Starting phenix.real_space_refine on Tue Dec 12 11:41:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c82_16469/12_2023/8c82_16469_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c82_16469/12_2023/8c82_16469.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c82_16469/12_2023/8c82_16469_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c82_16469/12_2023/8c82_16469_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c82_16469/12_2023/8c82_16469_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c82_16469/12_2023/8c82_16469.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c82_16469/12_2023/8c82_16469.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c82_16469/12_2023/8c82_16469_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c82_16469/12_2023/8c82_16469_updated.pdb" } resolution = 3.4 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= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 110 5.16 5 C 13534 2.51 5 N 3486 2.21 5 O 3938 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 236": "OD1" <-> "OD2" Residue "B TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 487": "OE1" <-> "OE2" Residue "B GLU 489": "OE1" <-> "OE2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 146": "OE1" <-> "OE2" Residue "C PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 181": "OE1" <-> "OE2" Residue "C TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 246": "OD1" <-> "OD2" Residue "C PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 452": "OD1" <-> "OD2" Residue "C GLU 551": "OE1" <-> "OE2" Residue "D PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 94": "OD1" <-> "OD2" Residue "F GLU 98": "OE1" <-> "OE2" Residue "F GLU 166": "OE1" <-> "OE2" Residue "F GLU 270": "OE1" <-> "OE2" Residue "F GLU 273": "OE1" <-> "OE2" Residue "F GLU 321": "OE1" <-> "OE2" Residue "F ASP 404": "OD1" <-> "OD2" Residue "F TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 463": "OE1" <-> "OE2" Residue "F PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 467": "OE1" <-> "OE2" Residue "G GLU 25": "OE1" <-> "OE2" Residue "G TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 95": "OE1" <-> "OE2" Residue "G GLU 146": "OE1" <-> "OE2" Residue "G PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 246": "OD1" <-> "OD2" Residue "G PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 551": "OE1" <-> "OE2" Residue "G ASP 556": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 21070 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1496 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 10, 'TRANS': 172} Chain: "B" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3943 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 25, 'TRANS': 479} Chain: "C" Number of atoms: 4382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4382 Classifications: {'peptide': 554} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 524} Chain: "D" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 569 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "E" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1496 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 10, 'TRANS': 172} Chain: "F" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3943 Classifications: {'peptide': 505} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 479} Chain: "G" Number of atoms: 4382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4382 Classifications: {'peptide': 554} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 524} Chain: "H" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 569 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'Z8A': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'PLP': 1, 'Q7G': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 130 Unusual residues: {'Q7G': 1, 'Z8A': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 10.03, per 1000 atoms: 0.48 Number of scatterers: 21070 At special positions: 0 Unit cell: (106.26, 175.56, 122.892, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 110 16.00 P 2 15.00 O 3938 8.00 N 3486 7.00 C 13534 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.95 Conformation dependent library (CDL) restraints added in 3.3 seconds 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4932 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 106 helices and 16 sheets defined 45.6% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.25 Creating SS restraints... Processing helix chain 'A' and resid 63 through 71 Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' Processing helix chain 'A' and resid 87 through 102 Processing helix chain 'A' and resid 108 through 127 Processing helix chain 'A' and resid 147 through 154 removed outlier: 6.276A pdb=" N ASP A 152 " --> pdb=" O TRP A 148 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ASP A 153 " --> pdb=" O GLU A 149 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLU A 154 " --> pdb=" O GLN A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 178 Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 183 through 197 removed outlier: 4.035A pdb=" N TRP A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 201 No H-bonds generated for 'chain 'A' and resid 199 through 201' Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'B' and resid 53 through 72 Processing helix chain 'B' and resid 82 through 85 removed outlier: 3.801A pdb=" N LYS B 85 " --> pdb=" O GLN B 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 82 through 85' Processing helix chain 'B' and resid 90 through 99 removed outlier: 3.662A pdb=" N ASP B 94 " --> pdb=" O PRO B 90 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA B 95 " --> pdb=" O GLN B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 119 removed outlier: 4.888A pdb=" N TRP B 116 " --> pdb=" O ASP B 112 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ARG B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL B 118 " --> pdb=" O GLN B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 175 removed outlier: 3.586A pdb=" N GLU B 166 " --> pdb=" O GLU B 162 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL B 167 " --> pdb=" O PRO B 163 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS B 169 " --> pdb=" O LYS B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 203 Processing helix chain 'B' and resid 214 through 216 No H-bonds generated for 'chain 'B' and resid 214 through 216' Processing helix chain 'B' and resid 218 through 225 Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 240 through 249 Processing helix chain 'B' and resid 261 through 278 Processing helix chain 'B' and resid 303 through 313 Processing helix chain 'B' and resid 335 through 339 removed outlier: 3.669A pdb=" N PHE B 339 " --> pdb=" O LEU B 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 335 through 339' Processing helix chain 'B' and resid 343 through 346 No H-bonds generated for 'chain 'B' and resid 343 through 346' Processing helix chain 'B' and resid 369 through 378 removed outlier: 4.193A pdb=" N ILE B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 383 No H-bonds generated for 'chain 'B' and resid 380 through 383' Processing helix chain 'B' and resid 390 through 405 Processing helix chain 'B' and resid 408 through 425 removed outlier: 3.593A pdb=" N PHE B 424 " --> pdb=" O LEU B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 432 removed outlier: 4.040A pdb=" N SER B 432 " --> pdb=" O SER B 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 429 through 432' Processing helix chain 'B' and resid 451 through 457 Processing helix chain 'B' and resid 462 through 475 Processing helix chain 'B' and resid 483 through 502 Processing helix chain 'B' and resid 514 through 516 No H-bonds generated for 'chain 'B' and resid 514 through 516' Processing helix chain 'B' and resid 535 through 553 Processing helix chain 'C' and resid 20 through 27 Processing helix chain 'C' and resid 34 through 36 No H-bonds generated for 'chain 'C' and resid 34 through 36' Processing helix chain 'C' and resid 58 through 84 Processing helix chain 'C' and resid 109 through 113 Processing helix chain 'C' and resid 116 through 121 removed outlier: 5.360A pdb=" N ASP C 120 " --> pdb=" O ARG C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 185 Processing helix chain 'C' and resid 201 through 214 Processing helix chain 'C' and resid 225 through 235 removed outlier: 4.321A pdb=" N PHE C 233 " --> pdb=" O ASN C 229 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ASN C 234 " --> pdb=" O ALA C 230 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ALA C 235 " --> pdb=" O ASN C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 260 Processing helix chain 'C' and resid 273 through 285 Processing helix chain 'C' and resid 314 through 324 Processing helix chain 'C' and resid 346 through 349 No H-bonds generated for 'chain 'C' and resid 346 through 349' Processing helix chain 'C' and resid 379 through 388 removed outlier: 4.026A pdb=" N ARG C 384 " --> pdb=" O TRP C 380 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 394 No H-bonds generated for 'chain 'C' and resid 391 through 394' Processing helix chain 'C' and resid 400 through 414 Processing helix chain 'C' and resid 422 through 443 Processing helix chain 'C' and resid 465 through 475 Processing helix chain 'C' and resid 505 through 522 Processing helix chain 'C' and resid 542 through 554 Proline residue: C 550 - end of helix removed outlier: 4.734A pdb=" N LYS C 554 " --> pdb=" O PRO C 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 21 Processing helix chain 'D' and resid 30 through 44 Processing helix chain 'D' and resid 53 through 68 Processing helix chain 'E' and resid 63 through 71 Processing helix chain 'E' and resid 87 through 102 Processing helix chain 'E' and resid 108 through 127 Processing helix chain 'E' and resid 147 through 154 removed outlier: 6.433A pdb=" N ASP E 152 " --> pdb=" O TRP E 148 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ASP E 153 " --> pdb=" O GLU E 149 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU E 154 " --> pdb=" O GLN E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 178 Proline residue: E 168 - end of helix Processing helix chain 'E' and resid 183 through 196 removed outlier: 3.556A pdb=" N TRP E 188 " --> pdb=" O LYS E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 201 No H-bonds generated for 'chain 'E' and resid 199 through 201' Processing helix chain 'F' and resid 54 through 72 removed outlier: 3.625A pdb=" N VAL F 59 " --> pdb=" O TYR F 55 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU F 60 " --> pdb=" O ARG F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 84 No H-bonds generated for 'chain 'F' and resid 82 through 84' Processing helix chain 'F' and resid 90 through 99 Processing helix chain 'F' and resid 111 through 119 removed outlier: 4.885A pdb=" N TRP F 116 " --> pdb=" O ASP F 112 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ARG F 117 " --> pdb=" O GLU F 113 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL F 118 " --> pdb=" O GLN F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 175 Processing helix chain 'F' and resid 190 through 203 Processing helix chain 'F' and resid 214 through 216 No H-bonds generated for 'chain 'F' and resid 214 through 216' Processing helix chain 'F' and resid 218 through 225 Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 240 through 249 Processing helix chain 'F' and resid 261 through 278 Processing helix chain 'F' and resid 303 through 313 Processing helix chain 'F' and resid 335 through 339 removed outlier: 3.677A pdb=" N PHE F 339 " --> pdb=" O LEU F 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 335 through 339' Processing helix chain 'F' and resid 343 through 346 No H-bonds generated for 'chain 'F' and resid 343 through 346' Processing helix chain 'F' and resid 369 through 378 removed outlier: 4.157A pdb=" N ILE F 377 " --> pdb=" O LEU F 373 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 383 No H-bonds generated for 'chain 'F' and resid 380 through 383' Processing helix chain 'F' and resid 390 through 405 Processing helix chain 'F' and resid 408 through 426 Processing helix chain 'F' and resid 451 through 458 Processing helix chain 'F' and resid 462 through 475 Processing helix chain 'F' and resid 483 through 502 removed outlier: 3.528A pdb=" N ASN F 502 " --> pdb=" O HIS F 498 " (cutoff:3.500A) Processing helix chain 'F' and resid 514 through 516 No H-bonds generated for 'chain 'F' and resid 514 through 516' Processing helix chain 'F' and resid 535 through 553 Processing helix chain 'G' and resid 20 through 27 Processing helix chain 'G' and resid 34 through 36 No H-bonds generated for 'chain 'G' and resid 34 through 36' Processing helix chain 'G' and resid 58 through 84 removed outlier: 3.501A pdb=" N TYR G 68 " --> pdb=" O THR G 64 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU G 71 " --> pdb=" O ASN G 67 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE G 72 " --> pdb=" O TYR G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 93 removed outlier: 3.731A pdb=" N LEU G 91 " --> pdb=" O ASN G 88 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ASP G 92 " --> pdb=" O LYS G 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 113 Processing helix chain 'G' and resid 116 through 121 removed outlier: 5.395A pdb=" N ASP G 120 " --> pdb=" O ARG G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 185 Processing helix chain 'G' and resid 201 through 214 Processing helix chain 'G' and resid 225 through 235 removed outlier: 4.338A pdb=" N PHE G 233 " --> pdb=" O ASN G 229 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ASN G 234 " --> pdb=" O ALA G 230 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ALA G 235 " --> pdb=" O ASN G 231 " (cutoff:3.500A) Processing helix chain 'G' and resid 251 through 260 Processing helix chain 'G' and resid 273 through 285 Processing helix chain 'G' and resid 314 through 324 Processing helix chain 'G' and resid 346 through 349 No H-bonds generated for 'chain 'G' and resid 346 through 349' Processing helix chain 'G' and resid 379 through 388 removed outlier: 3.927A pdb=" N ARG G 384 " --> pdb=" O TRP G 380 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU G 387 " --> pdb=" O ASP G 383 " (cutoff:3.500A) Processing helix chain 'G' and resid 391 through 394 No H-bonds generated for 'chain 'G' and resid 391 through 394' Processing helix chain 'G' and resid 400 through 414 Processing helix chain 'G' and resid 422 through 443 Processing helix chain 'G' and resid 465 through 475 Processing helix chain 'G' and resid 505 through 522 Processing helix chain 'G' and resid 542 through 554 Proline residue: G 550 - end of helix removed outlier: 4.761A pdb=" N LYS G 554 " --> pdb=" O PRO G 550 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 20 Processing helix chain 'H' and resid 26 through 44 removed outlier: 3.874A pdb=" N THR H 30 " --> pdb=" O GLY H 26 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ILE H 31 " --> pdb=" O ILE H 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 68 Processing sheet with id= A, first strand: chain 'A' and resid 55 through 57 Processing sheet with id= B, first strand: chain 'B' and resid 135 through 137 Processing sheet with id= C, first strand: chain 'B' and resid 207 through 211 removed outlier: 3.516A pdb=" N ILE B 349 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL B 231 " --> pdb=" O PHE B 287 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N VAL B 289 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL B 233 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N GLU B 291 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR B 252 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N ALA B 234 " --> pdb=" O THR B 252 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N TYR B 254 " --> pdb=" O ALA B 234 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 434 through 436 Processing sheet with id= E, first strand: chain 'C' and resid 133 through 137 Processing sheet with id= F, first strand: chain 'C' and resid 139 through 142 removed outlier: 4.184A pdb=" N TYR C 147 " --> pdb=" O HIS C 142 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 218 through 222 removed outlier: 3.652A pdb=" N GLY C 362 " --> pdb=" O TYR C 374 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE C 359 " --> pdb=" O LEU C 328 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET C 361 " --> pdb=" O ILE C 330 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU C 242 " --> pdb=" O LEU C 298 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N CYS C 300 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE C 244 " --> pdb=" O CYS C 300 " (cutoff:3.500A) removed outlier: 9.011A pdb=" N GLU C 302 " --> pdb=" O ILE C 244 " (cutoff:3.500A) removed outlier: 9.211A pdb=" N ASP C 246 " --> pdb=" O GLU C 302 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ALA C 263 " --> pdb=" O VAL C 243 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N SER C 245 " --> pdb=" O ALA C 263 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ARG C 265 " --> pdb=" O SER C 245 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 455 through 460 removed outlier: 3.563A pdb=" N ARG C 494 " --> pdb=" O VAL C 483 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL C 481 " --> pdb=" O ARG C 496 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 55 through 57 Processing sheet with id= J, first strand: chain 'F' and resid 135 through 137 removed outlier: 3.576A pdb=" N GLU F 142 " --> pdb=" O ARG F 137 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 207 through 211 removed outlier: 3.513A pdb=" N ILE F 349 " --> pdb=" O LEU F 317 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL F 231 " --> pdb=" O PHE F 287 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N VAL F 289 " --> pdb=" O VAL F 231 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL F 233 " --> pdb=" O VAL F 289 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N GLU F 291 " --> pdb=" O VAL F 233 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR F 252 " --> pdb=" O ILE F 232 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ALA F 234 " --> pdb=" O THR F 252 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N TYR F 254 " --> pdb=" O ALA F 234 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 434 through 436 Processing sheet with id= M, first strand: chain 'G' and resid 133 through 137 Processing sheet with id= N, first strand: chain 'G' and resid 139 through 142 removed outlier: 4.180A pdb=" N TYR G 147 " --> pdb=" O HIS G 142 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 218 through 222 removed outlier: 3.705A pdb=" N GLY G 362 " --> pdb=" O TYR G 374 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE G 359 " --> pdb=" O LEU G 328 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET G 361 " --> pdb=" O ILE G 330 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU G 242 " --> pdb=" O LEU G 298 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N CYS G 300 " --> pdb=" O LEU G 242 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE G 244 " --> pdb=" O CYS G 300 " (cutoff:3.500A) removed outlier: 8.891A pdb=" N GLU G 302 " --> pdb=" O ILE G 244 " (cutoff:3.500A) removed outlier: 9.048A pdb=" N ASP G 246 " --> pdb=" O GLU G 302 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA G 263 " --> pdb=" O VAL G 243 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N SER G 245 " --> pdb=" O ALA G 263 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ARG G 265 " --> pdb=" O SER G 245 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 455 through 460 removed outlier: 3.684A pdb=" N ARG G 494 " --> pdb=" O VAL G 483 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL G 481 " --> pdb=" O ARG G 496 " (cutoff:3.500A) 835 hydrogen bonds defined for protein. 2433 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: 5.74 Time building geometry restraints manager: 7.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5160 1.33 - 1.45: 4111 1.45 - 1.57: 12125 1.57 - 1.69: 2 1.69 - 1.81: 166 Bond restraints: 21564 Sorted by residual: bond pdb=" C04 Q7G E 302 " pdb=" C05 Q7G E 302 " ideal model delta sigma weight residual 1.836 1.531 0.305 2.00e-02 2.50e+03 2.32e+02 bond pdb=" C04 Q7G C 602 " pdb=" C05 Q7G C 602 " ideal model delta sigma weight residual 1.836 1.532 0.304 2.00e-02 2.50e+03 2.32e+02 bond pdb=" C13 Q7G C 602 " pdb=" C14 Q7G C 602 " ideal model delta sigma weight residual 1.599 1.325 0.274 2.00e-02 2.50e+03 1.88e+02 bond pdb=" C13 Q7G E 302 " pdb=" C14 Q7G E 302 " ideal model delta sigma weight residual 1.599 1.325 0.274 2.00e-02 2.50e+03 1.88e+02 bond pdb=" C07 Q7G C 602 " pdb=" C15 Q7G C 602 " ideal model delta sigma weight residual 1.779 1.525 0.254 2.00e-02 2.50e+03 1.61e+02 ... (remaining 21559 not shown) Histogram of bond angle deviations from ideal: 98.66 - 105.73: 541 105.73 - 112.79: 11539 112.79 - 119.86: 7182 119.86 - 126.93: 9744 126.93 - 133.99: 260 Bond angle restraints: 29266 Sorted by residual: angle pdb=" C GLN B 84 " pdb=" CA GLN B 84 " pdb=" CB GLN B 84 " ideal model delta sigma weight residual 110.88 104.00 6.88 1.57e+00 4.06e-01 1.92e+01 angle pdb=" N PHE D 48 " pdb=" CA PHE D 48 " pdb=" C PHE D 48 " ideal model delta sigma weight residual 114.31 109.01 5.30 1.29e+00 6.01e-01 1.69e+01 angle pdb=" CA LYS B 85 " pdb=" C LYS B 85 " pdb=" N PRO B 86 " ideal model delta sigma weight residual 118.44 124.52 -6.08 1.59e+00 3.96e-01 1.46e+01 angle pdb=" N PRO B 86 " pdb=" CA PRO B 86 " pdb=" CB PRO B 86 " ideal model delta sigma weight residual 103.25 107.00 -3.75 1.05e+00 9.07e-01 1.28e+01 angle pdb=" N PRO B 86 " pdb=" CA PRO B 86 " pdb=" C PRO B 86 " ideal model delta sigma weight residual 112.47 105.39 7.08 2.06e+00 2.36e-01 1.18e+01 ... (remaining 29261 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.93: 12476 28.93 - 57.86: 433 57.86 - 86.78: 55 86.78 - 115.71: 14 115.71 - 144.64: 2 Dihedral angle restraints: 12980 sinusoidal: 5324 harmonic: 7656 Sorted by residual: dihedral pdb=" CA LYS B 85 " pdb=" C LYS B 85 " pdb=" N PRO B 86 " pdb=" CA PRO B 86 " ideal model delta harmonic sigma weight residual -180.00 -53.94 -126.06 0 5.00e+00 4.00e-02 6.36e+02 dihedral pdb=" C4B Q7G C 602 " pdb=" C5B Q7G C 602 " pdb=" C6B Q7G C 602 " pdb=" O6B Q7G C 602 " ideal model delta sinusoidal sigma weight residual 143.94 -71.42 -144.64 1 3.00e+01 1.11e-03 1.94e+01 dihedral pdb=" CA TYR C 485 " pdb=" C TYR C 485 " pdb=" N PRO C 486 " pdb=" CA PRO C 486 " ideal model delta harmonic sigma weight residual 0.00 -20.05 20.05 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 12977 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.160: 3314 0.160 - 0.321: 11 0.321 - 0.481: 1 0.481 - 0.642: 0 0.642 - 0.802: 2 Chirality restraints: 3328 Sorted by residual: chirality pdb=" C02 Q7G C 602 " pdb=" C03 Q7G C 602 " pdb=" C06 Q7G C 602 " pdb=" C10 Q7G C 602 " both_signs ideal model delta sigma weight residual False 2.14 2.94 -0.80 2.00e-01 2.50e+01 1.61e+01 chirality pdb=" C02 Q7G E 302 " pdb=" C03 Q7G E 302 " pdb=" C06 Q7G E 302 " pdb=" C10 Q7G E 302 " both_signs ideal model delta sigma weight residual False 2.14 2.93 -0.79 2.00e-01 2.50e+01 1.57e+01 chirality pdb=" C2 Z8A E 301 " pdb=" C1 Z8A E 301 " pdb=" C3 Z8A E 301 " pdb=" N1 Z8A E 301 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.33 2.00e-01 2.50e+01 2.80e+00 ... (remaining 3325 not shown) Planarity restraints: 3688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 Q7G E 302 " -0.016 2.00e-02 2.50e+03 5.76e-02 4.15e+01 pdb=" C13 Q7G E 302 " -0.009 2.00e-02 2.50e+03 pdb=" C14 Q7G E 302 " -0.095 2.00e-02 2.50e+03 pdb=" C15 Q7G E 302 " 0.069 2.00e-02 2.50e+03 pdb=" C16 Q7G E 302 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 212 " -0.029 5.00e-02 4.00e+02 4.44e-02 3.15e+00 pdb=" N PRO A 213 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 213 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 213 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP G 556 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.11e+00 pdb=" C ASP G 556 " 0.031 2.00e-02 2.50e+03 pdb=" O ASP G 556 " -0.012 2.00e-02 2.50e+03 pdb=" N LYS G 557 " -0.010 2.00e-02 2.50e+03 ... (remaining 3685 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 206 2.67 - 3.22: 19138 3.22 - 3.78: 29454 3.78 - 4.34: 39088 4.34 - 4.90: 68898 Nonbonded interactions: 156784 Sorted by model distance: nonbonded pdb=" OD1 ASP C 238 " pdb=" N LYS C 239 " model vdw 2.108 2.520 nonbonded pdb=" OD1 ASP G 238 " pdb=" N LYS G 239 " model vdw 2.220 2.520 nonbonded pdb=" OH TYR F 460 " pdb=" OE1 GLU F 488 " model vdw 2.240 2.440 nonbonded pdb=" O PHE B 491 " pdb=" OG SER B 494 " model vdw 2.250 2.440 nonbonded pdb=" O GLN F 77 " pdb=" OG SER F 80 " model vdw 2.280 2.440 ... (remaining 156779 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 'E' and (resid 39 through 221 or resid 301)) } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 8 through 561 or resid 601)) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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: 7.060 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: 19.130 Check model and map are aligned: 0.330 Set scattering table: 0.180 Process input model: 49.660 Find NCS groups from input model: 1.380 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: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.305 21564 Z= 0.491 Angle : 0.666 10.193 29266 Z= 0.338 Chirality : 0.048 0.802 3328 Planarity : 0.004 0.058 3688 Dihedral : 15.026 144.639 8048 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.09 % Allowed : 0.17 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.76 % 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: 0.90 (0.16), residues: 2602 helix: 2.30 (0.16), residues: 1152 sheet: 0.69 (0.32), residues: 234 loop : -1.19 (0.16), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 112 HIS 0.006 0.001 HIS G 78 PHE 0.030 0.001 PHE E 163 TYR 0.018 0.001 TYR G 510 ARG 0.004 0.000 ARG B 456 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 338 time to evaluate : 2.478 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 340 average time/residue: 0.3479 time to fit residues: 180.1026 Evaluate side-chains 208 residues out of total 2314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 2.371 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 217 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 108 optimal weight: 0.0980 chunk 66 optimal weight: 0.2980 chunk 131 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 202 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 chunk 234 optimal weight: 0.2980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN B 91 GLN C 379 GLN E 69 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21564 Z= 0.170 Angle : 0.528 6.906 29266 Z= 0.268 Chirality : 0.042 0.236 3328 Planarity : 0.004 0.056 3688 Dihedral : 9.776 123.415 3040 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.99 % Allowed : 5.96 % Favored : 93.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.76 % 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: 1.05 (0.17), residues: 2602 helix: 2.48 (0.16), residues: 1144 sheet: 0.59 (0.32), residues: 258 loop : -1.13 (0.16), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 540 HIS 0.005 0.001 HIS G 78 PHE 0.018 0.001 PHE A 163 TYR 0.019 0.001 TYR C 510 ARG 0.006 0.000 ARG D 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 209 time to evaluate : 2.667 Fit side-chains outliers start: 23 outliers final: 18 residues processed: 221 average time/residue: 0.3524 time to fit residues: 119.0551 Evaluate side-chains 209 residues out of total 2314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 191 time to evaluate : 2.341 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2162 time to fit residues: 10.1780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 130 optimal weight: 10.0000 chunk 72 optimal weight: 0.0970 chunk 194 optimal weight: 0.7980 chunk 159 optimal weight: 0.2980 chunk 64 optimal weight: 0.8980 chunk 234 optimal weight: 0.9980 chunk 253 optimal weight: 2.9990 chunk 209 optimal weight: 0.0070 chunk 232 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN B 237 GLN E 69 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21564 Z= 0.128 Angle : 0.481 6.782 29266 Z= 0.240 Chirality : 0.040 0.186 3328 Planarity : 0.004 0.085 3688 Dihedral : 9.188 114.540 3040 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.39 % Allowed : 7.61 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.76 % 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: 1.17 (0.17), residues: 2602 helix: 2.65 (0.16), residues: 1128 sheet: 0.49 (0.31), residues: 282 loop : -1.08 (0.16), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 294 HIS 0.003 0.001 HIS G 203 PHE 0.020 0.001 PHE E 172 TYR 0.019 0.001 TYR B 71 ARG 0.005 0.000 ARG G 292 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 205 time to evaluate : 2.308 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 212 average time/residue: 0.3571 time to fit residues: 117.1925 Evaluate side-chains 189 residues out of total 2314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 186 time to evaluate : 2.342 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1992 time to fit residues: 4.3871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 231 optimal weight: 0.9980 chunk 176 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 112 optimal weight: 0.3980 chunk 157 optimal weight: 0.5980 chunk 235 optimal weight: 0.0170 chunk 249 optimal weight: 0.9990 chunk 123 optimal weight: 5.9990 chunk 223 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 overall best weight: 0.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN A 220 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 477 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 21564 Z= 0.148 Angle : 0.489 7.388 29266 Z= 0.244 Chirality : 0.041 0.184 3328 Planarity : 0.004 0.089 3688 Dihedral : 9.000 114.083 3040 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.99 % Allowed : 8.69 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.76 % 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: 1.23 (0.17), residues: 2602 helix: 2.65 (0.16), residues: 1140 sheet: 0.50 (0.30), residues: 282 loop : -1.01 (0.16), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 540 HIS 0.003 0.001 HIS G 203 PHE 0.021 0.001 PHE A 172 TYR 0.020 0.001 TYR F 71 ARG 0.003 0.000 ARG C 212 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 200 time to evaluate : 2.685 Fit side-chains outliers start: 23 outliers final: 16 residues processed: 211 average time/residue: 0.3812 time to fit residues: 123.2807 Evaluate side-chains 208 residues out of total 2314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 192 time to evaluate : 2.420 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2000 time to fit residues: 9.4266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.9146 > 50: distance: 55 - 60: 5.045 distance: 60 - 61: 18.062 distance: 61 - 62: 40.817 distance: 61 - 64: 27.497 distance: 62 - 63: 32.163 distance: 62 - 71: 39.968 distance: 64 - 65: 33.152 distance: 65 - 66: 21.572 distance: 66 - 67: 33.849 distance: 67 - 68: 17.249 distance: 68 - 69: 6.239 distance: 68 - 70: 4.298 distance: 71 - 72: 23.927 distance: 72 - 73: 6.393 distance: 72 - 75: 33.361 distance: 73 - 74: 16.352 distance: 73 - 77: 35.630 distance: 75 - 76: 26.726 distance: 77 - 78: 26.580 distance: 78 - 79: 67.812 distance: 78 - 81: 56.883 distance: 79 - 80: 51.752 distance: 79 - 89: 59.541 distance: 81 - 82: 16.446 distance: 82 - 83: 8.848 distance: 82 - 84: 6.064 distance: 83 - 85: 7.536 distance: 84 - 86: 9.656 distance: 85 - 87: 8.665 distance: 86 - 87: 11.466 distance: 87 - 88: 20.959 distance: 89 - 90: 38.869 distance: 90 - 91: 28.313 distance: 90 - 93: 34.005 distance: 91 - 92: 21.209 distance: 91 - 96: 51.111 distance: 93 - 94: 20.578 distance: 93 - 95: 26.310 distance: 96 - 97: 31.502 distance: 96 - 175: 24.088 distance: 97 - 98: 54.058 distance: 97 - 100: 35.074 distance: 98 - 99: 41.538 distance: 98 - 104: 37.563 distance: 99 - 172: 28.754 distance: 100 - 101: 29.464 distance: 100 - 102: 37.790 distance: 101 - 103: 8.027 distance: 104 - 105: 21.657 distance: 105 - 106: 46.256 distance: 105 - 108: 45.209 distance: 106 - 107: 36.427 distance: 106 - 111: 46.461 distance: 108 - 109: 31.011 distance: 108 - 110: 37.501 distance: 111 - 112: 40.359 distance: 112 - 113: 31.836 distance: 112 - 115: 45.094 distance: 113 - 114: 16.861 distance: 113 - 118: 49.166 distance: 115 - 116: 13.672 distance: 115 - 117: 43.321 distance: 118 - 119: 38.885 distance: 119 - 120: 56.398 distance: 119 - 122: 56.749 distance: 120 - 121: 38.937 distance: 120 - 124: 52.936 distance: 122 - 123: 20.386 distance: 124 - 125: 29.540 distance: 125 - 126: 46.438 distance: 125 - 128: 28.347 distance: 126 - 127: 18.436 distance: 126 - 130: 58.852 distance: 128 - 129: 46.086 distance: 130 - 131: 44.548 distance: 130 - 136: 36.292 distance: 131 - 132: 30.494 distance: 131 - 134: 25.399 distance: 132 - 133: 31.709 distance: 132 - 137: 28.933 distance: 134 - 135: 23.773 distance: 135 - 136: 32.624