Starting phenix.real_space_refine on Mon Aug 25 10:25:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e41_47497/08_2025/9e41_47497.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e41_47497/08_2025/9e41_47497.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9e41_47497/08_2025/9e41_47497.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e41_47497/08_2025/9e41_47497.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e41_47497/08_2025/9e41_47497.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e41_47497/08_2025/9e41_47497.map" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.013 sd= 0.093 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 S 90 5.16 5 C 8508 2.51 5 N 2277 2.21 5 O 2525 1.98 5 H 13101 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26507 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 7527 Classifications: {'peptide': 494} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 472} Chain: "B" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1210 Classifications: {'peptide': 75} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "E" Number of atoms: 7527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 7527 Classifications: {'peptide': 494} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 472} Chain: "F" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1210 Classifications: {'peptide': 75} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "C" Number of atoms: 7527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 7527 Classifications: {'peptide': 494} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 472} Chain: "D" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1210 Classifications: {'peptide': 75} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CPL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'CPL:plan-3': 2, 'CPL:plan-4': 2} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CPL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'CPL:plan-3': 2, 'CPL:plan-4': 2} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CPL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'CPL:plan-3': 2, 'CPL:plan-4': 2} Unresolved non-hydrogen planarities: 16 Time building chain proxies: 4.62, per 1000 atoms: 0.17 Number of scatterers: 26507 At special positions: 0 Unit cell: (117.12, 196.42, 98.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 90 16.00 P 6 15.00 O 2525 8.00 N 2277 7.00 C 8508 6.00 H 13101 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 30 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 105 " distance=2.03 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 116 " distance=2.03 Simple disulfide: pdb=" SG CYS A 186 " - pdb=" SG CYS A 290 " distance=2.04 Simple disulfide: pdb=" SG CYS A 307 " - pdb=" SG CYS A 339 " distance=2.03 Simple disulfide: pdb=" SG CYS E 3 " - pdb=" SG CYS E 30 " distance=2.03 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 121 " distance=2.03 Simple disulfide: pdb=" SG CYS E 74 " - pdb=" SG CYS E 105 " distance=2.04 Simple disulfide: pdb=" SG CYS E 92 " - pdb=" SG CYS E 116 " distance=2.03 Simple disulfide: pdb=" SG CYS E 186 " - pdb=" SG CYS E 290 " distance=2.03 Simple disulfide: pdb=" SG CYS E 307 " - pdb=" SG CYS E 339 " distance=2.03 Simple disulfide: pdb=" SG CYS C 3 " - pdb=" SG CYS C 30 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 121 " distance=2.03 Simple disulfide: pdb=" SG CYS C 74 " - pdb=" SG CYS C 105 " distance=2.03 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 116 " distance=2.03 Simple disulfide: pdb=" SG CYS C 186 " - pdb=" SG CYS C 290 " distance=2.03 Simple disulfide: pdb=" SG CYS C 307 " - pdb=" SG CYS C 339 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA G 3 " - " MAN G 4 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " NAG-ASN " NAG G 1 " - " ASN A 154 " " NAG H 1 " - " ASN E 154 " Time building additional restraints: 3.62 Conformation dependent library (CDL) restraints added in 810.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3096 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 28 sheets defined 30.5% alpha, 26.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 82 through 87 removed outlier: 3.663A pdb=" N HIS A 86 " --> pdb=" O PRO A 83 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN A 87 " --> pdb=" O GLU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 217 through 221 Processing helix chain 'A' and resid 260 through 267 Processing helix chain 'A' and resid 308 through 310 No H-bonds generated for 'chain 'A' and resid 308 through 310' Processing helix chain 'A' and resid 398 through 417 Processing helix chain 'A' and resid 418 through 424 removed outlier: 3.511A pdb=" N PHE A 424 " --> pdb=" O ALA A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 451 removed outlier: 3.817A pdb=" N SER A 433 " --> pdb=" O GLY A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 471 Processing helix chain 'A' and resid 474 through 494 removed outlier: 4.117A pdb=" N GLY A 494 " --> pdb=" O MET A 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 39 removed outlier: 3.659A pdb=" N ARG B 26 " --> pdb=" O GLY B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 54 Processing helix chain 'B' and resid 56 through 74 Proline residue: B 72 - end of helix Processing helix chain 'E' and resid 1 through 6 removed outlier: 3.915A pdb=" N LEU E 6 " --> pdb=" O CYS E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 87 Processing helix chain 'E' and resid 177 through 179 No H-bonds generated for 'chain 'E' and resid 177 through 179' Processing helix chain 'E' and resid 204 through 208 removed outlier: 3.513A pdb=" N ASP E 207 " --> pdb=" O SER E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 221 Processing helix chain 'E' and resid 237 through 240 removed outlier: 3.677A pdb=" N LYS E 240 " --> pdb=" O SER E 237 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 237 through 240' Processing helix chain 'E' and resid 260 through 268 Processing helix chain 'E' and resid 398 through 417 Processing helix chain 'E' and resid 418 through 424 removed outlier: 3.642A pdb=" N TRP E 422 " --> pdb=" O GLU E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 451 removed outlier: 3.613A pdb=" N LYS E 436 " --> pdb=" O SER E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 454 through 472 Processing helix chain 'E' and resid 474 through 492 Processing helix chain 'F' and resid 22 through 39 removed outlier: 4.088A pdb=" N ARG F 26 " --> pdb=" O GLY F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 54 Processing helix chain 'F' and resid 56 through 70 Processing helix chain 'C' and resid 1 through 6 Processing helix chain 'C' and resid 100 through 104 Processing helix chain 'C' and resid 188 through 191 Processing helix chain 'C' and resid 217 through 222 Processing helix chain 'C' and resid 237 through 240 Processing helix chain 'C' and resid 260 through 267 Processing helix chain 'C' and resid 308 through 310 No H-bonds generated for 'chain 'C' and resid 308 through 310' Processing helix chain 'C' and resid 398 through 417 Processing helix chain 'C' and resid 418 through 424 removed outlier: 3.508A pdb=" N ALA C 421 " --> pdb=" O GLY C 418 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TRP C 422 " --> pdb=" O GLU C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 451 Processing helix chain 'C' and resid 454 through 472 Processing helix chain 'C' and resid 474 through 493 Processing helix chain 'D' and resid 22 through 39 removed outlier: 3.531A pdb=" N ARG D 26 " --> pdb=" O GLY D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 54 Processing helix chain 'D' and resid 56 through 71 Processing helix chain 'D' and resid 72 through 75 Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 14 removed outlier: 6.552A pdb=" N ASP A 10 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N THR A 34 " --> pdb=" O ASP A 10 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VAL A 12 " --> pdb=" O THR A 34 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE A 48 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN A 50 " --> pdb=" O TYR A 281 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA A 212 " --> pdb=" O ALA A 274 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ALA A 127 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLU A 58 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 14 removed outlier: 6.552A pdb=" N ASP A 10 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N THR A 34 " --> pdb=" O ASP A 10 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VAL A 12 " --> pdb=" O THR A 34 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL A 140 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ILE A 48 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N THR A 138 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 21 through 26 Processing sheet with id=AA4, first strand: chain 'A' and resid 63 through 73 removed outlier: 6.574A pdb=" N LYS A 118 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N THR A 68 " --> pdb=" O CYS A 116 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N CYS A 116 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VAL A 70 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL A 114 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ALA A 72 " --> pdb=" O SER A 112 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N SER A 112 " --> pdb=" O ALA A 72 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 98 through 99 Processing sheet with id=AA6, first strand: chain 'A' and resid 173 through 175 Processing sheet with id=AA7, first strand: chain 'A' and resid 242 through 244 Processing sheet with id=AA8, first strand: chain 'A' and resid 312 through 320 removed outlier: 6.765A pdb=" N GLU A 329 " --> pdb=" O LYS A 315 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N VAL A 317 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL A 327 " --> pdb=" O VAL A 317 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 339 through 340 Processing sheet with id=AB1, first strand: chain 'A' and resid 343 through 347 Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 14 removed outlier: 6.777A pdb=" N VAL E 140 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ILE E 48 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR E 138 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 20 through 26 removed outlier: 4.291A pdb=" N THR E 289 " --> pdb=" O LYS E 187 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER E 183 " --> pdb=" O GLY E 293 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 54 through 55 removed outlier: 4.103A pdb=" N ALA E 212 " --> pdb=" O ALA E 274 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER E 275 " --> pdb=" O HIS E 282 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 58 through 59 Processing sheet with id=AB6, first strand: chain 'E' and resid 66 through 73 removed outlier: 5.981A pdb=" N ASN E 67 " --> pdb=" O LYS E 118 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LYS E 118 " --> pdb=" O ASN E 67 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 98 through 99 removed outlier: 3.531A pdb=" N GLY E 109 " --> pdb=" O ARG E 99 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 242 through 244 Processing sheet with id=AB9, first strand: chain 'E' and resid 305 through 306 removed outlier: 7.057A pdb=" N SER E 305 " --> pdb=" O ARG E 340 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 314 through 320 removed outlier: 6.459A pdb=" N GLU E 329 " --> pdb=" O LYS E 315 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N VAL E 317 " --> pdb=" O VAL E 327 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL E 327 " --> pdb=" O VAL E 317 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 343 through 347 Processing sheet with id=AC3, first strand: chain 'C' and resid 9 through 13 removed outlier: 6.403A pdb=" N ASP C 10 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N THR C 34 " --> pdb=" O ASP C 10 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL C 12 " --> pdb=" O THR C 34 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE C 41 " --> pdb=" O ILE C 33 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ILE C 48 " --> pdb=" O LEU C 283 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER C 275 " --> pdb=" O HIS C 282 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA C 212 " --> pdb=" O ALA C 274 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ALA C 127 " --> pdb=" O GLU C 58 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLU C 58 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N GLY C 129 " --> pdb=" O THR C 56 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA C 54 " --> pdb=" O VAL C 131 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 161 through 165 removed outlier: 3.889A pdb=" N ASP C 47 " --> pdb=" O VAL C 140 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LYS C 142 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N LEU C 45 " --> pdb=" O LYS C 142 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N GLU C 144 " --> pdb=" O VAL C 43 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N VAL C 43 " --> pdb=" O GLU C 144 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ILE C 48 " --> pdb=" O LEU C 283 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER C 275 " --> pdb=" O HIS C 282 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL C 271 " --> pdb=" O TRP D 19 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 20 through 26 removed outlier: 3.508A pdb=" N SER C 183 " --> pdb=" O GLY C 293 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 63 through 72 removed outlier: 4.386A pdb=" N THR C 68 " --> pdb=" O CYS C 116 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N CYS C 116 " --> pdb=" O THR C 68 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL C 70 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL C 114 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ALA C 72 " --> pdb=" O SER C 112 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N SER C 112 " --> pdb=" O ALA C 72 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY C 109 " --> pdb=" O ARG C 99 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 242 through 244 Processing sheet with id=AC8, first strand: chain 'C' and resid 312 through 320 removed outlier: 6.490A pdb=" N GLU C 329 " --> pdb=" O LYS C 315 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL C 317 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL C 327 " --> pdb=" O VAL C 317 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 339 through 340 Processing sheet with id=AD1, first strand: chain 'C' and resid 343 through 347 588 hydrogen bonds defined for protein. 1599 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: 5.29 Time building geometry restraints manager: 3.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 13101 1.04 - 1.23: 618 1.23 - 1.43: 5012 1.43 - 1.63: 7908 1.63 - 1.83: 156 Bond restraints: 26795 Sorted by residual: bond pdb=" C VAL A 292 " pdb=" N GLY A 293 " ideal model delta sigma weight residual 1.332 1.340 -0.008 5.00e-03 4.00e+04 2.60e+00 bond pdb=" C SER E 52 " pdb=" O SER E 52 " ideal model delta sigma weight residual 1.235 1.228 0.007 4.70e-03 4.53e+04 2.43e+00 bond pdb=" C VAL C 292 " pdb=" N GLY C 293 " ideal model delta sigma weight residual 1.332 1.326 0.006 5.00e-03 4.00e+04 1.59e+00 bond pdb=" N PRO A 342 " pdb=" CA PRO A 342 " ideal model delta sigma weight residual 1.469 1.484 -0.016 1.28e-02 6.10e+03 1.51e+00 bond pdb=" C VAL C 355 " pdb=" O VAL C 355 " ideal model delta sigma weight residual 1.236 1.224 0.013 1.19e-02 7.06e+03 1.13e+00 ... (remaining 26790 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.96: 44739 0.96 - 1.93: 3484 1.93 - 2.89: 155 2.89 - 3.86: 57 3.86 - 4.82: 6 Bond angle restraints: 48441 Sorted by residual: angle pdb=" CA GLY A 370 " pdb=" C GLY A 370 " pdb=" O GLY A 370 " ideal model delta sigma weight residual 122.37 120.19 2.18 7.30e-01 1.88e+00 8.94e+00 angle pdb=" CA GLY A 370 " pdb=" C GLY A 370 " pdb=" N GLY A 371 " ideal model delta sigma weight residual 114.13 117.34 -3.21 1.11e+00 8.12e-01 8.35e+00 angle pdb=" CA GLY C 452 " pdb=" C GLY C 452 " pdb=" N VAL C 453 " ideal model delta sigma weight residual 118.95 116.69 2.26 1.06e+00 8.90e-01 4.55e+00 angle pdb=" CA CYS A 186 " pdb=" CB CYS A 186 " pdb=" SG CYS A 186 " ideal model delta sigma weight residual 114.40 119.22 -4.82 2.30e+00 1.89e-01 4.40e+00 angle pdb=" N ILE A 341 " pdb=" CA ILE A 341 " pdb=" C ILE A 341 " ideal model delta sigma weight residual 107.76 109.71 -1.95 1.01e+00 9.80e-01 3.73e+00 ... (remaining 48436 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.84: 11911 23.84 - 47.69: 617 47.69 - 71.53: 195 71.53 - 95.37: 28 95.37 - 119.21: 3 Dihedral angle restraints: 12754 sinusoidal: 7096 harmonic: 5658 Sorted by residual: dihedral pdb=" CA CYS A 186 " pdb=" C CYS A 186 " pdb=" N LYS A 187 " pdb=" CA LYS A 187 " ideal model delta harmonic sigma weight residual -180.00 -157.48 -22.52 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA LYS A 315 " pdb=" C LYS A 315 " pdb=" N ARG A 316 " pdb=" CA ARG A 316 " ideal model delta harmonic sigma weight residual 180.00 159.77 20.23 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" C3 MAN G 4 " pdb=" C1 MAN G 4 " pdb=" C2 MAN G 4 " pdb=" O5 MAN G 4 " ideal model delta sinusoidal sigma weight residual -53.57 65.64 -119.21 1 3.00e+01 1.11e-03 1.59e+01 ... (remaining 12751 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1330 0.032 - 0.064: 578 0.064 - 0.097: 93 0.097 - 0.129: 110 0.129 - 0.161: 20 Chirality restraints: 2131 Sorted by residual: chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 3.72e+00 chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 1.97e+00 chirality pdb=" C1 BMA I 3 " pdb=" O4 NAG I 2 " pdb=" C2 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.42 0.02 2.00e-02 2.50e+03 7.64e-01 ... (remaining 2128 not shown) Planarity restraints: 3953 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE E 341 " 0.023 5.00e-02 4.00e+02 3.42e-02 1.87e+00 pdb=" N PRO E 342 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO E 342 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 342 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 360 " 0.020 5.00e-02 4.00e+02 2.96e-02 1.40e+00 pdb=" N PRO A 361 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 361 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 361 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 456 " 0.019 5.00e-02 4.00e+02 2.89e-02 1.33e+00 pdb=" N PRO A 457 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 457 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 457 " 0.016 5.00e-02 4.00e+02 ... (remaining 3950 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 957 2.16 - 2.77: 49439 2.77 - 3.38: 68156 3.38 - 3.99: 89682 3.99 - 4.60: 140243 Nonbonded interactions: 348477 Sorted by model distance: nonbonded pdb=" OE1 GLU C 26 " pdb=" HE ARG D 15 " model vdw 1.555 2.450 nonbonded pdb=" O LEU C 377 " pdb="HH22 ARG C 402 " model vdw 1.583 2.450 nonbonded pdb=" O SER A 97 " pdb=" H GLY A 111 " model vdw 1.619 2.450 nonbonded pdb=" OE2 GLU E 144 " pdb="HD21 ASN E 157 " model vdw 1.646 2.450 nonbonded pdb="HH12 ARG C 9 " pdb=" OE2 GLU C 374 " model vdw 1.666 2.450 ... (remaining 348472 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'I' } 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: 3.340 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: 0.180 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 23.730 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 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 : 0.003 0.024 13721 Z= 0.119 Angle : 0.503 4.822 18642 Z= 0.266 Chirality : 0.043 0.161 2131 Planarity : 0.003 0.034 2319 Dihedral : 12.224 119.213 5140 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.07 % Allowed : 0.00 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.21), residues: 1695 helix: 2.88 (0.25), residues: 426 sheet: 0.31 (0.24), residues: 474 loop : -0.82 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 344 TYR 0.013 0.002 TYR A 332 PHE 0.011 0.001 PHE C 450 TRP 0.008 0.001 TRP C 213 HIS 0.007 0.001 HIS C 348 Details of bonding type rmsd covalent geometry : bond 0.00257 (13694) covalent geometry : angle 0.49750 (18579) SS BOND : bond 0.00235 ( 18) SS BOND : angle 1.07227 ( 36) hydrogen bonds : bond 0.17946 ( 580) hydrogen bonds : angle 7.85833 ( 1599) link_ALPHA1-3 : bond 0.00193 ( 1) link_ALPHA1-3 : angle 1.46938 ( 3) link_BETA1-4 : bond 0.00465 ( 6) link_BETA1-4 : angle 1.66866 ( 18) link_NAG-ASN : bond 0.00293 ( 2) link_NAG-ASN : angle 1.47751 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 258 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 ASP cc_start: 0.7324 (t70) cc_final: 0.7005 (t0) REVERT: A 404 PHE cc_start: 0.8342 (t80) cc_final: 0.8008 (t80) REVERT: A 479 MET cc_start: 0.7238 (mtm) cc_final: 0.7002 (mmt) outliers start: 1 outliers final: 1 residues processed: 259 average time/residue: 1.0787 time to fit residues: 307.8056 Evaluate side-chains 184 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 154 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.0570 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.9102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 ASN F 39 ASN C 471 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.102694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.083169 restraints weight = 70625.565| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 3.07 r_work: 0.2976 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13721 Z= 0.123 Angle : 0.534 5.441 18642 Z= 0.278 Chirality : 0.042 0.183 2131 Planarity : 0.004 0.047 2319 Dihedral : 8.739 98.292 2124 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.84 % Allowed : 8.82 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.20), residues: 1695 helix: 2.97 (0.24), residues: 429 sheet: 0.17 (0.25), residues: 411 loop : -0.73 (0.20), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 20 TYR 0.012 0.001 TYR C 139 PHE 0.015 0.001 PHE A 119 TRP 0.008 0.001 TRP D 35 HIS 0.002 0.001 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00282 (13694) covalent geometry : angle 0.52933 (18579) SS BOND : bond 0.00187 ( 18) SS BOND : angle 1.03953 ( 36) hydrogen bonds : bond 0.03948 ( 580) hydrogen bonds : angle 5.80627 ( 1599) link_ALPHA1-3 : bond 0.00654 ( 1) link_ALPHA1-3 : angle 2.67673 ( 3) link_BETA1-4 : bond 0.00320 ( 6) link_BETA1-4 : angle 1.68539 ( 18) link_NAG-ASN : bond 0.00200 ( 2) link_NAG-ASN : angle 1.03186 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 194 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 GLU cc_start: 0.9100 (pm20) cc_final: 0.8840 (pm20) REVERT: A 324 ASP cc_start: 0.8493 (t70) cc_final: 0.7683 (t0) REVERT: A 479 MET cc_start: 0.7166 (mtm) cc_final: 0.6636 (mmt) REVERT: A 492 THR cc_start: 0.9009 (m) cc_final: 0.8679 (p) REVERT: B 26 ARG cc_start: 0.8365 (mtm-85) cc_final: 0.8065 (mtm-85) REVERT: B 74 TYR cc_start: 0.9095 (m-80) cc_final: 0.8505 (m-80) REVERT: E 7 GLU cc_start: 0.8944 (pm20) cc_final: 0.8695 (mt-10) REVERT: E 291 ASP cc_start: 0.7246 (t0) cc_final: 0.6966 (t0) REVERT: E 357 MET cc_start: 0.8814 (ttp) cc_final: 0.8423 (tmm) REVERT: F 57 TRP cc_start: 0.7017 (OUTLIER) cc_final: 0.5832 (t-100) REVERT: C 324 ASP cc_start: 0.7923 (t0) cc_final: 0.7332 (t0) REVERT: C 468 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9087 (mm) REVERT: C 471 ASN cc_start: 0.7891 (m-40) cc_final: 0.7665 (m110) outliers start: 12 outliers final: 5 residues processed: 200 average time/residue: 1.1119 time to fit residues: 245.0768 Evaluate side-chains 188 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 181 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain E residue 324 ASP Chi-restraints excluded: chain F residue 57 TRP Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 470 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 110 optimal weight: 3.9990 chunk 164 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 154 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.096828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.077309 restraints weight = 71892.063| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 3.05 r_work: 0.2860 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 13721 Z= 0.288 Angle : 0.578 5.953 18642 Z= 0.304 Chirality : 0.045 0.202 2131 Planarity : 0.004 0.041 2319 Dihedral : 8.639 96.828 2124 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.19 % Allowed : 9.52 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.20), residues: 1695 helix: 2.71 (0.24), residues: 429 sheet: -0.20 (0.24), residues: 420 loop : -0.77 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 217 TYR 0.013 0.002 TYR A 332 PHE 0.012 0.001 PHE A 372 TRP 0.014 0.001 TRP C 101 HIS 0.004 0.001 HIS A 439 Details of bonding type rmsd covalent geometry : bond 0.00656 (13694) covalent geometry : angle 0.57244 (18579) SS BOND : bond 0.00207 ( 18) SS BOND : angle 1.23459 ( 36) hydrogen bonds : bond 0.04087 ( 580) hydrogen bonds : angle 5.47453 ( 1599) link_ALPHA1-3 : bond 0.00750 ( 1) link_ALPHA1-3 : angle 3.22776 ( 3) link_BETA1-4 : bond 0.00309 ( 6) link_BETA1-4 : angle 1.76727 ( 18) link_NAG-ASN : bond 0.00097 ( 2) link_NAG-ASN : angle 1.05868 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 200 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 ASP cc_start: 0.8435 (t0) cc_final: 0.8211 (t0) REVERT: A 239 GLU cc_start: 0.9099 (pm20) cc_final: 0.8828 (pm20) REVERT: A 324 ASP cc_start: 0.8629 (t70) cc_final: 0.7844 (t0) REVERT: A 477 MET cc_start: 0.8311 (mpp) cc_final: 0.7927 (mpp) REVERT: A 479 MET cc_start: 0.7267 (mtm) cc_final: 0.6796 (mmt) REVERT: A 489 LEU cc_start: 0.8862 (mp) cc_final: 0.8467 (mp) REVERT: A 492 THR cc_start: 0.9003 (m) cc_final: 0.8727 (p) REVERT: E 388 ASP cc_start: 0.8984 (OUTLIER) cc_final: 0.8595 (t70) REVERT: F 10 LYS cc_start: 0.9336 (mptm) cc_final: 0.8980 (mmtm) REVERT: C 324 ASP cc_start: 0.8182 (t0) cc_final: 0.7609 (t0) REVERT: C 468 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9077 (mm) REVERT: C 471 ASN cc_start: 0.8137 (m-40) cc_final: 0.7833 (m-40) outliers start: 17 outliers final: 11 residues processed: 210 average time/residue: 0.8972 time to fit residues: 209.6885 Evaluate side-chains 200 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 187 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 324 ASP Chi-restraints excluded: chain E residue 388 ASP Chi-restraints excluded: chain E residue 442 LEU Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 470 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 11 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.097730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.078304 restraints weight = 71079.552| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 3.03 r_work: 0.2890 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13721 Z= 0.158 Angle : 0.518 5.443 18642 Z= 0.268 Chirality : 0.042 0.172 2131 Planarity : 0.004 0.064 2319 Dihedral : 8.307 95.196 2124 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.05 % Allowed : 11.48 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.21), residues: 1695 helix: 2.78 (0.24), residues: 432 sheet: -0.33 (0.24), residues: 444 loop : -0.64 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 20 TYR 0.012 0.001 TYR E 332 PHE 0.013 0.001 PHE C 450 TRP 0.010 0.001 TRP C 101 HIS 0.002 0.001 HIS E 104 Details of bonding type rmsd covalent geometry : bond 0.00365 (13694) covalent geometry : angle 0.51208 (18579) SS BOND : bond 0.00188 ( 18) SS BOND : angle 1.02471 ( 36) hydrogen bonds : bond 0.03410 ( 580) hydrogen bonds : angle 5.20523 ( 1599) link_ALPHA1-3 : bond 0.00845 ( 1) link_ALPHA1-3 : angle 3.12728 ( 3) link_BETA1-4 : bond 0.00296 ( 6) link_BETA1-4 : angle 1.68376 ( 18) link_NAG-ASN : bond 0.00098 ( 2) link_NAG-ASN : angle 0.71844 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 202 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 ASP cc_start: 0.8393 (t0) cc_final: 0.8178 (t0) REVERT: A 239 GLU cc_start: 0.9110 (pm20) cc_final: 0.8820 (pm20) REVERT: A 324 ASP cc_start: 0.8584 (t70) cc_final: 0.7807 (t0) REVERT: A 479 MET cc_start: 0.7361 (mtm) cc_final: 0.6869 (mmt) REVERT: A 489 LEU cc_start: 0.8838 (mp) cc_final: 0.8485 (mp) REVERT: A 492 THR cc_start: 0.8985 (m) cc_final: 0.8674 (p) REVERT: B 26 ARG cc_start: 0.8496 (mtm-85) cc_final: 0.8201 (mtm-85) REVERT: E 20 ARG cc_start: 0.8656 (ptm160) cc_final: 0.8441 (ptm160) REVERT: E 217 ARG cc_start: 0.8306 (ttp80) cc_final: 0.7895 (ttp80) REVERT: F 10 LYS cc_start: 0.9323 (mptm) cc_final: 0.8936 (mmtm) REVERT: C 324 ASP cc_start: 0.8083 (t0) cc_final: 0.7448 (t0) REVERT: C 468 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9095 (mm) REVERT: C 471 ASN cc_start: 0.8032 (m-40) cc_final: 0.7827 (m-40) REVERT: C 489 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8206 (mm) outliers start: 15 outliers final: 7 residues processed: 209 average time/residue: 1.1176 time to fit residues: 259.4312 Evaluate side-chains 200 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 191 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain E residue 324 ASP Chi-restraints excluded: chain E residue 442 LEU Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 489 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.1263 > 50: distance: 4 - 17: 4.048 distance: 17 - 18: 5.440 distance: 17 - 26: 15.580 distance: 17 - 543: 4.681 distance: 18 - 19: 8.727 distance: 18 - 21: 5.724 distance: 18 - 27: 7.310 distance: 19 - 20: 3.130 distance: 19 - 34: 7.912 distance: 20 - 540: 11.980 distance: 21 - 22: 3.923 distance: 21 - 28: 3.995 distance: 21 - 29: 5.632 distance: 22 - 23: 5.282 distance: 22 - 30: 3.409 distance: 22 - 31: 5.844 distance: 34 - 35: 6.489 distance: 34 - 43: 10.419 distance: 35 - 36: 25.420 distance: 35 - 38: 12.146 distance: 35 - 44: 12.701 distance: 36 - 37: 13.801 distance: 36 - 49: 6.685 distance: 38 - 39: 7.555 distance: 38 - 45: 8.022 distance: 38 - 46: 13.309 distance: 39 - 40: 5.122 distance: 39 - 48: 9.186 distance: 40 - 41: 6.585 distance: 40 - 42: 8.453 distance: 49 - 50: 6.986 distance: 49 - 55: 18.731 distance: 50 - 51: 12.125 distance: 50 - 53: 16.656 distance: 50 - 56: 24.798 distance: 51 - 52: 8.883 distance: 51 - 60: 4.543 distance: 53 - 54: 12.730 distance: 53 - 57: 7.878 distance: 53 - 58: 5.159 distance: 54 - 59: 3.271 distance: 60 - 61: 7.263 distance: 60 - 66: 7.725 distance: 61 - 62: 14.515 distance: 61 - 64: 6.613 distance: 61 - 67: 15.236 distance: 62 - 63: 24.934 distance: 62 - 74: 25.979 distance: 64 - 65: 4.674 distance: 64 - 68: 15.072 distance: 64 - 69: 8.253 distance: 65 - 66: 6.911 distance: 65 - 71: 10.919 distance: 66 - 72: 8.290 distance: 66 - 73: 9.947 distance: 74 - 75: 8.195 distance: 74 - 79: 20.764 distance: 75 - 78: 7.407 distance: 75 - 80: 9.563 distance: 76 - 77: 16.826 distance: 76 - 84: 10.265 distance: 77 - 259: 23.764 distance: 78 - 81: 7.740 distance: 78 - 82: 7.041 distance: 78 - 83: 8.924 distance: 84 - 85: 4.348 distance: 84 - 93: 8.964 distance: 85 - 86: 7.621 distance: 85 - 88: 4.300 distance: 85 - 94: 6.833 distance: 86 - 87: 13.070 distance: 86 - 99: 15.627 distance: 88 - 89: 4.240 distance: 88 - 96: 3.124 distance: 89 - 90: 4.366 distance: 89 - 98: 4.835 distance: 99 - 106: 18.384 distance: 99 - 239: 3.008 distance: 100 - 101: 4.484 distance: 101 - 113: 3.935 distance: 105 - 110: 5.107 distance: 105 - 111: 3.891 distance: 113 - 124: 4.543 distance: 114 - 115: 4.790 distance: 114 - 117: 4.837 distance: 114 - 125: 4.254 distance: 115 - 116: 19.585 distance: 115 - 137: 8.862 distance: 117 - 126: 3.337 distance: 137 - 138: 4.459 distance: 137 - 146: 10.375 distance: 137 - 445: 4.834 distance: 138 - 139: 5.951 distance: 138 - 141: 6.355 distance: 138 - 147: 5.270 distance: 139 - 140: 18.536 distance: 139 - 152: 11.259 distance: 140 - 442: 16.501 distance: 141 - 142: 8.425 distance: 141 - 148: 4.780 distance: 141 - 149: 4.563 distance: 142 - 151: 4.679 distance: 152 - 153: 10.573 distance: 152 - 164: 6.919 distance: 153 - 154: 5.890 distance: 153 - 156: 14.088 distance: 153 - 165: 12.341 distance: 154 - 155: 13.961 distance: 154 - 173: 9.772 distance: 156 - 157: 5.581 distance: 156 - 166: 18.431 distance: 156 - 167: 18.603 distance: 157 - 158: 5.628 distance: 157 - 159: 3.434 distance: 158 - 160: 7.041 distance: 158 - 168: 9.002 distance: 159 - 161: 6.729 distance: 159 - 169: 5.711 distance: 160 - 162: 5.195 distance: 160 - 170: 5.293 distance: 161 - 162: 6.668 distance: 161 - 171: 5.150 distance: 162 - 163: 5.146 distance: 163 - 172: 7.901