR C 498 " --> pdb=" O SER C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 540 removed outlier: 4.101A pdb=" N LEU C 515 " --> pdb=" O GLY C 511 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASP C 516 " --> pdb=" O ARG C 512 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE C 522 " --> pdb=" O LEU C 518 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ILE C 523 " --> pdb=" O LYS C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 543 No H-bonds generated for 'chain 'C' and resid 541 through 543' Processing helix chain 'C' and resid 567 through 580 removed outlier: 3.695A pdb=" N VAL C 579 " --> pdb=" O LEU C 575 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N PHE C 580 " --> pdb=" O PHE C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 588 removed outlier: 3.636A pdb=" N VAL C 587 " --> pdb=" O ASN C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 613 Processing helix chain 'C' and resid 614 through 633 removed outlier: 3.812A pdb=" N ASN C 618 " --> pdb=" O VAL C 614 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN C 629 " --> pdb=" O ASN C 625 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 630 " --> pdb=" O ASN C 626 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE C 631 " --> pdb=" O SER C 627 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASP C 633 " --> pdb=" O GLN C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 650 removed outlier: 3.701A pdb=" N TYR C 650 " --> pdb=" O LEU C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 731 Processing helix chain 'C' and resid 740 through 761 Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 44 through 59 removed outlier: 3.693A pdb=" N ILE D 57 " --> pdb=" O GLN D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 80 Processing helix chain 'D' and resid 82 through 92 Processing helix chain 'D' and resid 98 through 106 Processing helix chain 'D' and resid 108 through 118 Processing helix chain 'D' and resid 144 through 153 Processing helix chain 'D' and resid 154 through 164 removed outlier: 3.810A pdb=" N LYS D 164 " --> pdb=" O LEU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 188 Processing helix chain 'D' and resid 188 through 204 removed outlier: 3.504A pdb=" N SER D 193 " --> pdb=" O SER D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 211 Processing helix chain 'D' and resid 215 through 234 Processing helix chain 'D' and resid 237 through 258 removed outlier: 3.888A pdb=" N TYR D 241 " --> pdb=" O PHE D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 270 Processing helix chain 'D' and resid 287 through 296 Processing helix chain 'D' and resid 298 through 303 Processing helix chain 'D' and resid 304 through 316 Processing helix chain 'D' and resid 326 through 340 Processing helix chain 'D' and resid 340 through 351 Processing helix chain 'D' and resid 362 through 385 removed outlier: 3.912A pdb=" N SER D 385 " --> pdb=" O LEU D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 426 Proline residue: D 409 - end of helix Processing helix chain 'D' and resid 427 through 432 Processing helix chain 'D' and resid 435 through 460 Processing helix chain 'D' and resid 465 through 469 Processing helix chain 'D' and resid 473 through 492 Processing helix chain 'D' and resid 493 through 500 removed outlier: 3.782A pdb=" N THR D 498 " --> pdb=" O SER D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 540 removed outlier: 4.102A pdb=" N LEU D 515 " --> pdb=" O GLY D 511 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASP D 516 " --> pdb=" O ARG D 512 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE D 522 " --> pdb=" O LEU D 518 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE D 523 " --> pdb=" O LYS D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 543 No H-bonds generated for 'chain 'D' and resid 541 through 543' Processing helix chain 'D' and resid 567 through 580 removed outlier: 3.695A pdb=" N VAL D 579 " --> pdb=" O LEU D 575 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE D 580 " --> pdb=" O PHE D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 588 removed outlier: 3.635A pdb=" N VAL D 587 " --> pdb=" O ASN D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 613 Processing helix chain 'D' and resid 614 through 633 removed outlier: 3.812A pdb=" N ASN D 618 " --> pdb=" O VAL D 614 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN D 629 " --> pdb=" O ASN D 625 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU D 630 " --> pdb=" O ASN D 626 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE D 631 " --> pdb=" O SER D 627 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASP D 633 " --> pdb=" O GLN D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 650 removed outlier: 3.701A pdb=" N TYR D 650 " --> pdb=" O LEU D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 731 Processing helix chain 'D' and resid 740 through 761 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 20 removed outlier: 4.149A pdb=" N VAL B 166 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 168 removed outlier: 4.148A pdb=" N VAL A 166 " --> pdb=" O LEU D 20 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 18 through 20 removed outlier: 4.148A pdb=" N VAL C 166 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 18 through 20 removed outlier: 4.149A pdb=" N VAL D 166 " --> pdb=" O LEU C 20 " (cutoff:3.500A) 1432 hydrogen bonds defined for protein. 4200 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: 7.71 Time building geometry restraints manager: 10.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3500 1.32 - 1.44: 6112 1.44 - 1.57: 12960 1.57 - 1.69: 16 1.69 - 1.81: 188 Bond restraints: 22776 Sorted by residual: bond pdb=" C12 YZY D 806 " pdb=" C13 YZY D 806 " ideal model delta sigma weight residual 1.524 1.320 0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C12 YZY A 806 " pdb=" C13 YZY A 806 " ideal model delta sigma weight residual 1.524 1.320 0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C12 YZY C 806 " pdb=" C13 YZY C 806 " ideal model delta sigma weight residual 1.524 1.320 0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C12 YZY B 806 " pdb=" C13 YZY B 806 " ideal model delta sigma weight residual 1.524 1.320 0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C28 YZY B 806 " pdb=" C29 YZY B 806 " ideal model delta sigma weight residual 1.332 1.504 -0.172 2.00e-02 2.50e+03 7.40e+01 ... (remaining 22771 not shown) Histogram of bond angle deviations from ideal: 99.86 - 106.69: 604 106.69 - 113.52: 12666 113.52 - 120.36: 8693 120.36 - 127.19: 8549 127.19 - 134.02: 272 Bond angle restraints: 30784 Sorted by residual: angle pdb=" C27 YZY D 806 " pdb=" C28 YZY D 806 " pdb=" C29 YZY D 806 " ideal model delta sigma weight residual 128.13 107.59 20.54 3.00e+00 1.11e-01 4.69e+01 angle pdb=" C27 YZY A 806 " pdb=" C28 YZY A 806 " pdb=" C29 YZY A 806 " ideal model delta sigma weight residual 128.13 107.62 20.51 3.00e+00 1.11e-01 4.68e+01 angle pdb=" C27 YZY C 806 " pdb=" C28 YZY C 806 " pdb=" C29 YZY C 806 " ideal model delta sigma weight residual 128.13 107.64 20.49 3.00e+00 1.11e-01 4.67e+01 angle pdb=" C27 YZY B 806 " pdb=" C28 YZY B 806 " pdb=" C29 YZY B 806 " ideal model delta sigma weight residual 128.13 107.65 20.48 3.00e+00 1.11e-01 4.66e+01 angle pdb=" C21 YZY C 806 " pdb=" C20 YZY C 806 " pdb=" O4 YZY C 806 " ideal model delta sigma weight residual 111.77 126.25 -14.48 3.00e+00 1.11e-01 2.33e+01 ... (remaining 30779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.84: 13632 34.84 - 69.68: 236 69.68 - 104.52: 16 104.52 - 139.36: 8 139.36 - 174.21: 12 Dihedral angle restraints: 13904 sinusoidal: 6040 harmonic: 7864 Sorted by residual: dihedral pdb=" C26 YZY B 806 " pdb=" C27 YZY B 806 " pdb=" C28 YZY B 806 " pdb=" C29 YZY B 806 " ideal model delta sinusoidal sigma weight residual 119.11 -66.68 -174.21 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C26 YZY A 806 " pdb=" C27 YZY A 806 " pdb=" C28 YZY A 806 " pdb=" C29 YZY A 806 " ideal model delta sinusoidal sigma weight residual 119.11 -66.70 -174.19 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C26 YZY C 806 " pdb=" C27 YZY C 806 " pdb=" C28 YZY C 806 " pdb=" C29 YZY C 806 " ideal model delta sinusoidal sigma weight residual 119.11 -66.70 -174.19 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 13901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2832 0.046 - 0.092: 520 0.092 - 0.138: 76 0.138 - 0.185: 8 0.185 - 0.231: 8 Chirality restraints: 3444 Sorted by residual: chirality pdb=" CBI Y01 A 803 " pdb=" CAU Y01 A 803 " pdb=" CBE Y01 A 803 " pdb=" CBG Y01 A 803 " both_signs ideal model delta sigma weight residual False 2.94 2.71 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CBI Y01 B 803 " pdb=" CAU Y01 B 803 " pdb=" CBE Y01 B 803 " pdb=" CBG Y01 B 803 " both_signs ideal model delta sigma weight residual False 2.94 2.71 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CBI Y01 C 803 " pdb=" CAU Y01 C 803 " pdb=" CBE Y01 C 803 " pdb=" CBG Y01 C 803 " both_signs ideal model delta sigma weight residual False 2.94 2.71 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 3441 not shown) Planarity restraints: 3784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN C 573 " 0.006 2.00e-02 2.50e+03 1.26e-02 1.59e+00 pdb=" C GLN C 573 " -0.022 2.00e-02 2.50e+03 pdb=" O GLN C 573 " 0.008 2.00e-02 2.50e+03 pdb=" N SER C 574 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 573 " 0.006 2.00e-02 2.50e+03 1.26e-02 1.59e+00 pdb=" C GLN B 573 " -0.022 2.00e-02 2.50e+03 pdb=" O GLN B 573 " 0.008 2.00e-02 2.50e+03 pdb=" N SER B 574 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 573 " 0.006 2.00e-02 2.50e+03 1.26e-02 1.59e+00 pdb=" C GLN D 573 " -0.022 2.00e-02 2.50e+03 pdb=" O GLN D 573 " 0.008 2.00e-02 2.50e+03 pdb=" N SER D 574 " 0.007 2.00e-02 2.50e+03 ... (remaining 3781 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 5587 2.80 - 3.33: 21748 3.33 - 3.85: 37197 3.85 - 4.38: 44011 4.38 - 4.90: 75825 Nonbonded interactions: 184368 Sorted by model distance: nonbonded pdb=" OG1 THR B 140 " pdb=" OD1 ASP B 142 " model vdw 2.278 2.440 nonbonded pdb=" OG1 THR D 140 " pdb=" OD1 ASP D 142 " model vdw 2.279 2.440 nonbonded pdb=" OG1 THR C 140 " pdb=" OD1 ASP C 142 " model vdw 2.279 2.440 nonbonded pdb=" OG1 THR A 140 " pdb=" OD1 ASP A 142 " model vdw 2.279 2.440 nonbonded pdb=" OD1 ASP C 215 " pdb=" OH TYR C 713 " model vdw 2.328 2.440 ... (remaining 184363 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 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: 0.030 Extract box with map and model: 5.980 Check model and map are aligned: 0.330 Set scattering table: 0.210 Process input model: 63.550 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.150 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:15.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6569 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 : 0.007 0.204 22776 Z= 0.416 Angle : 0.786 20.541 30784 Z= 0.323 Chirality : 0.036 0.231 3444 Planarity : 0.003 0.029 3784 Dihedral : 14.086 174.205 8772 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.01 % Allowed : 3.21 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.77 (0.15), residues: 2608 helix: 0.88 (0.11), residues: 1948 sheet: None (None), residues: 0 loop : -0.35 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 639 HIS 0.001 0.000 HIS A 370 PHE 0.014 0.001 PHE D 341 TYR 0.010 0.001 TYR A 524 ARG 0.003 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 484 time to evaluate : 2.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 10 residues processed: 500 average time/residue: 1.4372 time to fit residues: 811.3731 Evaluate side-chains 252 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 242 time to evaluate : 2.736 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 7 residues processed: 3 average time/residue: 1.3140 time to fit residues: 8.0058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 2.9990 chunk 200 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 134 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 206 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 125 optimal weight: 1.9990 chunk 154 optimal weight: 5.9990 chunk 239 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 GLN A 609 ASN ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 GLN B 609 ASN ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 GLN C 609 ASN ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 573 GLN D 609 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6671 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 22776 Z= 0.378 Angle : 0.593 7.451 30784 Z= 0.295 Chirality : 0.039 0.152 3444 Planarity : 0.004 0.040 3784 Dihedral : 14.566 175.640 3544 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 4.27 % Allowed : 11.82 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.69 (0.16), residues: 2608 helix: 1.49 (0.11), residues: 1952 sheet: None (None), residues: 0 loop : 0.20 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 315 HIS 0.005 0.002 HIS A 634 PHE 0.021 0.002 PHE D 341 TYR 0.015 0.002 TYR B 539 ARG 0.004 0.001 ARG C 323 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 271 time to evaluate : 2.559 Fit side-chains outliers start: 101 outliers final: 52 residues processed: 324 average time/residue: 1.2255 time to fit residues: 458.2269 Evaluate side-chains 282 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 230 time to evaluate : 2.568 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 40 residues processed: 12 average time/residue: 0.5388 time to fit residues: 12.0889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 199 optimal weight: 9.9990 chunk 163 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 240 optimal weight: 0.8980 chunk 259 optimal weight: 0.9990 chunk 213 optimal weight: 7.9990 chunk 238 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 chunk 192 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN B 135 GLN C 135 GLN C 192 HIS D 135 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6670 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 22776 Z= 0.249 Angle : 0.495 7.039 30784 Z= 0.252 Chirality : 0.037 0.150 3444 Planarity : 0.004 0.034 3784 Dihedral : 14.488 178.204 3544 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 5.49 % Allowed : 12.37 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.15 (0.16), residues: 2608 helix: 1.85 (0.11), residues: 1948 sheet: None (None), residues: 0 loop : 0.28 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 315 HIS 0.004 0.001 HIS D 92 PHE 0.022 0.001 PHE C 341 TYR 0.010 0.001 TYR A 524 ARG 0.003 0.000 ARG C 194 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 246 time to evaluate : 2.674 Fit side-chains outliers start: 130 outliers final: 44 residues processed: 323 average time/residue: 1.2933 time to fit residues: 479.5012 Evaluate side-chains 274 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 230 time to evaluate : 2.303 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 36 residues processed: 8 average time/residue: 0.2146 time to fit residues: 6.3496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 10.0000 chunk 180 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 161 optimal weight: 0.8980 chunk 241 optimal weight: 0.7980 chunk 255 optimal weight: 4.9990 chunk 125 optimal weight: 0.9980 chunk 228 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 634 HIS B 135 GLN B 634 HIS C 135 GLN C 192 HIS C 634 HIS D 135 GLN D 634 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6674 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22776 Z= 0.250 Angle : 0.494 8.645 30784 Z= 0.249 Chirality : 0.036 0.148 3444 Planarity : 0.004 0.035 3784 Dihedral : 13.719 169.119 3544 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 4.43 % Allowed : 14.10 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.30 (0.16), residues: 2608 helix: 1.95 (0.11), residues: 1952 sheet: None (None), residues: 0 loop : 0.35 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 315 HIS 0.003 0.001 HIS B 92 PHE 0.023 0.002 PHE D 341 TYR 0.009 0.001 TYR A 539 ARG 0.002 0.000 ARG B 170 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 261 time to evaluate : 2.685 Fit side-chains outliers start: 105 outliers final: 57 residues processed: 325 average time/residue: 1.3178 time to fit residues: 490.6295 Evaluate side-chains 295 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 238 time to evaluate : 2.569 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 44 residues processed: 16 average time/residue: 0.4851 time to fit residues: 14.1852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 9.9990 chunk 144 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 chunk 190 optimal weight: 0.8980 chunk 105 optimal weight: 10.0000 chunk 217 optimal weight: 6.9990 chunk 176 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 229 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 overall best weight: 2.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 HIS ** C 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 22776 Z= 0.320 Angle : 0.526 10.551 30784 Z= 0.268 Chirality : 0.038 0.148 3444 Planarity : 0.004 0.035 3784 Dihedral : 13.526 167.105 3544 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 4.60 % Allowed : 14.74 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.17 (0.16), residues: 2608 helix: 1.89 (0.11), residues: 1944 sheet: None (None), residues: 0 loop : 0.21 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 315 HIS 0.003 0.001 HIS A 473 PHE 0.024 0.002 PHE D 341 TYR 0.010 0.001 TYR C 539 ARG 0.002 0.000 ARG A 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 244 time to evaluate : 2.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 109 outliers final: 58 residues processed: 313 average time/residue: 1.3159 time to fit residues: 472.2504 Evaluate side-chains 288 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 230 time to evaluate : 2.374 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 45 residues processed: 13 average time/residue: 0.5415 time to fit residues: 12.6388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 6.9990 chunk 229 optimal weight: 0.7980 chunk 50 optimal weight: 7.9990 chunk 149 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 255 optimal weight: 3.9990 chunk 212 optimal weight: 10.0000 chunk 118 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 134 optimal weight: 10.0000 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN B 135 GLN C 135 GLN C 192 HIS D 135 GLN D 551 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 22776 Z= 0.298 Angle : 0.508 9.837 30784 Z= 0.259 Chirality : 0.038 0.147 3444 Planarity : 0.004 0.034 3784 Dihedral : 13.356 169.798 3544 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 5.03 % Allowed : 14.53 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.13 (0.16), residues: 2608 helix: 1.89 (0.11), residues: 1944 sheet: None (None), residues: 0 loop : 0.09 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 315 HIS 0.003 0.001 HIS A 473 PHE 0.024 0.002 PHE B 341 TYR 0.008 0.001 TYR A 586 ARG 0.004 0.000 ARG A 194 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 248 time to evaluate : 2.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 119 outliers final: 72 residues processed: 325 average time/residue: 1.2879 time to fit residues: 482.3191 Evaluate side-chains 303 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 231 time to evaluate : 2.619 Switching outliers to nearest non-outliers outliers start: 72 outliers final: 52 residues processed: 20 average time/residue: 0.7873 time to fit residues: 23.1283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 145 optimal weight: 8.9990 chunk 186 optimal weight: 6.9990 chunk 144 optimal weight: 0.8980 chunk 215 optimal weight: 0.7980 chunk 142 optimal weight: 0.6980 chunk 254 optimal weight: 0.7980 chunk 159 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 117 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN B 247 GLN C 192 HIS C 247 GLN D 247 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6655 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22776 Z= 0.145 Angle : 0.448 8.264 30784 Z= 0.233 Chirality : 0.035 0.145 3444 Planarity : 0.003 0.035 3784 Dihedral : 12.822 171.741 3544 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.89 % Allowed : 15.96 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.49 (0.16), residues: 2608 helix: 2.16 (0.11), residues: 1952 sheet: None (None), residues: 0 loop : 0.16 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 315 HIS 0.002 0.001 HIS A 92 PHE 0.022 0.001 PHE B 341 TYR 0.011 0.001 TYR B 200 ARG 0.002 0.000 ARG C 71 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 275 time to evaluate : 2.623 Fit side-chains outliers start: 92 outliers final: 56 residues processed: 340 average time/residue: 1.1992 time to fit residues: 471.0451 Evaluate side-chains 295 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 239 time to evaluate : 2.351 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 54 residues processed: 5 average time/residue: 0.2432 time to fit residues: 5.3584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 0.0980 chunk 101 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 161 optimal weight: 0.8980 chunk 173 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 200 optimal weight: 9.9990 chunk 231 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 GLN C 135 GLN C 192 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22776 Z= 0.183 Angle : 0.484 6.808 30784 Z= 0.250 Chirality : 0.036 0.143 3444 Planarity : 0.004 0.035 3784 Dihedral : 12.624 173.392 3544 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.05 % Allowed : 16.77 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.48 (0.16), residues: 2608 helix: 2.12 (0.11), residues: 1948 sheet: None (None), residues: 0 loop : 0.30 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 315 HIS 0.002 0.001 HIS B 92 PHE 0.028 0.001 PHE C 359 TYR 0.009 0.001 TYR B 586 ARG 0.003 0.000 ARG D 71 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 250 time to evaluate : 3.049 Fit side-chains outliers start: 96 outliers final: 64 residues processed: 309 average time/residue: 1.2531 time to fit residues: 448.2951 Evaluate side-chains 303 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 239 time to evaluate : 2.575 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 53 residues processed: 13 average time/residue: 0.2331 time to fit residues: 8.9126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 0.9980 chunk 222 optimal weight: 0.0770 chunk 237 optimal weight: 9.9990 chunk 142 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 186 optimal weight: 7.9990 chunk 72 optimal weight: 9.9990 chunk 214 optimal weight: 0.9990 chunk 224 optimal weight: 0.5980 chunk 236 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 ASN B 731 ASN C 192 HIS C 731 ASN D 731 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22776 Z= 0.179 Angle : 0.480 7.057 30784 Z= 0.248 Chirality : 0.036 0.142 3444 Planarity : 0.004 0.035 3784 Dihedral : 12.342 175.731 3544 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 4.18 % Allowed : 16.22 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.49 (0.16), residues: 2608 helix: 2.13 (0.11), residues: 1952 sheet: None (None), residues: 0 loop : 0.25 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 315 HIS 0.002 0.000 HIS B 92 PHE 0.024 0.001 PHE C 341 TYR 0.009 0.001 TYR C 586 ARG 0.004 0.000 ARG D 191 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 262 time to evaluate : 2.746 Fit side-chains outliers start: 99 outliers final: 62 residues processed: 332 average time/residue: 1.2469 time to fit residues: 478.2620 Evaluate side-chains 306 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 244 time to evaluate : 2.549 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 53 residues processed: 12 average time/residue: 0.2357 time to fit residues: 8.5072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 0.8980 chunk 153 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 174 optimal weight: 0.9990 chunk 263 optimal weight: 5.9990 chunk 242 optimal weight: 0.4980 chunk 209 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 chunk 128 optimal weight: 4.9990 chunk 166 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 ASN B 731 ASN ** B 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 731 ASN ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 731 ASN ** D 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22776 Z= 0.154 Angle : 0.489 8.730 30784 Z= 0.255 Chirality : 0.035 0.139 3444 Planarity : 0.003 0.036 3784 Dihedral : 11.830 177.867 3544 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.08 % Allowed : 17.78 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.61 (0.16), residues: 2608 helix: 2.21 (0.12), residues: 1956 sheet: None (None), residues: 0 loop : 0.32 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 315 HIS 0.002 0.000 HIS B 92 PHE 0.014 0.001 PHE D 427 TYR 0.010 0.001 TYR B 200 ARG 0.005 0.000 ARG B 191 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 253 time to evaluate : 2.444 Fit side-chains outliers start: 73 outliers final: 61 residues processed: 307 average time/residue: 1.3433 time to fit residues: 475.4405 Evaluate side-chains 290 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 229 time to evaluate : 2.616 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 52 residues processed: 12 average time/residue: 0.2749 time to fit residues: 8.9878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.3406 > 50: distance: 20 - 36: 3.268 distance: 24 - 47: 11.523 distance: 31 - 36: 4.146 distance: 36 - 37: 7.220 distance: 37 - 38: 6.799 distance: 37 - 40: 10.746 distance: 38 - 47: 4.690 distance: 40 - 41: 4.782 distance: 41 - 42: 10.395 distance: 42 - 43: 3.275 distance: 43 - 44: 13.232 distance: 44 - 45: 14.580 distance: 44 - 46: 12.741 distance: 47 - 48: 3.541 distance: 48 - 49: 5.922 distance: 48 - 51: 3.264 distance: 49 - 50: 6.632 distance: 51 - 52: 7.704 distance: 52 - 54: 4.509 distance: 55 - 56: 9.751 distance: 56 - 57: 32.995 distance: 56 - 59: 24.331 distance: 57 - 58: 34.929 distance: 57 - 62: 31.627 distance: 59 - 60: 5.831 distance: 59 - 61: 31.014 distance: 62 - 63: 29.237 distance: 63 - 64: 8.729 distance: 63 - 66: 15.296 distance: 64 - 65: 47.444 distance: 64 - 71: 28.502 distance: 65 - 99: 30.449 distance: 66 - 67: 39.829 distance: 67 - 68: 39.751 distance: 68 - 69: 24.186 distance: 68 - 70: 35.744 distance: 71 - 72: 19.209 distance: 72 - 73: 14.277 distance: 72 - 75: 34.330 distance: 73 - 74: 17.985 distance: 73 - 80: 16.163 distance: 74 - 108: 28.478 distance: 75 - 76: 12.077 distance: 76 - 77: 24.440 distance: 77 - 78: 17.672 distance: 77 - 79: 35.196 distance: 80 - 81: 23.807 distance: 81 - 82: 8.605 distance: 81 - 84: 18.441 distance: 82 - 83: 15.156 distance: 82 - 88: 12.031 distance: 83 - 117: 27.188 distance: 84 - 85: 23.953 distance: 85 - 86: 5.270 distance: 85 - 87: 11.432 distance: 88 - 89: 13.834 distance: 89 - 90: 10.441 distance: 89 - 92: 9.632 distance: 90 - 91: 10.752 distance: 90 - 99: 20.928 distance: 91 - 125: 22.371 distance: 92 - 93: 7.045 distance: 93 - 94: 6.175 distance: 93 - 95: 11.483 distance: 94 - 96: 5.259 distance: 95 - 97: 4.758 distance: 96 - 98: 8.109 distance: 97 - 98: 9.864 distance: 99 - 100: 15.890 distance: 100 - 101: 13.004 distance: 100 - 103: 10.307 distance: 101 - 102: 9.176 distance: 101 - 108: 12.898 distance: 102 - 134: 33.194 distance: 103 - 104: 5.929 distance: 104 - 105: 15.159 distance: 105 - 106: 14.236 distance: 106 - 107: 7.872 distance: 108 - 109: 29.406 distance: 109 - 110: 26.065 distance: 109 - 112: 50.820 distance: 110 - 111: 35.363 distance: 110 - 117: 26.926 distance: 111 - 141: 36.624 distance: 112 - 113: 48.391 distance: 113 - 114: 30.613 distance: 114 - 115: 19.500 distance: 114 - 116: 26.382 distance: 117 - 118: 49.869 distance: 118 - 119: 37.876 distance: 118 - 121: 37.541 distance: 119 - 120: 42.304 distance: 119 - 125: 30.038 distance: 120 - 148: 31.975 distance: 121 - 122: 4.168 distance: 122 - 124: 16.464