Starting phenix.real_space_refine (version: 1.21rc1) on Thu Jul 6 02:51:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6idf_9648/07_2023/6idf_9648_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6idf_9648/07_2023/6idf_9648.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6idf_9648/07_2023/6idf_9648.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6idf_9648/07_2023/6idf_9648.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6idf_9648/07_2023/6idf_9648_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6idf_9648/07_2023/6idf_9648_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 4 5.49 5 S 44 5.16 5 C 7344 2.51 5 N 1762 2.21 5 O 2034 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 108": "NH1" <-> "NH2" Residue "B ARG 128": "NH1" <-> "NH2" Residue "B ARG 377": "NH1" <-> "NH2" Residue "D ARG 39": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 11188 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 5235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 5235 Classifications: {'peptide': 667} Link IDs: {'PTRANS': 37, 'TRANS': 629} Chain: "B" Number of atoms: 2414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2414 Classifications: {'peptide': 312} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 10, 'TRANS': 301} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1872 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 7, 'TRANS': 235} Chain: "D" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 850 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "E" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 263 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 3, 'TRANS': 37} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 2, 'TYR:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 85 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 95 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "C" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 134 Unusual residues: {'CLR': 3, 'PC1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Time building chain proxies: 6.05, per 1000 atoms: 0.54 Number of scatterers: 11188 At special positions: 0 Unit cell: (110.191, 94.917, 133.102, 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 44 16.00 P 4 15.00 O 2034 8.00 N 1762 7.00 C 7344 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 62 " distance=2.04 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 248 " distance=2.02 Simple disulfide: pdb=" SG CYS A 586 " - pdb=" SG CYS A 620 " distance=2.03 Simple disulfide: pdb=" SG CYS B 112 " - pdb=" SG CYS E 9 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-3 " BMA G 3 " - " BMA G 4 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " BETA1-6 " BMA G 3 " - " BMA G 5 " NAG-ASN " NAG A 810 " - " ASN A 387 " " NAG A 817 " - " ASN A 464 " " NAG A 818 " - " ASN A 506 " " NAG A 819 " - " ASN A 264 " " NAG A 820 " - " ASN A 187 " " NAG F 1 " - " ASN A 45 " " NAG G 1 " - " ASN A 55 " " NAG H 1 " - " ASN A 435 " " NAG I 1 " - " ASN A 573 " " NAG J 1 " - " ASN A 530 " " NAG K 1 " - " ASN A 562 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.87 Conformation dependent library (CDL) restraints added in 3.1 seconds 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2566 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 4 sheets defined 50.1% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 81 through 87 removed outlier: 3.862A pdb=" N VAL A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 113 removed outlier: 4.170A pdb=" N GLY A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 154 through 156 No H-bonds generated for 'chain 'A' and resid 154 through 156' Processing helix chain 'A' and resid 186 through 199 Processing helix chain 'A' and resid 227 through 236 removed outlier: 3.998A pdb=" N ARG A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER A 235 " --> pdb=" O MET A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 313 Processing helix chain 'A' and resid 338 through 349 removed outlier: 3.572A pdb=" N ARG A 342 " --> pdb=" O ILE A 338 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 386 No H-bonds generated for 'chain 'A' and resid 384 through 386' Processing helix chain 'A' and resid 388 through 404 removed outlier: 3.561A pdb=" N ASP A 396 " --> pdb=" O ASN A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 432 removed outlier: 4.163A pdb=" N LEU A 431 " --> pdb=" O GLN A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 502 removed outlier: 3.705A pdb=" N ALA A 486 " --> pdb=" O ASP A 482 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 526 Processing helix chain 'A' and resid 534 through 536 No H-bonds generated for 'chain 'A' and resid 534 through 536' Processing helix chain 'A' and resid 540 through 545 removed outlier: 3.743A pdb=" N ARG A 543 " --> pdb=" O GLN A 540 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N SER A 544 " --> pdb=" O ASP A 541 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR A 545 " --> pdb=" O LEU A 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 540 through 545' Processing helix chain 'A' and resid 562 through 575 Processing helix chain 'A' and resid 583 through 587 Processing helix chain 'A' and resid 633 through 635 No H-bonds generated for 'chain 'A' and resid 633 through 635' Processing helix chain 'A' and resid 666 through 692 removed outlier: 3.560A pdb=" N LEU A 673 " --> pdb=" O GLU A 669 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER A 683 " --> pdb=" O ILE A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 697 No H-bonds generated for 'chain 'A' and resid 694 through 697' Processing helix chain 'B' and resid 75 through 102 removed outlier: 3.902A pdb=" N HIS B 81 " --> pdb=" O TYR B 77 " (cutoff:3.500A) Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 125 through 153 removed outlier: 3.881A pdb=" N HIS B 131 " --> pdb=" O GLN B 127 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL B 142 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE B 143 " --> pdb=" O MET B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 165 Processing helix chain 'B' and resid 168 through 174 removed outlier: 4.334A pdb=" N LEU B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 188 Processing helix chain 'B' and resid 195 through 213 removed outlier: 3.764A pdb=" N TRP B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 239 Processing helix chain 'B' and resid 243 through 262 removed outlier: 3.552A pdb=" N VAL B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 277 removed outlier: 3.765A pdb=" N LEU B 271 " --> pdb=" O PRO B 267 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 398 removed outlier: 3.871A pdb=" N ALA B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 428 Processing helix chain 'B' and resid 435 through 449 Processing helix chain 'B' and resid 454 through 462 Processing helix chain 'C' and resid 4 through 13 removed outlier: 3.564A pdb=" N VAL C 12 " --> pdb=" O GLY C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 24 Processing helix chain 'C' and resid 29 through 60 removed outlier: 4.150A pdb=" N ILE C 33 " --> pdb=" O PRO C 29 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE C 34 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TRP C 53 " --> pdb=" O ALA C 49 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 106 removed outlier: 3.712A pdb=" N GLU C 84 " --> pdb=" O VAL C 80 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL C 85 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE C 86 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG C 87 " --> pdb=" O GLN C 83 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER C 103 " --> pdb=" O GLU C 99 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU C 104 " --> pdb=" O GLY C 100 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N SER C 105 " --> pdb=" O LEU C 101 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 141 removed outlier: 3.597A pdb=" N PHE C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ASN C 136 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ILE C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA C 139 " --> pdb=" O ILE C 135 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP C 140 " --> pdb=" O ASN C 136 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA C 141 " --> pdb=" O ILE C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 184 removed outlier: 3.785A pdb=" N ALA C 166 " --> pdb=" O PHE C 162 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE C 167 " --> pdb=" O LEU C 163 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL C 176 " --> pdb=" O THR C 172 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG C 184 " --> pdb=" O ASP C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 202 removed outlier: 3.929A pdb=" N VAL C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 206 No H-bonds generated for 'chain 'C' and resid 204 through 206' Processing helix chain 'C' and resid 210 through 212 No H-bonds generated for 'chain 'C' and resid 210 through 212' Processing helix chain 'C' and resid 215 through 231 Processing helix chain 'C' and resid 236 through 242 Processing helix chain 'D' and resid 8 through 23 removed outlier: 4.134A pdb=" N LEU D 12 " --> pdb=" O ASN D 8 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS D 17 " --> pdb=" O ASN D 13 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLY D 22 " --> pdb=" O TYR D 18 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE D 23 " --> pdb=" O TYR D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 41 removed outlier: 3.560A pdb=" N PHE D 37 " --> pdb=" O ASN D 33 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ARG D 39 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N GLU D 40 " --> pdb=" O TRP D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 58 Processing helix chain 'D' and resid 60 through 80 removed outlier: 3.575A pdb=" N PHE D 64 " --> pdb=" O SER D 60 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU D 65 " --> pdb=" O ALA D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 91 No H-bonds generated for 'chain 'D' and resid 88 through 91' Processing helix chain 'E' and resid 4 through 7 removed outlier: 3.657A pdb=" N VAL E 7 " --> pdb=" O SER E 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 4 through 7' Processing helix chain 'E' and resid 17 through 22 removed outlier: 3.972A pdb=" N ALA E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 27 No H-bonds generated for 'chain 'E' and resid 24 through 27' Processing sheet with id= A, first strand: chain 'A' and resid 42 through 44 removed outlier: 4.497A pdb=" N ALA A 658 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 13.679A pdb=" N VAL A 75 " --> pdb=" O PRO A 211 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N CYS A 213 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS A 74 " --> pdb=" O MET A 95 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLU A 99 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 626 through 630 removed outlier: 7.237A pdb=" N VAL A 277 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N PHE A 362 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ALA A 279 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLU A 364 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N ARG A 281 " --> pdb=" O GLU A 364 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE A 412 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N MET A 378 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ARG A 414 " --> pdb=" O MET A 378 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 577 through 579 removed outlier: 4.299A pdb=" N CYS A 620 " --> pdb=" O VAL A 579 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER A 603 " --> pdb=" O VAL A 621 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 287 through 289 472 hydrogen bonds defined for protein. 1383 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.95 Time building geometry restraints manager: 4.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1680 1.31 - 1.44: 3232 1.44 - 1.57: 6471 1.57 - 1.70: 13 1.70 - 1.83: 66 Bond restraints: 11462 Sorted by residual: bond pdb=" C29 PC1 C 301 " pdb=" C2A PC1 C 301 " ideal model delta sigma weight residual 1.524 1.347 0.177 2.00e-02 2.50e+03 7.85e+01 bond pdb=" C29 PC1 B 501 " pdb=" C2A PC1 B 501 " ideal model delta sigma weight residual 1.524 1.348 0.176 2.00e-02 2.50e+03 7.75e+01 bond pdb=" C29 PC1 B 502 " pdb=" C2A PC1 B 502 " ideal model delta sigma weight residual 1.524 1.349 0.175 2.00e-02 2.50e+03 7.69e+01 bond pdb=" C29 PC1 D 201 " pdb=" C2A PC1 D 201 " ideal model delta sigma weight residual 1.524 1.349 0.175 2.00e-02 2.50e+03 7.67e+01 bond pdb=" C31 PC1 B 502 " pdb=" O31 PC1 B 502 " ideal model delta sigma weight residual 1.330 1.426 -0.096 2.00e-02 2.50e+03 2.32e+01 ... (remaining 11457 not shown) Histogram of bond angle deviations from ideal: 94.89 - 102.72: 43 102.72 - 110.54: 3438 110.54 - 118.37: 5493 118.37 - 126.19: 6427 126.19 - 134.01: 214 Bond angle restraints: 15615 Sorted by residual: angle pdb=" O12 PC1 C 301 " pdb=" P PC1 C 301 " pdb=" O14 PC1 C 301 " ideal model delta sigma weight residual 123.67 100.19 23.48 3.00e+00 1.11e-01 6.12e+01 angle pdb=" O12 PC1 B 501 " pdb=" P PC1 B 501 " pdb=" O14 PC1 B 501 " ideal model delta sigma weight residual 123.67 101.07 22.60 3.00e+00 1.11e-01 5.68e+01 angle pdb=" O12 PC1 D 201 " pdb=" P PC1 D 201 " pdb=" O14 PC1 D 201 " ideal model delta sigma weight residual 123.67 101.14 22.53 3.00e+00 1.11e-01 5.64e+01 angle pdb=" O12 PC1 B 502 " pdb=" P PC1 B 502 " pdb=" O14 PC1 B 502 " ideal model delta sigma weight residual 123.67 101.17 22.50 3.00e+00 1.11e-01 5.62e+01 angle pdb=" N PRO B 117 " pdb=" CA PRO B 117 " pdb=" CB PRO B 117 " ideal model delta sigma weight residual 103.25 110.99 -7.74 1.05e+00 9.07e-01 5.44e+01 ... (remaining 15610 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 6126 16.79 - 33.59: 287 33.59 - 50.38: 89 50.38 - 67.18: 15 67.18 - 83.97: 11 Dihedral angle restraints: 6528 sinusoidal: 2551 harmonic: 3977 Sorted by residual: dihedral pdb=" CB CYS A 140 " pdb=" SG CYS A 140 " pdb=" SG CYS A 159 " pdb=" CB CYS A 159 " ideal model delta sinusoidal sigma weight residual -86.00 -169.97 83.97 1 1.00e+01 1.00e-02 8.59e+01 dihedral pdb=" CB CYS A 586 " pdb=" SG CYS A 586 " pdb=" SG CYS A 620 " pdb=" CB CYS A 620 " ideal model delta sinusoidal sigma weight residual -86.00 -164.97 78.97 1 1.00e+01 1.00e-02 7.76e+01 dihedral pdb=" CA PHE A 210 " pdb=" C PHE A 210 " pdb=" N PRO A 211 " pdb=" CA PRO A 211 " ideal model delta harmonic sigma weight residual 180.00 137.02 42.98 0 5.00e+00 4.00e-02 7.39e+01 ... (remaining 6525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1707 0.097 - 0.194: 146 0.194 - 0.291: 10 0.291 - 0.388: 3 0.388 - 0.485: 2 Chirality restraints: 1868 Sorted by residual: chirality pdb=" C2 NAG J 2 " pdb=" C1 NAG J 2 " pdb=" C3 NAG J 2 " pdb=" N2 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.01 -0.48 2.00e-01 2.50e+01 5.87e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A 573 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.46e+00 chirality pdb=" C1 NAG A 819 " pdb=" ND2 ASN A 264 " pdb=" C2 NAG A 819 " pdb=" O5 NAG A 819 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.32e+00 ... (remaining 1865 not shown) Planarity restraints: 1888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 210 " -0.055 5.00e-02 4.00e+02 8.36e-02 1.12e+01 pdb=" N PRO A 211 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 211 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 211 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 227 " -0.020 2.00e-02 2.50e+03 1.73e-02 7.45e+00 pdb=" CG TRP C 227 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP C 227 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP C 227 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 227 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 227 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 227 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 227 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 227 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 227 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 559 " -0.041 5.00e-02 4.00e+02 6.27e-02 6.29e+00 pdb=" N PRO A 560 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 560 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 560 " -0.036 5.00e-02 4.00e+02 ... (remaining 1885 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2843 2.80 - 3.33: 9818 3.33 - 3.85: 18037 3.85 - 4.38: 20936 4.38 - 4.90: 36250 Nonbonded interactions: 87884 Sorted by model distance: nonbonded pdb=" O VAL A 383 " pdb=" O6 NAG H 1 " model vdw 2.279 2.440 nonbonded pdb=" OG SER A 286 " pdb=" O VAL A 291 " model vdw 2.285 2.440 nonbonded pdb=" O PRO A 130 " pdb=" OH TYR A 452 " model vdw 2.318 2.440 nonbonded pdb=" O PHE C 162 " pdb=" OH TYR C 218 " model vdw 2.323 2.440 nonbonded pdb=" OG SER A 202 " pdb=" O SER A 206 " model vdw 2.329 2.440 ... (remaining 87879 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 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 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: 0.010 Extract box with map and model: 7.340 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 28.780 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.060 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:13.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.0000 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: