Starting phenix.real_space_refine on Mon May 19 14:47:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e29_47446/05_2025/9e29_47446.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e29_47446/05_2025/9e29_47446.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e29_47446/05_2025/9e29_47446.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e29_47446/05_2025/9e29_47446.map" model { file = "/net/cci-nas-00/data/ceres_data/9e29_47446/05_2025/9e29_47446.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e29_47446/05_2025/9e29_47446.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.043 sd= 0.103 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 14 5.49 5 Mg 6 5.21 5 S 100 5.16 5 C 11394 2.51 5 N 3432 2.21 5 O 3552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 18498 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3053 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 17, 'TRANS': 404} Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 257 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 105 Chain: "B" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3054 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 17, 'TRANS': 404} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 105 Chain: "C" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3054 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 17, 'TRANS': 404} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 105 Chain: "D" Number of atoms: 3053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3053 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 17, 'TRANS': 404} Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 257 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 105 Chain: "E" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3054 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 17, 'TRANS': 404} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 105 Chain: "F" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3054 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 17, 'TRANS': 404} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 105 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 11.52, per 1000 atoms: 0.62 Number of scatterers: 18498 At special positions: 0 Unit cell: (144.2, 144.2, 91.67, 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 100 16.00 P 14 15.00 Mg 6 11.99 O 3552 8.00 N 3432 7.00 C 11394 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM18494 O4' ADP F 601 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.51 Conformation dependent library (CDL) restraints added in 2.4 seconds 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4644 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 14 sheets defined 44.3% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.21 Creating SS restraints... Processing helix chain 'A' and resid 80 through 95 removed outlier: 3.935A pdb=" N ASN A 95 " --> pdb=" O ASN A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 105 Processing helix chain 'A' and resid 106 through 126 removed outlier: 3.720A pdb=" N GLU A 112 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASP A 116 " --> pdb=" O GLU A 112 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 146 Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 151 through 157 removed outlier: 3.537A pdb=" N ALA A 156 " --> pdb=" O GLU A 152 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG A 157 " --> pdb=" O PRO A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 202 Processing helix chain 'A' and resid 249 through 256 Processing helix chain 'A' and resid 260 through 273 Processing helix chain 'A' and resid 286 through 296 Processing helix chain 'A' and resid 337 through 346 Processing helix chain 'A' and resid 361 through 372 removed outlier: 3.993A pdb=" N ASP A 365 " --> pdb=" O PRO A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 400 Processing helix chain 'A' and resid 405 through 417 Processing helix chain 'A' and resid 480 through 487 Processing helix chain 'A' and resid 489 through 500 removed outlier: 3.577A pdb=" N ASP A 498 " --> pdb=" O ALA A 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 97 Processing helix chain 'B' and resid 98 through 105 Processing helix chain 'B' and resid 106 through 126 Processing helix chain 'B' and resid 130 through 147 Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 151 through 157 Processing helix chain 'B' and resid 188 through 202 Processing helix chain 'B' and resid 249 through 256 Processing helix chain 'B' and resid 260 through 273 Processing helix chain 'B' and resid 286 through 296 Processing helix chain 'B' and resid 337 through 346 Processing helix chain 'B' and resid 361 through 372 removed outlier: 4.031A pdb=" N ASP B 365 " --> pdb=" O PRO B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 400 Processing helix chain 'B' and resid 405 through 417 Processing helix chain 'B' and resid 480 through 488 Processing helix chain 'B' and resid 489 through 500 Processing helix chain 'C' and resid 81 through 97 removed outlier: 3.782A pdb=" N ASN C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 105 removed outlier: 3.846A pdb=" N ALA C 103 " --> pdb=" O LEU C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 120 removed outlier: 4.165A pdb=" N ASP C 116 " --> pdb=" O GLU C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 146 removed outlier: 3.666A pdb=" N HIS C 136 " --> pdb=" O ALA C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 157 removed outlier: 4.713A pdb=" N LEU C 154 " --> pdb=" O PRO C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 202 Processing helix chain 'C' and resid 249 through 256 Processing helix chain 'C' and resid 260 through 273 Processing helix chain 'C' and resid 286 through 296 Processing helix chain 'C' and resid 337 through 346 removed outlier: 3.775A pdb=" N ASN C 344 " --> pdb=" O ASP C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 372 removed outlier: 3.889A pdb=" N ASP C 365 " --> pdb=" O PRO C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 399 Processing helix chain 'C' and resid 405 through 417 Processing helix chain 'C' and resid 480 through 487 Processing helix chain 'C' and resid 489 through 498 Processing helix chain 'D' and resid 81 through 94 removed outlier: 3.581A pdb=" N LEU D 94 " --> pdb=" O PHE D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 103 removed outlier: 3.618A pdb=" N LEU D 102 " --> pdb=" O ASP D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 124 removed outlier: 3.772A pdb=" N ASP D 116 " --> pdb=" O GLU D 112 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 146 Processing helix chain 'D' and resid 150 through 157 removed outlier: 4.509A pdb=" N LEU D 154 " --> pdb=" O PRO D 150 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG D 157 " --> pdb=" O PRO D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 202 Processing helix chain 'D' and resid 249 through 256 Processing helix chain 'D' and resid 260 through 273 Processing helix chain 'D' and resid 286 through 296 Processing helix chain 'D' and resid 337 through 346 Processing helix chain 'D' and resid 361 through 368 removed outlier: 3.747A pdb=" N ASP D 365 " --> pdb=" O PRO D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 400 Processing helix chain 'D' and resid 405 through 417 Processing helix chain 'D' and resid 480 through 487 Processing helix chain 'D' and resid 489 through 500 Processing helix chain 'E' and resid 81 through 97 Processing helix chain 'E' and resid 98 through 105 removed outlier: 3.562A pdb=" N LEU E 102 " --> pdb=" O ASP E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 126 Processing helix chain 'E' and resid 130 through 146 Processing helix chain 'E' and resid 150 through 157 removed outlier: 4.520A pdb=" N LEU E 154 " --> pdb=" O PRO E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 203 removed outlier: 4.299A pdb=" N VAL E 203 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 256 Processing helix chain 'E' and resid 260 through 272 Processing helix chain 'E' and resid 286 through 296 Processing helix chain 'E' and resid 337 through 346 Processing helix chain 'E' and resid 361 through 372 removed outlier: 4.036A pdb=" N ASP E 365 " --> pdb=" O PRO E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 400 Processing helix chain 'E' and resid 405 through 417 Processing helix chain 'E' and resid 480 through 488 Processing helix chain 'E' and resid 489 through 500 Processing helix chain 'F' and resid 81 through 97 removed outlier: 4.036A pdb=" N LEU F 94 " --> pdb=" O PHE F 90 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ASN F 95 " --> pdb=" O ASN F 91 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR F 96 " --> pdb=" O ALA F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 104 removed outlier: 3.542A pdb=" N ALA F 103 " --> pdb=" O SER F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 115 removed outlier: 3.655A pdb=" N ARG F 115 " --> pdb=" O GLY F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 124 removed outlier: 4.047A pdb=" N GLU F 120 " --> pdb=" O ASP F 116 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL F 122 " --> pdb=" O VAL F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 146 Processing helix chain 'F' and resid 148 through 150 No H-bonds generated for 'chain 'F' and resid 148 through 150' Processing helix chain 'F' and resid 151 through 157 Processing helix chain 'F' and resid 188 through 202 Processing helix chain 'F' and resid 249 through 256 Processing helix chain 'F' and resid 260 through 273 Processing helix chain 'F' and resid 286 through 297 removed outlier: 3.696A pdb=" N LEU F 291 " --> pdb=" O LYS F 287 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE F 297 " --> pdb=" O THR F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 346 Processing helix chain 'F' and resid 347 through 349 No H-bonds generated for 'chain 'F' and resid 347 through 349' Processing helix chain 'F' and resid 361 through 371 removed outlier: 4.061A pdb=" N ASP F 365 " --> pdb=" O PRO F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 398 removed outlier: 3.777A pdb=" N THR F 398 " --> pdb=" O GLU F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 417 Processing helix chain 'F' and resid 480 through 488 Processing helix chain 'F' and resid 489 through 500 Processing sheet with id=AA1, first strand: chain 'A' and resid 178 through 181 removed outlier: 4.056A pdb=" N ASP A 162 " --> pdb=" O GLU A 174 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 320 through 324 removed outlier: 6.653A pdb=" N VAL A 304 " --> pdb=" O VAL A 321 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N LEU A 323 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR A 306 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL A 305 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N GLY A 356 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N CYS A 307 " --> pdb=" O GLY A 356 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N VAL A 358 " --> pdb=" O CYS A 307 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR A 380 " --> pdb=" O VAL A 355 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLU A 357 " --> pdb=" O THR A 380 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N HIS A 382 " --> pdb=" O GLU A 357 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU A 277 " --> pdb=" O GLY A 379 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N LEU A 381 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ILE A 279 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR A 437 " --> pdb=" O ILE A 420 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ALA A 424 " --> pdb=" O ILE A 433 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ILE A 433 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N VAL A 439 " --> pdb=" O GLN A 450 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLN A 450 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY A 441 " --> pdb=" O VAL A 448 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 453 through 460 removed outlier: 7.080A pdb=" N VAL A 467 " --> pdb=" O THR A 458 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 178 through 181 removed outlier: 3.851A pdb=" N ASP B 162 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 320 through 324 removed outlier: 6.528A pdb=" N VAL B 304 " --> pdb=" O VAL B 321 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N LEU B 323 " --> pdb=" O VAL B 304 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N THR B 306 " --> pdb=" O LEU B 323 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL B 305 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ILE B 353 " --> pdb=" O MET B 378 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N THR B 380 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N VAL B 355 " --> pdb=" O THR B 380 " (cutoff:3.500A) removed outlier: 9.841A pdb=" N HIS B 382 " --> pdb=" O VAL B 355 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU B 277 " --> pdb=" O GLY B 379 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N LEU B 381 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ILE B 279 " --> pdb=" O LEU B 381 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE B 420 " --> pdb=" O ILE B 436 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ILE B 436 " --> pdb=" O ILE B 420 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLN B 422 " --> pdb=" O THR B 434 " (cutoff:3.500A) removed outlier: 13.761A pdb=" N ARG B 432 " --> pdb=" O ILE B 457 " (cutoff:3.500A) removed outlier: 11.289A pdb=" N ILE B 457 " --> pdb=" O ARG B 432 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N THR B 434 " --> pdb=" O TYR B 455 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE B 453 " --> pdb=" O ILE B 436 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N GLU B 438 " --> pdb=" O ASP B 451 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ASP B 451 " --> pdb=" O GLU B 438 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL B 440 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N THR B 449 " --> pdb=" O VAL B 440 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU B 442 " --> pdb=" O ILE B 447 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILE B 447 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL B 467 " --> pdb=" O THR B 458 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 178 through 181 removed outlier: 4.081A pdb=" N ASP C 162 " --> pdb=" O GLU C 174 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 320 through 324 removed outlier: 6.574A pdb=" N ILE C 353 " --> pdb=" O MET C 378 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N THR C 380 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N VAL C 355 " --> pdb=" O THR C 380 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N HIS C 382 " --> pdb=" O VAL C 355 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL C 278 " --> pdb=" O ILE C 421 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ALA C 423 " --> pdb=" O VAL C 278 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N SER C 280 " --> pdb=" O ALA C 423 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N ARG C 425 " --> pdb=" O SER C 280 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE C 420 " --> pdb=" O ILE C 436 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ILE C 436 " --> pdb=" O ILE C 420 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLN C 422 " --> pdb=" O THR C 434 " (cutoff:3.500A) removed outlier: 10.699A pdb=" N ILE C 433 " --> pdb=" O GLU C 456 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N GLU C 456 " --> pdb=" O ILE C 433 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N HIS C 435 " --> pdb=" O VAL C 454 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL C 454 " --> pdb=" O HIS C 435 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N THR C 437 " --> pdb=" O LEU C 452 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LEU C 452 " --> pdb=" O THR C 437 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N VAL C 439 " --> pdb=" O GLN C 450 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLN C 450 " --> pdb=" O VAL C 439 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY C 441 " --> pdb=" O VAL C 448 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS C 469 " --> pdb=" O GLU C 456 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 178 through 181 removed outlier: 3.988A pdb=" N ASP D 162 " --> pdb=" O GLU D 174 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 378 through 382 removed outlier: 6.101A pdb=" N ILE D 420 " --> pdb=" O ILE D 436 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ILE D 436 " --> pdb=" O ILE D 420 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLN D 422 " --> pdb=" O THR D 434 " (cutoff:3.500A) removed outlier: 16.624A pdb=" N ARG D 431 " --> pdb=" O THR D 458 " (cutoff:3.500A) removed outlier: 13.632A pdb=" N THR D 458 " --> pdb=" O ARG D 431 " (cutoff:3.500A) removed outlier: 10.558A pdb=" N ILE D 433 " --> pdb=" O GLU D 456 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N GLU D 456 " --> pdb=" O ILE D 433 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N HIS D 435 " --> pdb=" O VAL D 454 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL D 454 " --> pdb=" O HIS D 435 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N THR D 437 " --> pdb=" O LEU D 452 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N LEU D 452 " --> pdb=" O THR D 437 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N VAL D 439 " --> pdb=" O GLN D 450 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN D 450 " --> pdb=" O VAL D 439 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY D 441 " --> pdb=" O VAL D 448 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N VAL D 467 " --> pdb=" O THR D 458 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 320 through 324 removed outlier: 6.751A pdb=" N VAL D 304 " --> pdb=" O VAL D 321 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N LEU D 323 " --> pdb=" O VAL D 304 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N THR D 306 " --> pdb=" O LEU D 323 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 178 through 181 removed outlier: 3.581A pdb=" N ARG E 170 " --> pdb=" O ASN E 166 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP E 162 " --> pdb=" O GLU E 174 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 320 through 324 removed outlier: 6.295A pdb=" N VAL E 305 " --> pdb=" O ILE E 354 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ILE E 353 " --> pdb=" O MET E 378 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N THR E 380 " --> pdb=" O ILE E 353 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N VAL E 355 " --> pdb=" O THR E 380 " (cutoff:3.500A) removed outlier: 9.915A pdb=" N HIS E 382 " --> pdb=" O VAL E 355 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ILE E 279 " --> pdb=" O LEU E 381 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE E 420 " --> pdb=" O ILE E 436 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE E 436 " --> pdb=" O ILE E 420 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLN E 422 " --> pdb=" O THR E 434 " (cutoff:3.500A) removed outlier: 17.379A pdb=" N ARG E 431 " --> pdb=" O THR E 458 " (cutoff:3.500A) removed outlier: 13.924A pdb=" N THR E 458 " --> pdb=" O ARG E 431 " (cutoff:3.500A) removed outlier: 10.422A pdb=" N ILE E 433 " --> pdb=" O GLU E 456 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N GLU E 456 " --> pdb=" O ILE E 433 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N HIS E 435 " --> pdb=" O VAL E 454 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL E 454 " --> pdb=" O HIS E 435 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N THR E 437 " --> pdb=" O LEU E 452 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N LEU E 452 " --> pdb=" O THR E 437 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N VAL E 439 " --> pdb=" O GLN E 450 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN E 450 " --> pdb=" O VAL E 439 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLY E 441 " --> pdb=" O VAL E 448 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL E 467 " --> pdb=" O THR E 458 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 178 through 182 removed outlier: 4.694A pdb=" N VAL F 171 " --> pdb=" O THR F 182 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG F 170 " --> pdb=" O ASN F 166 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASP F 162 " --> pdb=" O GLU F 174 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER F 222 " --> pdb=" O LEU F 218 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 320 through 324 removed outlier: 6.597A pdb=" N VAL F 304 " --> pdb=" O VAL F 321 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N LEU F 323 " --> pdb=" O VAL F 304 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N THR F 306 " --> pdb=" O LEU F 323 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR F 380 " --> pdb=" O VAL F 355 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU F 277 " --> pdb=" O GLY F 379 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LEU F 381 " --> pdb=" O LEU F 277 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE F 279 " --> pdb=" O LEU F 381 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA F 424 " --> pdb=" O ILE F 433 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ILE F 433 " --> pdb=" O ALA F 424 " (cutoff:3.500A) removed outlier: 9.557A pdb=" N ILE F 433 " --> pdb=" O GLU F 456 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N GLU F 456 " --> pdb=" O ILE F 433 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N HIS F 435 " --> pdb=" O VAL F 454 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL F 454 " --> pdb=" O HIS F 435 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N THR F 437 " --> pdb=" O LEU F 452 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N LEU F 452 " --> pdb=" O THR F 437 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N VAL F 439 " --> pdb=" O GLN F 450 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLN F 450 " --> pdb=" O VAL F 439 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY F 441 " --> pdb=" O VAL F 448 " (cutoff:3.500A) 939 hydrogen bonds defined for protein. 2733 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: 5.89 Time building geometry restraints manager: 6.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6550 1.34 - 1.46: 2964 1.46 - 1.58: 9038 1.58 - 1.69: 14 1.69 - 1.81: 166 Bond restraints: 18732 Sorted by residual: bond pdb=" CA PHE F 256 " pdb=" C PHE F 256 " ideal model delta sigma weight residual 1.523 1.492 0.031 1.80e-02 3.09e+03 3.03e+00 bond pdb=" O3A ATP A 602 " pdb=" PA ATP A 602 " ideal model delta sigma weight residual 1.592 1.544 0.048 3.00e-02 1.11e+03 2.60e+00 bond pdb=" CA PHE E 256 " pdb=" C PHE E 256 " ideal model delta sigma weight residual 1.523 1.497 0.026 1.80e-02 3.09e+03 2.08e+00 bond pdb=" C4 ADP F 601 " pdb=" C5 ADP F 601 " ideal model delta sigma weight residual 1.490 1.462 0.028 2.00e-02 2.50e+03 1.95e+00 bond pdb=" C4 ADP B 602 " pdb=" C5 ADP B 602 " ideal model delta sigma weight residual 1.490 1.463 0.027 2.00e-02 2.50e+03 1.87e+00 ... (remaining 18727 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 24591 1.31 - 2.63: 639 2.63 - 3.94: 160 3.94 - 5.25: 38 5.25 - 6.56: 30 Bond angle restraints: 25458 Sorted by residual: angle pdb=" C3' ATP A 602 " pdb=" C4' ATP A 602 " pdb=" C5' ATP A 602 " ideal model delta sigma weight residual 115.19 110.10 5.09 1.76e+00 3.23e-01 8.37e+00 angle pdb=" C ARG C 347 " pdb=" N MET C 348 " pdb=" CA MET C 348 " ideal model delta sigma weight residual 123.17 119.46 3.71 1.49e+00 4.50e-01 6.20e+00 angle pdb=" CA GLU E 411 " pdb=" CB GLU E 411 " pdb=" CG GLU E 411 " ideal model delta sigma weight residual 114.10 118.86 -4.76 2.00e+00 2.50e-01 5.65e+00 angle pdb=" C3' ATP D 602 " pdb=" C4' ATP D 602 " pdb=" C5' ATP D 602 " ideal model delta sigma weight residual 115.19 111.03 4.16 1.76e+00 3.23e-01 5.58e+00 angle pdb=" C1' ATP D 602 " pdb=" C2' ATP D 602 " pdb=" O2' ATP D 602 " ideal model delta sigma weight residual 110.58 104.02 6.56 2.79e+00 1.28e-01 5.52e+00 ... (remaining 25453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 10299 17.71 - 35.42: 941 35.42 - 53.12: 189 53.12 - 70.83: 48 70.83 - 88.54: 27 Dihedral angle restraints: 11504 sinusoidal: 4304 harmonic: 7200 Sorted by residual: dihedral pdb=" C5' ADP C 602 " pdb=" O5' ADP C 602 " pdb=" PA ADP C 602 " pdb=" O2A ADP C 602 " ideal model delta sinusoidal sigma weight residual -60.00 -146.12 86.12 1 2.00e+01 2.50e-03 2.24e+01 dihedral pdb=" CA ALA D 369 " pdb=" C ALA D 369 " pdb=" N MET D 370 " pdb=" CA MET D 370 " ideal model delta harmonic sigma weight residual 180.00 158.55 21.45 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA LEU D 367 " pdb=" C LEU D 367 " pdb=" N GLN D 368 " pdb=" CA GLN D 368 " ideal model delta harmonic sigma weight residual 180.00 158.59 21.41 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 11501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2506 0.059 - 0.117: 469 0.117 - 0.176: 37 0.176 - 0.234: 0 0.234 - 0.292: 6 Chirality restraints: 3018 Sorted by residual: chirality pdb=" C2' ATP D 602 " pdb=" C1' ATP D 602 " pdb=" C3' ATP D 602 " pdb=" O2' ATP D 602 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" C3' ATP A 602 " pdb=" C2' ATP A 602 " pdb=" C4' ATP A 602 " pdb=" O3' ATP A 602 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C3' ATP D 602 " pdb=" C2' ATP D 602 " pdb=" C4' ATP D 602 " pdb=" O3' ATP D 602 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.29 2.00e-01 2.50e+01 2.03e+00 ... (remaining 3015 not shown) Planarity restraints: 3366 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY E 235 " -0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO E 236 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO E 236 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 236 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 235 " 0.026 5.00e-02 4.00e+02 3.96e-02 2.52e+00 pdb=" N PRO B 236 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 228 " 0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO D 229 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO D 229 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 229 " 0.022 5.00e-02 4.00e+02 ... (remaining 3363 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.39: 97 2.39 - 3.02: 12930 3.02 - 3.65: 28141 3.65 - 4.27: 40884 4.27 - 4.90: 69158 Nonbonded interactions: 151210 Sorted by model distance: nonbonded pdb="MG MG A 601 " pdb=" O2B ATP A 602 " model vdw 1.765 2.170 nonbonded pdb="MG MG B 601 " pdb=" O1B ADP B 602 " model vdw 1.792 2.170 nonbonded pdb=" O3B ADP E 601 " pdb="MG MG E 602 " model vdw 1.817 2.170 nonbonded pdb="MG MG D 601 " pdb=" O2B ATP D 602 " model vdw 1.850 2.170 nonbonded pdb=" O3B ADP F 601 " pdb="MG MG F 602 " model vdw 1.857 2.170 ... (remaining 151205 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: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and resid 80 through 501) selection = (chain 'B' and (resid 80 through 274 or (resid 275 and (name N or name CA or nam \ e C or name O or name CB )) or resid 276 through 501)) selection = (chain 'C' and (resid 80 through 274 or (resid 275 and (name N or name CA or nam \ e C or name O or name CB )) or resid 276 through 501)) selection = (chain 'D' and resid 80 through 501) selection = (chain 'E' and (resid 80 through 274 or (resid 275 and (name N or name CA or nam \ e C or name O or name CB )) or resid 276 through 501)) selection = (chain 'F' and (resid 80 through 274 or (resid 275 and (name N or name CA or nam \ e C or name O or name CB )) or resid 276 through 501)) } 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: 0.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.720 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 43.180 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.070 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 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 : 0.004 0.048 18732 Z= 0.215 Angle : 0.593 6.563 25458 Z= 0.306 Chirality : 0.045 0.292 3018 Planarity : 0.004 0.041 3366 Dihedral : 15.008 88.537 6860 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.17 % Allowed : 13.42 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.17), residues: 2520 helix: 1.66 (0.17), residues: 1064 sheet: -0.86 (0.23), residues: 496 loop : -0.75 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 481 HIS 0.003 0.001 HIS D 435 PHE 0.017 0.001 PHE C 364 TYR 0.011 0.001 TYR C 402 ARG 0.003 0.000 ARG D 206 Details of bonding type rmsd hydrogen bonds : bond 0.13277 ( 939) hydrogen bonds : angle 6.06708 ( 2733) covalent geometry : bond 0.00448 (18732) covalent geometry : angle 0.59349 (25458) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 705 time to evaluate : 2.007 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: 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: 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: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.6322 (mtt) cc_final: 0.6003 (mpp) REVERT: A 172 PHE cc_start: 0.8072 (m-80) cc_final: 0.7485 (m-80) REVERT: A 233 LEU cc_start: 0.9285 (mt) cc_final: 0.9063 (mp) REVERT: A 266 VAL cc_start: 0.7653 (t) cc_final: 0.7343 (p) REVERT: A 448 VAL cc_start: 0.7292 (t) cc_final: 0.6601 (t) REVERT: A 479 ARG cc_start: 0.7428 (ttt180) cc_final: 0.7218 (mtp180) REVERT: B 174 GLU cc_start: 0.7549 (tt0) cc_final: 0.7025 (mt-10) REVERT: B 241 ARG cc_start: 0.7154 (mtp180) cc_final: 0.6837 (mtp-110) REVERT: B 283 THR cc_start: 0.8178 (t) cc_final: 0.7445 (m) REVERT: B 294 MET cc_start: 0.7656 (mmm) cc_final: 0.7121 (ttp) REVERT: B 317 GLN cc_start: 0.6671 (mp-120) cc_final: 0.6351 (mm-40) REVERT: B 365 ASP cc_start: 0.7244 (m-30) cc_final: 0.6389 (m-30) REVERT: B 381 LEU cc_start: 0.6004 (tp) cc_final: 0.5465 (tt) REVERT: C 148 TYR cc_start: 0.7423 (m-80) cc_final: 0.6699 (m-80) REVERT: C 240 ILE cc_start: 0.6813 (mm) cc_final: 0.6449 (mt) REVERT: C 275 CYS cc_start: 0.3692 (m) cc_final: 0.3064 (m) REVERT: C 276 ASN cc_start: 0.6350 (m-40) cc_final: 0.6000 (m110) REVERT: C 279 ILE cc_start: 0.6500 (mt) cc_final: 0.6261 (mt) REVERT: C 299 ASP cc_start: 0.8187 (t0) cc_final: 0.7903 (t0) REVERT: C 315 LEU cc_start: 0.7905 (mp) cc_final: 0.7501 (mp) REVERT: C 348 MET cc_start: 0.7150 (ptp) cc_final: 0.6384 (ptt) REVERT: C 364 PHE cc_start: 0.7359 (t80) cc_final: 0.6458 (t80) REVERT: C 407 LYS cc_start: 0.8935 (tptt) cc_final: 0.8577 (mmmt) REVERT: C 408 THR cc_start: 0.9348 (m) cc_final: 0.8863 (p) REVERT: C 452 LEU cc_start: 0.7541 (mt) cc_final: 0.7048 (mp) REVERT: C 487 TYR cc_start: 0.6744 (m-80) cc_final: 0.6500 (m-80) REVERT: D 173 ILE cc_start: 0.9168 (pt) cc_final: 0.8722 (pt) REVERT: D 180 GLN cc_start: 0.8261 (pt0) cc_final: 0.7788 (pm20) REVERT: D 279 ILE cc_start: 0.8006 (mt) cc_final: 0.7765 (mt) REVERT: D 324 GLU cc_start: 0.8138 (tt0) cc_final: 0.7006 (pt0) REVERT: D 367 LEU cc_start: 0.8480 (mm) cc_final: 0.8107 (mt) REVERT: D 390 ILE cc_start: 0.7938 (mt) cc_final: 0.7647 (mt) REVERT: D 397 ILE cc_start: 0.9191 (mt) cc_final: 0.8845 (mm) REVERT: D 404 LEU cc_start: 0.8266 (mp) cc_final: 0.8036 (mp) REVERT: D 409 ILE cc_start: 0.8543 (mm) cc_final: 0.8169 (mt) REVERT: D 421 ILE cc_start: 0.8089 (mt) cc_final: 0.7869 (mt) REVERT: D 446 VAL cc_start: 0.8407 (p) cc_final: 0.7950 (t) REVERT: E 173 ILE cc_start: 0.8027 (pt) cc_final: 0.7387 (pt) REVERT: E 175 VAL cc_start: 0.9010 (t) cc_final: 0.8702 (m) REVERT: E 178 LYS cc_start: 0.8643 (tttt) cc_final: 0.8420 (mmmt) REVERT: E 180 GLN cc_start: 0.8401 (mt0) cc_final: 0.8133 (mp10) REVERT: E 183 ASN cc_start: 0.8916 (m-40) cc_final: 0.8562 (p0) REVERT: E 202 GLN cc_start: 0.8477 (mp10) cc_final: 0.8246 (mp10) REVERT: E 306 THR cc_start: 0.8575 (m) cc_final: 0.8312 (p) REVERT: E 324 GLU cc_start: 0.6190 (tt0) cc_final: 0.5791 (tt0) REVERT: E 336 VAL cc_start: 0.6618 (t) cc_final: 0.6053 (m) REVERT: E 338 MET cc_start: 0.8375 (tpp) cc_final: 0.8160 (tpp) REVERT: E 359 ARG cc_start: 0.8282 (ttm110) cc_final: 0.7913 (ttp80) REVERT: E 410 LYS cc_start: 0.8953 (mttt) cc_final: 0.8425 (mttm) REVERT: E 414 VAL cc_start: 0.8260 (t) cc_final: 0.7883 (t) REVERT: E 492 GLU cc_start: 0.9010 (mm-30) cc_final: 0.8385 (tp30) REVERT: F 175 VAL cc_start: 0.6610 (m) cc_final: 0.5985 (t) REVERT: F 320 VAL cc_start: 0.7301 (t) cc_final: 0.6248 (t) outliers start: 3 outliers final: 0 residues processed: 705 average time/residue: 0.3657 time to fit residues: 362.2745 Evaluate side-chains 471 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 471 time to evaluate : 2.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 80.0000 chunk 191 optimal weight: 20.0000 chunk 105 optimal weight: 5.9990 chunk 65 optimal weight: 8.9990 chunk 128 optimal weight: 40.0000 chunk 102 optimal weight: 8.9990 chunk 197 optimal weight: 5.9990 chunk 76 optimal weight: 20.0000 chunk 120 optimal weight: 0.0970 chunk 147 optimal weight: 5.9990 chunk 228 optimal weight: 8.9990 overall best weight: 5.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 ASN B 317 GLN B 435 HIS C 314 GLN C 344 ASN ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 HIS ** C 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 GLN D 225 ASN ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 344 ASN ** F 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 225 ASN F 292 ASN F 317 GLN ** F 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 435 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.086991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.069055 restraints weight = 63499.228| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 5.06 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 18732 Z= 0.217 Angle : 0.830 11.229 25458 Z= 0.422 Chirality : 0.052 0.321 3018 Planarity : 0.007 0.084 3366 Dihedral : 7.555 92.724 2866 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 5.30 % Allowed : 21.48 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.17), residues: 2520 helix: 1.29 (0.16), residues: 1068 sheet: -0.46 (0.25), residues: 398 loop : -0.65 (0.19), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.004 TRP F 481 HIS 0.011 0.002 HIS C 319 PHE 0.023 0.003 PHE A 364 TYR 0.022 0.003 TYR B 402 ARG 0.013 0.001 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.04098 ( 939) hydrogen bonds : angle 4.89984 ( 2733) covalent geometry : bond 0.00505 (18732) covalent geometry : angle 0.82951 (25458) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 555 time to evaluate : 1.985 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: 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 162 ASP cc_start: 0.4125 (p0) cc_final: 0.3640 (p0) REVERT: A 172 PHE cc_start: 0.8252 (m-80) cc_final: 0.7906 (m-80) REVERT: A 215 ASP cc_start: 0.7366 (p0) cc_final: 0.6779 (p0) REVERT: A 237 THR cc_start: 0.7877 (m) cc_final: 0.7616 (m) REVERT: A 244 LYS cc_start: 0.8883 (tppt) cc_final: 0.7662 (ttpt) REVERT: A 324 GLU cc_start: 0.6817 (pp20) cc_final: 0.6459 (pm20) REVERT: A 343 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7698 (ttpp) REVERT: A 368 GLN cc_start: 0.7136 (mp10) cc_final: 0.6915 (mp10) REVERT: A 388 GLU cc_start: 0.7752 (tt0) cc_final: 0.7108 (tp30) REVERT: A 412 MET cc_start: 0.9182 (tpp) cc_final: 0.8829 (tmm) REVERT: A 482 ASP cc_start: 0.9293 (t0) cc_final: 0.9070 (p0) REVERT: B 174 GLU cc_start: 0.7509 (tt0) cc_final: 0.7041 (tt0) REVERT: B 193 MET cc_start: 0.8061 (tmm) cc_final: 0.7859 (tmm) REVERT: B 225 ASN cc_start: 0.7731 (t0) cc_final: 0.7357 (t0) REVERT: B 450 GLN cc_start: 0.7724 (pt0) cc_final: 0.7453 (pm20) REVERT: B 486 TYR cc_start: 0.7211 (t80) cc_final: 0.6799 (t80) REVERT: C 223 ARG cc_start: 0.7838 (tpp80) cc_final: 0.7609 (tpp80) REVERT: C 270 ILE cc_start: 0.6619 (OUTLIER) cc_final: 0.6414 (tp) REVERT: C 299 ASP cc_start: 0.8217 (t0) cc_final: 0.7312 (t0) REVERT: C 319 HIS cc_start: 0.7984 (t-170) cc_final: 0.7596 (t-90) REVERT: C 355 VAL cc_start: 0.9007 (t) cc_final: 0.8752 (p) REVERT: C 396 MET cc_start: 0.8390 (mtm) cc_final: 0.7093 (mtt) REVERT: C 469 LYS cc_start: 0.8823 (mtmm) cc_final: 0.8463 (mtmm) REVERT: D 164 MET cc_start: 0.8467 (mtm) cc_final: 0.8231 (ttm) REVERT: D 243 PHE cc_start: 0.8624 (t80) cc_final: 0.8417 (t80) REVERT: D 247 LYS cc_start: 0.8873 (mmmt) cc_final: 0.8455 (mmtm) REVERT: D 279 ILE cc_start: 0.8096 (mt) cc_final: 0.7862 (mt) REVERT: D 324 GLU cc_start: 0.8336 (tt0) cc_final: 0.7786 (tm-30) REVERT: D 343 LYS cc_start: 0.8820 (mtmm) cc_final: 0.8455 (mtmm) REVERT: D 345 CYS cc_start: 0.9025 (m) cc_final: 0.8624 (m) REVERT: D 378 MET cc_start: 0.7739 (mtm) cc_final: 0.7477 (mtm) REVERT: D 402 TYR cc_start: 0.6805 (m-80) cc_final: 0.6568 (m-10) REVERT: D 421 ILE cc_start: 0.8184 (mt) cc_final: 0.7883 (mt) REVERT: E 164 MET cc_start: 0.7536 (mtm) cc_final: 0.7316 (mtm) REVERT: E 173 ILE cc_start: 0.8375 (pt) cc_final: 0.8034 (pt) REVERT: E 175 VAL cc_start: 0.9210 (t) cc_final: 0.8813 (m) REVERT: E 180 GLN cc_start: 0.8663 (mt0) cc_final: 0.8420 (mp10) REVERT: E 208 ASP cc_start: 0.8945 (t0) cc_final: 0.8558 (m-30) REVERT: E 246 ASP cc_start: 0.8562 (p0) cc_final: 0.8338 (p0) REVERT: E 251 LYS cc_start: 0.9410 (mmmt) cc_final: 0.9136 (mmmt) REVERT: E 252 ASN cc_start: 0.8970 (m110) cc_final: 0.8461 (m-40) REVERT: E 324 GLU cc_start: 0.6768 (tt0) cc_final: 0.6395 (tt0) REVERT: E 338 MET cc_start: 0.8599 (tpp) cc_final: 0.8161 (tpp) REVERT: E 341 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7888 (mm) REVERT: E 344 ASN cc_start: 0.7876 (t0) cc_final: 0.7357 (t0) REVERT: E 348 MET cc_start: 0.8266 (mtt) cc_final: 0.8035 (mpp) REVERT: E 437 THR cc_start: 0.7476 (OUTLIER) cc_final: 0.7189 (t) REVERT: F 164 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7607 (mtp) REVERT: F 172 PHE cc_start: 0.7824 (m-80) cc_final: 0.7524 (m-10) REVERT: F 194 ASN cc_start: 0.9699 (t0) cc_final: 0.9483 (t0) REVERT: F 202 GLN cc_start: 0.8697 (tm-30) cc_final: 0.8374 (tm-30) REVERT: F 227 ILE cc_start: 0.8099 (mm) cc_final: 0.7829 (mm) REVERT: F 345 CYS cc_start: 0.8011 (m) cc_final: 0.7696 (m) REVERT: F 388 GLU cc_start: 0.8869 (tt0) cc_final: 0.8518 (tt0) REVERT: F 399 MET cc_start: 0.7941 (ptp) cc_final: 0.7475 (ptp) REVERT: F 443 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7387 (mp0) outliers start: 94 outliers final: 39 residues processed: 600 average time/residue: 0.3175 time to fit residues: 278.2883 Evaluate side-chains 488 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 444 time to evaluate : 2.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 LYS Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 251 LYS Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 202 GLN Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 421 ILE Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 348 MET Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 244 LYS Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 380 THR Chi-restraints excluded: chain F residue 398 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 16 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 85 optimal weight: 0.0170 chunk 84 optimal weight: 9.9990 chunk 12 optimal weight: 20.0000 chunk 164 optimal weight: 7.9990 chunk 72 optimal weight: 0.4980 chunk 228 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 151 optimal weight: 20.0000 chunk 130 optimal weight: 7.9990 overall best weight: 2.7022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN A 225 ASN ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 GLN C 316 GLN ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 GLN D 225 ASN D 314 GLN D 368 GLN ** E 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 180 GLN F 189 ASN ** F 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 435 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.087309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.069416 restraints weight = 63320.475| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 4.97 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.5179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18732 Z= 0.159 Angle : 0.729 8.888 25458 Z= 0.360 Chirality : 0.048 0.299 3018 Planarity : 0.005 0.048 3366 Dihedral : 7.290 81.235 2866 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.57 % Allowed : 24.52 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.17), residues: 2520 helix: 1.33 (0.16), residues: 1074 sheet: -0.64 (0.24), residues: 440 loop : -0.62 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 481 HIS 0.006 0.001 HIS B 374 PHE 0.013 0.002 PHE C 364 TYR 0.020 0.002 TYR D 402 ARG 0.008 0.001 ARG B 205 Details of bonding type rmsd hydrogen bonds : bond 0.03496 ( 939) hydrogen bonds : angle 4.46256 ( 2733) covalent geometry : bond 0.00361 (18732) covalent geometry : angle 0.72946 (25458) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 488 time to evaluate : 2.273 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 PHE cc_start: 0.8394 (m-80) cc_final: 0.8090 (m-10) REVERT: A 189 ASN cc_start: 0.7999 (p0) cc_final: 0.7537 (t0) REVERT: A 244 LYS cc_start: 0.8878 (tppt) cc_final: 0.8277 (tptp) REVERT: A 246 ASP cc_start: 0.8730 (m-30) cc_final: 0.8257 (m-30) REVERT: A 250 MET cc_start: 0.6718 (pmm) cc_final: 0.5761 (mmm) REVERT: A 324 GLU cc_start: 0.6926 (pp20) cc_final: 0.6556 (pm20) REVERT: A 370 MET cc_start: 0.7085 (mmp) cc_final: 0.6827 (mmt) REVERT: A 381 LEU cc_start: 0.7960 (mt) cc_final: 0.7751 (mp) REVERT: A 388 GLU cc_start: 0.8067 (tt0) cc_final: 0.7211 (tp30) REVERT: B 174 GLU cc_start: 0.7583 (tt0) cc_final: 0.7317 (tt0) REVERT: B 193 MET cc_start: 0.8280 (tmm) cc_final: 0.7946 (tpt) REVERT: B 250 MET cc_start: 0.7090 (tpt) cc_final: 0.6574 (tmm) REVERT: B 348 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7996 (ttm) REVERT: B 410 LYS cc_start: 0.8497 (mmmt) cc_final: 0.8143 (mmtp) REVERT: B 450 GLN cc_start: 0.7623 (pt0) cc_final: 0.7318 (pm20) REVERT: C 195 ILE cc_start: 0.8215 (mm) cc_final: 0.7971 (mm) REVERT: C 299 ASP cc_start: 0.8481 (t0) cc_final: 0.8091 (t0) REVERT: C 308 GLU cc_start: 0.7686 (pm20) cc_final: 0.7190 (pt0) REVERT: C 316 GLN cc_start: 0.8895 (mm110) cc_final: 0.8670 (pm20) REVERT: C 319 HIS cc_start: 0.8032 (t-170) cc_final: 0.7621 (t-90) REVERT: C 351 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7936 (mp0) REVERT: C 355 VAL cc_start: 0.9334 (t) cc_final: 0.9065 (p) REVERT: C 396 MET cc_start: 0.7782 (mtm) cc_final: 0.7219 (mtt) REVERT: C 411 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8639 (mp0) REVERT: C 450 GLN cc_start: 0.7209 (tm130) cc_final: 0.6910 (tm-30) REVERT: D 164 MET cc_start: 0.8607 (mtm) cc_final: 0.8291 (ttm) REVERT: D 205 ARG cc_start: 0.9161 (mtp-110) cc_final: 0.8877 (mtp-110) REVERT: D 243 PHE cc_start: 0.8690 (t80) cc_final: 0.8489 (t80) REVERT: D 247 LYS cc_start: 0.9020 (mmmt) cc_final: 0.8687 (mmtm) REVERT: D 277 LEU cc_start: 0.8650 (tp) cc_final: 0.8405 (tt) REVERT: D 324 GLU cc_start: 0.8259 (tt0) cc_final: 0.7732 (tm-30) REVERT: D 341 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.7910 (mp) REVERT: D 345 CYS cc_start: 0.8979 (m) cc_final: 0.8699 (m) REVERT: D 378 MET cc_start: 0.8082 (mtm) cc_final: 0.7595 (mtm) REVERT: D 393 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8842 (mp) REVERT: D 402 TYR cc_start: 0.6978 (m-80) cc_final: 0.6669 (m-10) REVERT: E 173 ILE cc_start: 0.8429 (pt) cc_final: 0.8015 (pt) REVERT: E 175 VAL cc_start: 0.9240 (t) cc_final: 0.8865 (m) REVERT: E 178 LYS cc_start: 0.8886 (mmmt) cc_final: 0.8203 (mmmt) REVERT: E 180 GLN cc_start: 0.8684 (mt0) cc_final: 0.8476 (mp10) REVERT: E 208 ASP cc_start: 0.8903 (t0) cc_final: 0.8516 (m-30) REVERT: E 215 ASP cc_start: 0.7933 (p0) cc_final: 0.7696 (p0) REVERT: E 256 PHE cc_start: 0.8342 (m-10) cc_final: 0.7972 (m-10) REVERT: E 324 GLU cc_start: 0.6782 (tt0) cc_final: 0.6465 (tt0) REVERT: E 341 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8122 (mm) REVERT: E 344 ASN cc_start: 0.8041 (t0) cc_final: 0.7812 (t0) REVERT: E 348 MET cc_start: 0.8279 (mtt) cc_final: 0.7959 (mtm) REVERT: E 396 MET cc_start: 0.9148 (ttp) cc_final: 0.8733 (ttp) REVERT: E 407 LYS cc_start: 0.9017 (ptmm) cc_final: 0.8549 (ptmm) REVERT: E 410 LYS cc_start: 0.9106 (mttt) cc_final: 0.8692 (mttm) REVERT: E 492 GLU cc_start: 0.9152 (mm-30) cc_final: 0.8801 (tp30) REVERT: F 172 PHE cc_start: 0.8260 (m-80) cc_final: 0.7893 (m-10) REVERT: F 202 GLN cc_start: 0.8889 (tm-30) cc_final: 0.8559 (tm-30) REVERT: F 345 CYS cc_start: 0.8218 (m) cc_final: 0.7857 (m) REVERT: F 368 GLN cc_start: 0.8827 (tm-30) cc_final: 0.8591 (tp40) REVERT: F 399 MET cc_start: 0.8307 (ptp) cc_final: 0.8045 (ptp) REVERT: F 491 ARG cc_start: 0.9264 (ptp90) cc_final: 0.8992 (ptp90) outliers start: 81 outliers final: 42 residues processed: 528 average time/residue: 0.3050 time to fit residues: 242.1832 Evaluate side-chains 479 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 432 time to evaluate : 1.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 245 LYS Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 421 ILE Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 348 MET Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 368 GLN Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 463 HIS Chi-restraints excluded: chain D residue 469 LYS Chi-restraints excluded: chain D residue 472 SER Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 160 ILE Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 244 LYS Chi-restraints excluded: chain F residue 380 THR Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain F residue 435 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-dev-5687/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-dev-5687/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-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-dev-5687/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-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-dev-5687/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-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.0744 > 50: distance: 21 - 25: 5.014 distance: 25 - 26: 7.979 distance: 26 - 27: 5.826 distance: 26 - 29: 10.988 distance: 27 - 28: 5.657 distance: 27 - 33: 11.707 distance: 29 - 30: 7.608 distance: 29 - 31: 4.086 distance: 30 - 32: 16.020 distance: 34 - 37: 6.976 distance: 35 - 36: 5.431 distance: 35 - 39: 5.855 distance: 36 - 59: 11.814 distance: 37 - 38: 11.526 distance: 39 - 40: 6.435 distance: 39 - 45: 14.337 distance: 40 - 41: 12.976 distance: 40 - 43: 13.737 distance: 41 - 42: 16.540 distance: 41 - 46: 15.198 distance: 42 - 64: 18.040 distance: 43 - 44: 11.598 distance: 44 - 45: 14.150 distance: 46 - 47: 31.106 distance: 47 - 48: 18.579 distance: 47 - 50: 12.749 distance: 48 - 49: 8.453 distance: 48 - 55: 10.964 distance: 49 - 75: 17.428 distance: 50 - 51: 24.957 distance: 51 - 52: 38.886 distance: 52 - 53: 30.111 distance: 52 - 54: 20.278 distance: 55 - 56: 4.490 distance: 56 - 57: 8.334 distance: 57 - 58: 7.670 distance: 58 - 82: 3.462 distance: 59 - 60: 7.914 distance: 60 - 63: 4.296 distance: 61 - 62: 7.907 distance: 61 - 64: 9.907 distance: 62 - 90: 9.277 distance: 64 - 65: 12.640 distance: 65 - 66: 5.433 distance: 65 - 68: 9.213 distance: 66 - 67: 4.687 distance: 66 - 75: 6.003 distance: 67 - 94: 4.964 distance: 68 - 69: 13.035 distance: 69 - 70: 9.728 distance: 70 - 71: 14.517 distance: 71 - 72: 6.082 distance: 72 - 73: 9.476 distance: 72 - 74: 10.253 distance: 76 - 77: 5.440 distance: 76 - 79: 6.449 distance: 77 - 78: 8.428 distance: 77 - 82: 7.006 distance: 78 - 101: 4.404 distance: 79 - 80: 5.110 distance: 79 - 81: 9.950 distance: 83 - 86: 5.881 distance: 84 - 90: 5.154 distance: 85 - 109: 3.882 distance: 86 - 87: 4.548 distance: 87 - 88: 12.795 distance: 87 - 89: 10.346 distance: 90 - 91: 3.518 distance: 91 - 92: 4.194 distance: 92 - 93: 5.556 distance: 92 - 94: 4.565 distance: 93 - 113: 9.584