Starting phenix.real_space_refine on Mon Jun 16 12:26:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e29_47446/06_2025/9e29_47446.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e29_47446/06_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_47446/06_2025/9e29_47446.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e29_47446/06_2025/9e29_47446.map" model { file = "/net/cci-nas-00/data/ceres_data/9e29_47446/06_2025/9e29_47446.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e29_47446/06_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-5710/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: 12.88, per 1000 atoms: 0.70 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: 5.47 Conformation dependent library (CDL) restraints added in 2.7 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: 2.63 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: 6.14 Time building geometry restraints manager: 6.33 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: 0.05 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: 0.120 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: 0.850 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 46.820 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.080 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:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.490 ------------------------------------------------------------------------------- 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 : 2.141 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: 0.6004 (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: 0.7219 (mtp180) REVERT: B 174 GLU cc_start: 0.7549 (tt0) cc_final: 0.7024 (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: 0.6350 (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: 0.7502 (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: 0.7870 (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: 0.3729 time to fit residues: 368.5920 Evaluate side-chains 472 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 472 time to evaluate : 2.004 ------------------------------------------------------------------------------- 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** B 180 GLN 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 = 0.3712 r_free = 0.3712 target = 0.086917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.068991 restraints weight = 63589.979| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 5.05 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 18732 Z= 0.212 Angle : 0.839 11.024 25458 Z= 0.426 Chirality : 0.052 0.335 3018 Planarity : 0.007 0.081 3366 Dihedral : 7.520 92.728 2866 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 5.58 % Allowed : 21.59 % Favored : 72.83 % 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: 0.24 (0.17), residues: 2520 helix: 1.25 (0.16), residues: 1068 sheet: -0.42 (0.25), residues: 394 loop : -0.67 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP F 481 HIS 0.012 0.002 HIS C 319 PHE 0.023 0.003 PHE B 364 TYR 0.023 0.003 TYR B 402 ARG 0.014 0.001 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.04104 ( 939) hydrogen bonds : angle 4.91739 ( 2733) covalent geometry : bond 0.00473 (18732) covalent geometry : angle 0.83886 (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 656 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 557 time to evaluate : 2.063 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: A 162 ASP cc_start: 0.4199 (p0) cc_final: 0.3213 (p0) REVERT: A 172 PHE cc_start: 0.8241 (m-80) cc_final: 0.7876 (m-80) REVERT: A 206 ARG cc_start: 0.7267 (OUTLIER) cc_final: 0.6519 (mmp80) REVERT: A 215 ASP cc_start: 0.7460 (p0) cc_final: 0.6899 (p0) REVERT: A 237 THR cc_start: 0.7886 (m) cc_final: 0.7625 (m) REVERT: A 248 LEU cc_start: 0.6442 (OUTLIER) cc_final: 0.6218 (mt) REVERT: A 324 GLU cc_start: 0.6695 (OUTLIER) cc_final: 0.6109 (pm20) REVERT: A 367 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8312 (mm) REVERT: A 388 GLU cc_start: 0.7742 (tt0) cc_final: 0.7087 (tp30) REVERT: A 412 MET cc_start: 0.9182 (tpp) cc_final: 0.8820 (tmm) REVERT: A 482 ASP cc_start: 0.9305 (t0) cc_final: 0.9098 (p0) REVERT: B 174 GLU cc_start: 0.7518 (tt0) cc_final: 0.7116 (tt0) REVERT: B 180 GLN cc_start: 0.8166 (mt0) cc_final: 0.7937 (mp10) REVERT: B 193 MET cc_start: 0.8065 (tmm) cc_final: 0.7701 (tpt) REVERT: B 225 ASN cc_start: 0.7770 (t0) cc_final: 0.7444 (t0) REVERT: B 450 GLN cc_start: 0.7728 (pt0) cc_final: 0.7460 (pm20) REVERT: B 486 TYR cc_start: 0.7204 (t80) cc_final: 0.6799 (t80) REVERT: C 223 ARG cc_start: 0.7872 (tpp80) cc_final: 0.7636 (tpp80) REVERT: C 270 ILE cc_start: 0.6726 (OUTLIER) cc_final: 0.6505 (tp) REVERT: C 299 ASP cc_start: 0.8225 (t0) cc_final: 0.7303 (t0) REVERT: C 319 HIS cc_start: 0.8016 (t-170) cc_final: 0.7567 (t-90) REVERT: C 355 VAL cc_start: 0.9043 (t) cc_final: 0.8784 (p) REVERT: C 396 MET cc_start: 0.8432 (mtm) cc_final: 0.7171 (mtt) REVERT: C 469 LYS cc_start: 0.8851 (mtmm) cc_final: 0.8520 (mtmm) REVERT: D 164 MET cc_start: 0.8460 (mtm) cc_final: 0.8219 (ttm) REVERT: D 243 PHE cc_start: 0.8629 (t80) cc_final: 0.8428 (t80) REVERT: D 247 LYS cc_start: 0.8885 (mmmt) cc_final: 0.8475 (mmtm) REVERT: D 279 ILE cc_start: 0.8073 (mt) cc_final: 0.7814 (mt) REVERT: D 324 GLU cc_start: 0.8350 (tt0) cc_final: 0.7260 (pt0) REVERT: D 343 LYS cc_start: 0.8819 (mtmm) cc_final: 0.8363 (mtmm) REVERT: D 345 CYS cc_start: 0.9031 (m) cc_final: 0.8633 (m) REVERT: D 378 MET cc_start: 0.7771 (mtm) cc_final: 0.7505 (mtm) REVERT: D 421 ILE cc_start: 0.8212 (mt) cc_final: 0.7915 (mt) REVERT: E 164 MET cc_start: 0.7552 (mtm) cc_final: 0.7329 (mtm) REVERT: E 173 ILE cc_start: 0.8420 (pt) cc_final: 0.8077 (pt) REVERT: E 175 VAL cc_start: 0.9220 (t) cc_final: 0.8830 (m) REVERT: E 180 GLN cc_start: 0.8675 (mt0) cc_final: 0.8434 (mp10) REVERT: E 208 ASP cc_start: 0.8949 (t0) cc_final: 0.8561 (m-30) REVERT: E 251 LYS cc_start: 0.9410 (mmmt) cc_final: 0.9138 (mmmt) REVERT: E 252 ASN cc_start: 0.8977 (m110) cc_final: 0.8464 (m-40) REVERT: E 324 GLU cc_start: 0.6812 (tt0) cc_final: 0.6433 (tt0) REVERT: E 338 MET cc_start: 0.8608 (tpp) cc_final: 0.8173 (tpp) REVERT: E 341 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7921 (mm) REVERT: E 344 ASN cc_start: 0.7909 (t0) cc_final: 0.7530 (t0) REVERT: E 348 MET cc_start: 0.8258 (mtt) cc_final: 0.7971 (mtm) REVERT: E 437 THR cc_start: 0.7489 (OUTLIER) cc_final: 0.7203 (t) REVERT: E 452 LEU cc_start: 0.9217 (tp) cc_final: 0.9014 (mp) REVERT: F 164 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7592 (mtp) REVERT: F 172 PHE cc_start: 0.7818 (m-80) cc_final: 0.7523 (m-10) REVERT: F 194 ASN cc_start: 0.9701 (t0) cc_final: 0.9487 (t0) REVERT: F 202 GLN cc_start: 0.8742 (tm-30) cc_final: 0.8433 (tm-30) REVERT: F 227 ILE cc_start: 0.8097 (mm) cc_final: 0.7828 (mm) REVERT: F 345 CYS cc_start: 0.7971 (m) cc_final: 0.7669 (m) REVERT: F 349 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7577 (ptm160) REVERT: F 399 MET cc_start: 0.7924 (ptp) cc_final: 0.7436 (ptp) REVERT: F 443 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7417 (mp0) outliers start: 99 outliers final: 41 residues processed: 606 average time/residue: 0.3340 time to fit residues: 295.6036 Evaluate side-chains 489 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 439 time to evaluate : 2.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 245 LYS Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 182 THR 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 B residue 475 ILE 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 D residue 469 LYS Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 275 CYS 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 248 LEU Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 349 ARG 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: 20.0000 chunk 11 optimal weight: 6.9990 chunk 85 optimal weight: 0.0970 chunk 84 optimal weight: 10.0000 chunk 12 optimal weight: 30.0000 chunk 164 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 228 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 151 optimal weight: 20.0000 chunk 130 optimal weight: 8.9990 overall best weight: 4.0186 ------------------------------------------------------------------------------- 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** A 292 ASN B 180 GLN B 368 GLN B 450 GLN C 316 GLN ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.085912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.067941 restraints weight = 63576.684| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 4.99 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.5376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 18732 Z= 0.177 Angle : 0.735 8.970 25458 Z= 0.365 Chirality : 0.049 0.315 3018 Planarity : 0.006 0.058 3366 Dihedral : 7.228 81.099 2866 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.96 % Allowed : 24.52 % Favored : 70.52 % 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: 0.18 (0.17), residues: 2520 helix: 1.29 (0.16), residues: 1076 sheet: -0.76 (0.23), residues: 448 loop : -0.67 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 481 HIS 0.010 0.001 HIS C 463 PHE 0.014 0.002 PHE C 364 TYR 0.031 0.003 TYR D 402 ARG 0.009 0.001 ARG C 491 Details of bonding type rmsd hydrogen bonds : bond 0.03518 ( 939) hydrogen bonds : angle 4.55270 ( 2733) covalent geometry : bond 0.00412 (18732) covalent geometry : angle 0.73527 (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 574 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 486 time to evaluate : 2.405 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: A 172 PHE cc_start: 0.8451 (m-80) cc_final: 0.8137 (m-80) REVERT: A 189 ASN cc_start: 0.8027 (p0) cc_final: 0.7518 (t0) REVERT: A 324 GLU cc_start: 0.7060 (pp20) cc_final: 0.6497 (pm20) REVERT: A 388 GLU cc_start: 0.8275 (tt0) cc_final: 0.7377 (tp30) REVERT: A 396 MET cc_start: 0.7478 (ptm) cc_final: 0.7263 (ptm) REVERT: A 410 LYS cc_start: 0.8614 (ptmt) cc_final: 0.8405 (ptmm) REVERT: B 174 GLU cc_start: 0.7727 (tt0) cc_final: 0.7476 (tt0) REVERT: B 180 GLN cc_start: 0.8571 (mt0) cc_final: 0.8251 (mp10) REVERT: B 193 MET cc_start: 0.8171 (tmm) cc_final: 0.7771 (tpt) REVERT: B 233 LEU cc_start: 0.8683 (mt) cc_final: 0.7840 (mt) REVERT: B 270 ILE cc_start: 0.7853 (mm) cc_final: 0.7614 (mm) REVERT: B 357 GLU cc_start: 0.7844 (pm20) cc_final: 0.7132 (pm20) REVERT: B 450 GLN cc_start: 0.7695 (pt0) cc_final: 0.7377 (pm20) REVERT: C 195 ILE cc_start: 0.8242 (mm) cc_final: 0.8022 (mm) REVERT: C 239 THR cc_start: 0.7927 (p) cc_final: 0.7649 (p) REVERT: C 299 ASP cc_start: 0.8578 (t0) cc_final: 0.8200 (t0) REVERT: C 308 GLU cc_start: 0.7724 (pm20) cc_final: 0.7294 (pt0) REVERT: C 316 GLN cc_start: 0.8901 (mm110) cc_final: 0.8700 (pm20) REVERT: C 319 HIS cc_start: 0.8161 (t-170) cc_final: 0.7705 (t-90) REVERT: C 355 VAL cc_start: 0.9378 (t) cc_final: 0.9122 (p) REVERT: C 396 MET cc_start: 0.7898 (mtm) cc_final: 0.7313 (mtt) REVERT: C 407 LYS cc_start: 0.9038 (mmmt) cc_final: 0.7971 (tppt) REVERT: C 411 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8617 (mp0) REVERT: C 445 ASP cc_start: 0.7719 (m-30) cc_final: 0.7471 (m-30) REVERT: D 164 MET cc_start: 0.8648 (mtm) cc_final: 0.8157 (ttm) REVERT: D 205 ARG cc_start: 0.9164 (mtp-110) cc_final: 0.8874 (mtp-110) REVERT: D 243 PHE cc_start: 0.8721 (t80) cc_final: 0.8519 (t80) REVERT: D 247 LYS cc_start: 0.9098 (mmmt) cc_final: 0.8750 (mmtm) REVERT: D 251 LYS cc_start: 0.9389 (ptmm) cc_final: 0.9146 (tmmt) REVERT: D 324 GLU cc_start: 0.8259 (tt0) cc_final: 0.7714 (tm-30) REVERT: D 341 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.7786 (mp) REVERT: D 343 LYS cc_start: 0.8870 (mtmm) cc_final: 0.8538 (mtmm) REVERT: D 345 CYS cc_start: 0.9057 (m) cc_final: 0.8737 (m) REVERT: D 378 MET cc_start: 0.8135 (mtm) cc_final: 0.7795 (mtp) REVERT: D 393 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8825 (mp) REVERT: D 397 ILE cc_start: 0.9465 (mt) cc_final: 0.9225 (mm) REVERT: D 407 LYS cc_start: 0.8872 (mmmt) cc_final: 0.8572 (mmmt) REVERT: D 411 GLU cc_start: 0.9075 (mt-10) cc_final: 0.8777 (mt-10) REVERT: D 421 ILE cc_start: 0.8483 (mt) cc_final: 0.8250 (mt) REVERT: E 173 ILE cc_start: 0.8491 (pt) cc_final: 0.8085 (pt) REVERT: E 175 VAL cc_start: 0.9284 (t) cc_final: 0.8910 (m) REVERT: E 178 LYS cc_start: 0.8928 (mmmt) cc_final: 0.8339 (mmmt) REVERT: E 180 GLN cc_start: 0.8735 (mt0) cc_final: 0.8521 (mp10) REVERT: E 208 ASP cc_start: 0.8941 (t0) cc_final: 0.8521 (m-30) REVERT: E 256 PHE cc_start: 0.8441 (m-10) cc_final: 0.8053 (m-10) REVERT: E 324 GLU cc_start: 0.6858 (tt0) cc_final: 0.6494 (tt0) REVERT: E 338 MET cc_start: 0.8800 (tpp) cc_final: 0.8420 (tpp) REVERT: E 341 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8144 (mm) REVERT: E 348 MET cc_start: 0.8421 (mtt) cc_final: 0.8005 (mtp) REVERT: E 399 MET cc_start: 0.8610 (tmm) cc_final: 0.8397 (ptt) REVERT: E 410 LYS cc_start: 0.9140 (mttt) cc_final: 0.8729 (mttm) REVERT: E 492 GLU cc_start: 0.9164 (mm-30) cc_final: 0.8801 (tp30) REVERT: F 172 PHE cc_start: 0.8403 (m-80) cc_final: 0.8009 (m-10) REVERT: F 202 GLN cc_start: 0.8916 (tm-30) cc_final: 0.8602 (tm-30) REVERT: F 245 LYS cc_start: 0.9527 (mmmm) cc_final: 0.9033 (mmtt) REVERT: F 343 LYS cc_start: 0.8684 (tptm) cc_final: 0.8328 (ttpt) REVERT: F 345 CYS cc_start: 0.8307 (m) cc_final: 0.7923 (m) REVERT: F 365 ASP cc_start: 0.8667 (t70) cc_final: 0.8359 (t0) REVERT: F 368 GLN cc_start: 0.8807 (tm-30) cc_final: 0.8558 (tp-100) REVERT: F 399 MET cc_start: 0.8300 (ptp) cc_final: 0.8038 (ptp) REVERT: F 491 ARG cc_start: 0.9305 (ptp90) cc_final: 0.9022 (ptp90) outliers start: 88 outliers final: 41 residues processed: 528 average time/residue: 0.3057 time to fit residues: 242.6633 Evaluate side-chains 470 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 425 time to evaluate : 2.030 ------------------------------------------------------------------------------- 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 A residue 367 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 367 LEU 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 186 PHE 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 411 GLU Chi-restraints excluded: chain C residue 421 ILE 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 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 199 ILE Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 244 LYS Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 367 LEU 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 ************** Weight determination summary: number of chunks: 252 random chunks: chunk 161 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 188 optimal weight: 30.0000 chunk 5 optimal weight: 10.0000 chunk 217 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 137 optimal weight: 8.9990 chunk 3 optimal weight: 50.0000 chunk 19 optimal weight: 5.9990 chunk 180 optimal weight: 7.9990 chunk 88 optimal weight: 0.2980 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 ASN A 384 ASN B 292 ASN ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 382 HIS ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 435 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.085975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.067793 restraints weight = 63697.119| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 5.04 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.6223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 18732 Z= 0.161 Angle : 0.717 11.536 25458 Z= 0.354 Chirality : 0.048 0.311 3018 Planarity : 0.005 0.060 3366 Dihedral : 7.119 78.051 2866 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 5.07 % Allowed : 25.14 % Favored : 69.79 % 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: 0.19 (0.17), residues: 2520 helix: 1.30 (0.16), residues: 1078 sheet: -0.77 (0.22), residues: 490 loop : -0.62 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 481 HIS 0.017 0.001 HIS F 435 PHE 0.021 0.002 PHE F 243 TYR 0.037 0.002 TYR D 402 ARG 0.027 0.001 ARG E 491 Details of bonding type rmsd hydrogen bonds : bond 0.03360 ( 939) hydrogen bonds : angle 4.53227 ( 2733) covalent geometry : bond 0.00377 (18732) covalent geometry : angle 0.71734 (25458) *********************** REFINEMENT MACRO_CYCLE 4 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 542 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 452 time to evaluate : 2.187 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: A 172 PHE cc_start: 0.8640 (m-80) cc_final: 0.8413 (m-10) REVERT: A 206 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.7215 (mmm160) REVERT: A 250 MET cc_start: 0.7128 (pmm) cc_final: 0.6260 (mmm) REVERT: A 324 GLU cc_start: 0.7273 (pp20) cc_final: 0.6852 (pm20) REVERT: A 370 MET cc_start: 0.7704 (mmp) cc_final: 0.7504 (mmt) REVERT: A 410 LYS cc_start: 0.8628 (ptmt) cc_final: 0.8366 (ptmm) REVERT: B 174 GLU cc_start: 0.7760 (tt0) cc_final: 0.7257 (tt0) REVERT: B 180 GLN cc_start: 0.8634 (mt0) cc_final: 0.8315 (mp10) REVERT: B 193 MET cc_start: 0.8432 (tmm) cc_final: 0.8194 (tpt) REVERT: B 270 ILE cc_start: 0.8215 (mm) cc_final: 0.7946 (mm) REVERT: B 396 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8385 (mtm) REVERT: B 410 LYS cc_start: 0.8495 (mmmt) cc_final: 0.8182 (mmtp) REVERT: B 412 MET cc_start: 0.9191 (tmm) cc_final: 0.8926 (tmm) REVERT: C 239 THR cc_start: 0.8308 (p) cc_final: 0.7950 (p) REVERT: C 243 PHE cc_start: 0.7851 (t80) cc_final: 0.7615 (t80) REVERT: C 299 ASP cc_start: 0.8681 (t0) cc_final: 0.8240 (t0) REVERT: C 355 VAL cc_start: 0.9478 (t) cc_final: 0.9203 (p) REVERT: C 396 MET cc_start: 0.8210 (mtm) cc_final: 0.7183 (mtm) REVERT: C 407 LYS cc_start: 0.8951 (mmmt) cc_final: 0.7941 (tppt) REVERT: C 411 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8608 (mp0) REVERT: D 164 MET cc_start: 0.8490 (mtm) cc_final: 0.8134 (ttm) REVERT: D 205 ARG cc_start: 0.9269 (mtp-110) cc_final: 0.8975 (mtp-110) REVERT: D 247 LYS cc_start: 0.9225 (mmmt) cc_final: 0.8929 (mmtm) REVERT: D 324 GLU cc_start: 0.8313 (tt0) cc_final: 0.7781 (tm-30) REVERT: D 341 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.7903 (mp) REVERT: D 345 CYS cc_start: 0.9159 (m) cc_final: 0.8743 (m) REVERT: D 396 MET cc_start: 0.9238 (mtt) cc_final: 0.8807 (mtt) REVERT: D 407 LYS cc_start: 0.8970 (mmmt) cc_final: 0.8697 (mmmt) REVERT: D 411 GLU cc_start: 0.9110 (mt-10) cc_final: 0.8752 (mt-10) REVERT: E 164 MET cc_start: 0.8261 (mtm) cc_final: 0.7606 (mtm) REVERT: E 173 ILE cc_start: 0.8636 (pt) cc_final: 0.8286 (pt) REVERT: E 175 VAL cc_start: 0.9268 (t) cc_final: 0.8837 (m) REVERT: E 178 LYS cc_start: 0.8918 (mmmt) cc_final: 0.8428 (mmmt) REVERT: E 180 GLN cc_start: 0.8779 (mt0) cc_final: 0.8571 (mp10) REVERT: E 208 ASP cc_start: 0.8972 (t0) cc_final: 0.8526 (m-30) REVERT: E 243 PHE cc_start: 0.8305 (t80) cc_final: 0.8072 (t80) REVERT: E 324 GLU cc_start: 0.7107 (tt0) cc_final: 0.6675 (tt0) REVERT: E 338 MET cc_start: 0.8770 (tpp) cc_final: 0.8441 (tpp) REVERT: E 341 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8190 (mm) REVERT: E 399 MET cc_start: 0.8604 (tmm) cc_final: 0.8388 (tmm) REVERT: E 407 LYS cc_start: 0.9065 (ptmm) cc_final: 0.8629 (ptmm) REVERT: E 410 LYS cc_start: 0.9233 (mttt) cc_final: 0.8766 (mttm) REVERT: E 492 GLU cc_start: 0.9242 (mm-30) cc_final: 0.8772 (tp30) REVERT: F 148 TYR cc_start: 0.8332 (m-80) cc_final: 0.7840 (m-80) REVERT: F 164 MET cc_start: 0.8316 (mtp) cc_final: 0.7495 (mtp) REVERT: F 172 PHE cc_start: 0.8592 (m-80) cc_final: 0.8285 (m-10) REVERT: F 190 LEU cc_start: 0.9658 (mm) cc_final: 0.9409 (pp) REVERT: F 202 GLN cc_start: 0.9051 (tm-30) cc_final: 0.8707 (tm-30) REVERT: F 220 ASP cc_start: 0.8861 (m-30) cc_final: 0.8609 (p0) REVERT: F 245 LYS cc_start: 0.9620 (mmmm) cc_final: 0.9194 (mmtt) REVERT: F 343 LYS cc_start: 0.8831 (tptm) cc_final: 0.8523 (ttpt) REVERT: F 365 ASP cc_start: 0.8817 (t70) cc_final: 0.8574 (t0) REVERT: F 378 MET cc_start: 0.8713 (mtm) cc_final: 0.8093 (mtm) REVERT: F 399 MET cc_start: 0.8596 (ptp) cc_final: 0.8033 (ptp) REVERT: F 443 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.6955 (mp0) REVERT: F 451 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.6189 (t0) REVERT: F 491 ARG cc_start: 0.9309 (ptp90) cc_final: 0.9038 (ptp90) outliers start: 90 outliers final: 51 residues processed: 499 average time/residue: 0.2951 time to fit residues: 221.4018 Evaluate side-chains 467 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 409 time to evaluate : 2.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 245 LYS Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 323 LEU 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 448 VAL Chi-restraints excluded: chain D residue 306 THR 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 463 HIS Chi-restraints excluded: chain D residue 469 LYS Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 307 CYS Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 368 GLN Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 180 GLN Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 213 ILE 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 354 ILE Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 443 GLU Chi-restraints excluded: chain F residue 448 VAL Chi-restraints excluded: chain F residue 451 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 143 optimal weight: 8.9990 chunk 27 optimal weight: 0.5980 chunk 94 optimal weight: 20.0000 chunk 33 optimal weight: 7.9990 chunk 147 optimal weight: 1.9990 chunk 237 optimal weight: 0.4980 chunk 167 optimal weight: 7.9990 chunk 108 optimal weight: 10.0000 chunk 73 optimal weight: 20.0000 chunk 63 optimal weight: 9.9990 chunk 239 optimal weight: 6.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 GLN ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 344 ASN ** F 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 374 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.085287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.067282 restraints weight = 64251.352| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 4.96 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.6985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 18732 Z= 0.154 Angle : 0.710 10.422 25458 Z= 0.350 Chirality : 0.047 0.311 3018 Planarity : 0.005 0.044 3366 Dihedral : 6.864 71.177 2866 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 5.30 % Allowed : 26.27 % Favored : 68.43 % 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: 0.18 (0.17), residues: 2520 helix: 1.30 (0.16), residues: 1090 sheet: -0.63 (0.23), residues: 458 loop : -0.77 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 481 HIS 0.010 0.001 HIS F 382 PHE 0.022 0.002 PHE F 243 TYR 0.029 0.002 TYR D 402 ARG 0.010 0.001 ARG F 425 Details of bonding type rmsd hydrogen bonds : bond 0.03209 ( 939) hydrogen bonds : angle 4.42737 ( 2733) covalent geometry : bond 0.00358 (18732) covalent geometry : angle 0.71030 (25458) *********************** REFINEMENT MACRO_CYCLE 5 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 530 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 436 time to evaluate : 2.048 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 182 THR cc_start: 0.8291 (OUTLIER) cc_final: 0.8085 (t) REVERT: A 197 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7878 (mm110) REVERT: A 250 MET cc_start: 0.7323 (pmm) cc_final: 0.6507 (mmm) REVERT: A 324 GLU cc_start: 0.7498 (pp20) cc_final: 0.7097 (pm20) REVERT: A 384 ASN cc_start: 0.8713 (m110) cc_final: 0.8262 (m-40) REVERT: A 387 ARG cc_start: 0.8560 (mmm160) cc_final: 0.8229 (mmm160) REVERT: A 388 GLU cc_start: 0.8730 (tt0) cc_final: 0.7739 (tp30) REVERT: B 174 GLU cc_start: 0.8037 (tt0) cc_final: 0.7695 (tt0) REVERT: B 250 MET cc_start: 0.6416 (tmm) cc_final: 0.6181 (tpt) REVERT: B 270 ILE cc_start: 0.8497 (mm) cc_final: 0.8227 (mm) REVERT: B 339 ARG cc_start: 0.8443 (ttp80) cc_final: 0.7903 (ttp80) REVERT: B 343 LYS cc_start: 0.8724 (mtmt) cc_final: 0.8522 (mtmm) REVERT: B 358 VAL cc_start: 0.8686 (t) cc_final: 0.8447 (m) REVERT: B 410 LYS cc_start: 0.8484 (mmmt) cc_final: 0.8158 (mmtp) REVERT: B 412 MET cc_start: 0.9213 (tmm) cc_final: 0.8940 (tmm) REVERT: B 450 GLN cc_start: 0.7965 (pt0) cc_final: 0.7558 (pm20) REVERT: B 473 THR cc_start: 0.8812 (OUTLIER) cc_final: 0.8578 (p) REVERT: C 215 ASP cc_start: 0.8646 (OUTLIER) cc_final: 0.8416 (m-30) REVERT: C 239 THR cc_start: 0.8467 (p) cc_final: 0.8113 (p) REVERT: C 299 ASP cc_start: 0.8789 (t0) cc_final: 0.8316 (t0) REVERT: C 303 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8185 (ttt180) REVERT: C 313 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8435 (mm) REVERT: C 345 CYS cc_start: 0.9353 (m) cc_final: 0.9072 (m) REVERT: C 355 VAL cc_start: 0.9521 (t) cc_final: 0.9242 (p) REVERT: C 396 MET cc_start: 0.8494 (mtm) cc_final: 0.7718 (mtm) REVERT: C 407 LYS cc_start: 0.8862 (mmmt) cc_final: 0.8129 (tppt) REVERT: D 164 MET cc_start: 0.8544 (mtm) cc_final: 0.7589 (ttm) REVERT: D 244 LYS cc_start: 0.9532 (mmmm) cc_final: 0.9308 (mmmm) REVERT: D 247 LYS cc_start: 0.9277 (mmmt) cc_final: 0.8959 (mmtm) REVERT: D 324 GLU cc_start: 0.8298 (tt0) cc_final: 0.7245 (pt0) REVERT: D 341 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8168 (mp) REVERT: D 345 CYS cc_start: 0.9186 (m) cc_final: 0.8801 (m) REVERT: D 351 GLU cc_start: 0.8416 (mm-30) cc_final: 0.7641 (mp0) REVERT: D 411 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8669 (mt-10) REVERT: E 164 MET cc_start: 0.8382 (mtm) cc_final: 0.7709 (mtm) REVERT: E 173 ILE cc_start: 0.8751 (pt) cc_final: 0.8388 (pt) REVERT: E 175 VAL cc_start: 0.9295 (t) cc_final: 0.8758 (m) REVERT: E 178 LYS cc_start: 0.9069 (mmmt) cc_final: 0.8526 (mmmt) REVERT: E 180 GLN cc_start: 0.8797 (mt0) cc_final: 0.8501 (mp10) REVERT: E 208 ASP cc_start: 0.9008 (t0) cc_final: 0.8508 (m-30) REVERT: E 324 GLU cc_start: 0.7225 (tt0) cc_final: 0.6949 (tt0) REVERT: E 338 MET cc_start: 0.8865 (tpp) cc_final: 0.8571 (tpp) REVERT: E 348 MET cc_start: 0.8752 (mtp) cc_final: 0.8168 (mpp) REVERT: E 370 MET cc_start: 0.8652 (tpp) cc_final: 0.8378 (tpp) REVERT: E 399 MET cc_start: 0.8757 (tmm) cc_final: 0.8531 (tmm) REVERT: E 407 LYS cc_start: 0.9069 (ptmm) cc_final: 0.8737 (ptmm) REVERT: E 410 LYS cc_start: 0.9299 (mttt) cc_final: 0.8990 (mttm) REVERT: E 437 THR cc_start: 0.7574 (OUTLIER) cc_final: 0.7283 (t) REVERT: E 492 GLU cc_start: 0.9275 (mm-30) cc_final: 0.8868 (tp30) REVERT: F 148 TYR cc_start: 0.8380 (m-80) cc_final: 0.7878 (m-80) REVERT: F 172 PHE cc_start: 0.8792 (m-80) cc_final: 0.8570 (m-10) REVERT: F 190 LEU cc_start: 0.9650 (mm) cc_final: 0.9390 (pp) REVERT: F 202 GLN cc_start: 0.9038 (tm-30) cc_final: 0.8684 (tm-30) REVERT: F 220 ASP cc_start: 0.8889 (m-30) cc_final: 0.8654 (p0) REVERT: F 245 LYS cc_start: 0.9621 (mmmm) cc_final: 0.9272 (mmtt) REVERT: F 275 CYS cc_start: 0.7872 (m) cc_final: 0.7447 (m) REVERT: F 343 LYS cc_start: 0.8937 (tptm) cc_final: 0.8612 (ttpt) REVERT: F 365 ASP cc_start: 0.9047 (t70) cc_final: 0.8571 (t0) REVERT: F 368 GLN cc_start: 0.8747 (tp40) cc_final: 0.8473 (tp40) REVERT: F 399 MET cc_start: 0.8791 (ptp) cc_final: 0.8434 (ptp) REVERT: F 443 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7362 (mp0) outliers start: 94 outliers final: 57 residues processed: 485 average time/residue: 0.2967 time to fit residues: 217.5105 Evaluate side-chains 456 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 390 time to evaluate : 2.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 245 LYS Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 303 ARG Chi-restraints excluded: chain C residue 307 CYS Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 338 MET Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 421 ILE Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 306 THR 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 380 THR Chi-restraints excluded: chain D residue 463 HIS Chi-restraints excluded: chain D residue 469 LYS Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 307 CYS Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 393 ILE Chi-restraints excluded: chain E residue 417 VAL 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 180 GLN Chi-restraints excluded: chain F residue 199 ILE 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 354 ILE Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 443 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 211 optimal weight: 8.9990 chunk 216 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 171 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 208 optimal weight: 8.9990 chunk 94 optimal weight: 0.9980 chunk 148 optimal weight: 0.6980 chunk 241 optimal weight: 20.0000 chunk 125 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 overall best weight: 4.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 344 ASN F 435 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.083641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.065482 restraints weight = 64825.336| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 4.98 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.7785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 18732 Z= 0.165 Angle : 0.699 9.613 25458 Z= 0.345 Chirality : 0.047 0.307 3018 Planarity : 0.005 0.049 3366 Dihedral : 6.774 70.218 2866 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 5.69 % Allowed : 27.00 % Favored : 67.31 % 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: 0.22 (0.17), residues: 2520 helix: 1.36 (0.16), residues: 1092 sheet: -0.59 (0.24), residues: 462 loop : -0.81 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 481 HIS 0.012 0.001 HIS F 319 PHE 0.023 0.002 PHE F 243 TYR 0.021 0.002 TYR D 402 ARG 0.023 0.001 ARG B 352 Details of bonding type rmsd hydrogen bonds : bond 0.03190 ( 939) hydrogen bonds : angle 4.41440 ( 2733) covalent geometry : bond 0.00390 (18732) covalent geometry : angle 0.69941 (25458) *********************** REFINEMENT MACRO_CYCLE 6 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 504 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 403 time to evaluate : 3.411 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 182 THR cc_start: 0.8588 (OUTLIER) cc_final: 0.8365 (t) REVERT: A 193 MET cc_start: 0.8667 (tpt) cc_final: 0.7921 (tpp) REVERT: A 197 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7870 (mm-40) REVERT: A 250 MET cc_start: 0.7577 (pmm) cc_final: 0.6964 (mmm) REVERT: A 324 GLU cc_start: 0.7820 (pp20) cc_final: 0.7521 (pm20) REVERT: A 351 GLU cc_start: 0.8387 (mp0) cc_final: 0.7823 (mp0) REVERT: A 368 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7771 (mp10) REVERT: A 384 ASN cc_start: 0.8903 (m110) cc_final: 0.8677 (m-40) REVERT: A 387 ARG cc_start: 0.8566 (mmm160) cc_final: 0.8326 (mmm160) REVERT: B 174 GLU cc_start: 0.8081 (tt0) cc_final: 0.7628 (tt0) REVERT: B 239 THR cc_start: 0.8996 (m) cc_final: 0.8586 (p) REVERT: B 250 MET cc_start: 0.6536 (tmm) cc_final: 0.6315 (tpt) REVERT: B 343 LYS cc_start: 0.8970 (mtmt) cc_final: 0.8640 (mtpt) REVERT: B 347 ARG cc_start: 0.8680 (ptp-110) cc_final: 0.8322 (ptp90) REVERT: B 351 GLU cc_start: 0.8512 (mp0) cc_final: 0.8307 (mp0) REVERT: B 378 MET cc_start: 0.7502 (ptm) cc_final: 0.7093 (ptm) REVERT: B 394 GLU cc_start: 0.8973 (tt0) cc_final: 0.8736 (mt-10) REVERT: B 412 MET cc_start: 0.9233 (tmm) cc_final: 0.8919 (tmm) REVERT: B 417 VAL cc_start: 0.7068 (OUTLIER) cc_final: 0.6606 (p) REVERT: B 420 ILE cc_start: 0.8252 (mt) cc_final: 0.8049 (tp) REVERT: B 450 GLN cc_start: 0.8004 (pt0) cc_final: 0.7646 (pm20) REVERT: B 473 THR cc_start: 0.8886 (OUTLIER) cc_final: 0.8649 (p) REVERT: B 479 ARG cc_start: 0.7895 (ptm160) cc_final: 0.7393 (ttt180) REVERT: C 299 ASP cc_start: 0.8856 (t0) cc_final: 0.8485 (t0) REVERT: C 303 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8370 (ttt180) REVERT: C 355 VAL cc_start: 0.9573 (t) cc_final: 0.9270 (p) REVERT: C 370 MET cc_start: 0.9280 (mtt) cc_final: 0.8625 (mtt) REVERT: C 396 MET cc_start: 0.8779 (mtm) cc_final: 0.7973 (mtm) REVERT: C 407 LYS cc_start: 0.8795 (mmmt) cc_final: 0.7612 (tppt) REVERT: C 411 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8548 (mp0) REVERT: C 469 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8737 (ptpp) REVERT: D 164 MET cc_start: 0.8740 (mtm) cc_final: 0.7752 (mtm) REVERT: D 243 PHE cc_start: 0.8777 (t80) cc_final: 0.8527 (t80) REVERT: D 245 LYS cc_start: 0.9110 (mmtm) cc_final: 0.8902 (mmmt) REVERT: D 351 GLU cc_start: 0.8554 (mm-30) cc_final: 0.7878 (mp0) REVERT: D 396 MET cc_start: 0.9363 (mtt) cc_final: 0.8990 (mtt) REVERT: D 402 TYR cc_start: 0.8588 (m-80) cc_final: 0.8171 (m-10) REVERT: D 407 LYS cc_start: 0.8921 (mmmt) cc_final: 0.8381 (tppt) REVERT: D 411 GLU cc_start: 0.9076 (mt-10) cc_final: 0.8687 (mt-10) REVERT: E 164 MET cc_start: 0.8482 (mtm) cc_final: 0.7693 (mtm) REVERT: E 173 ILE cc_start: 0.8958 (pt) cc_final: 0.8664 (pt) REVERT: E 175 VAL cc_start: 0.9302 (t) cc_final: 0.8706 (m) REVERT: E 178 LYS cc_start: 0.9166 (mmmt) cc_final: 0.8635 (mmmt) REVERT: E 180 GLN cc_start: 0.8866 (mt0) cc_final: 0.8476 (mp10) REVERT: E 206 ARG cc_start: 0.7830 (ptm160) cc_final: 0.6966 (ttp80) REVERT: E 324 GLU cc_start: 0.7650 (tt0) cc_final: 0.7441 (tt0) REVERT: E 348 MET cc_start: 0.8858 (mtp) cc_final: 0.8205 (mpp) REVERT: E 399 MET cc_start: 0.8837 (tmm) cc_final: 0.8586 (tmm) REVERT: E 437 THR cc_start: 0.7718 (OUTLIER) cc_final: 0.7462 (t) REVERT: E 452 LEU cc_start: 0.9230 (tp) cc_final: 0.8989 (mp) REVERT: E 492 GLU cc_start: 0.9293 (mm-30) cc_final: 0.8876 (tp30) REVERT: F 148 TYR cc_start: 0.8471 (m-80) cc_final: 0.8029 (m-80) REVERT: F 202 GLN cc_start: 0.9088 (tm-30) cc_final: 0.8734 (tm-30) REVERT: F 220 ASP cc_start: 0.8990 (m-30) cc_final: 0.8782 (p0) REVERT: F 245 LYS cc_start: 0.9630 (mmmm) cc_final: 0.9296 (mmtt) REVERT: F 246 ASP cc_start: 0.9152 (m-30) cc_final: 0.8759 (t0) REVERT: F 251 LYS cc_start: 0.9375 (mmtm) cc_final: 0.8895 (mmmm) REVERT: F 275 CYS cc_start: 0.8466 (m) cc_final: 0.8154 (m) REVERT: F 343 LYS cc_start: 0.9014 (tptm) cc_final: 0.8784 (ttpt) REVERT: F 365 ASP cc_start: 0.9095 (t70) cc_final: 0.8570 (t0) REVERT: F 368 GLN cc_start: 0.8684 (tp40) cc_final: 0.8399 (tp40) REVERT: F 399 MET cc_start: 0.8803 (ptp) cc_final: 0.8276 (ptp) REVERT: F 443 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7715 (mp0) REVERT: F 451 ASP cc_start: 0.7990 (m-30) cc_final: 0.6972 (t70) outliers start: 101 outliers final: 56 residues processed: 468 average time/residue: 0.4162 time to fit residues: 297.3650 Evaluate side-chains 446 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 380 time to evaluate : 3.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 245 LYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 368 GLN Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 303 ARG Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 421 ILE Chi-restraints excluded: chain C residue 469 LYS Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 259 ILE 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 348 MET Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 368 GLN Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 463 HIS Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain F residue 180 GLN Chi-restraints excluded: chain F residue 199 ILE 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 396 MET Chi-restraints excluded: chain F residue 397 ILE Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain F residue 435 HIS Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 443 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 60 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 149 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 246 optimal weight: 30.0000 chunk 63 optimal weight: 7.9990 chunk 240 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 156 optimal weight: 7.9990 chunk 139 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN A 384 ASN A 470 HIS ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.083156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.065141 restraints weight = 64267.083| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 4.91 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.8328 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= 0.157 Angle : 0.704 11.378 25458 Z= 0.346 Chirality : 0.047 0.317 3018 Planarity : 0.005 0.049 3366 Dihedral : 6.560 67.849 2866 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.62 % Allowed : 28.24 % Favored : 67.14 % 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: 0.22 (0.17), residues: 2520 helix: 1.32 (0.16), residues: 1098 sheet: -0.55 (0.24), residues: 462 loop : -0.79 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 481 HIS 0.029 0.001 HIS F 435 PHE 0.023 0.002 PHE F 243 TYR 0.014 0.001 TYR D 402 ARG 0.011 0.001 ARG B 205 Details of bonding type rmsd hydrogen bonds : bond 0.03157 ( 939) hydrogen bonds : angle 4.37907 ( 2733) covalent geometry : bond 0.00367 (18732) covalent geometry : angle 0.70439 (25458) *********************** REFINEMENT MACRO_CYCLE 7 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 467 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 385 time to evaluate : 2.009 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 193 MET cc_start: 0.8781 (tpt) cc_final: 0.8048 (tpp) REVERT: A 197 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.8025 (mm-40) REVERT: A 250 MET cc_start: 0.7615 (pmm) cc_final: 0.7200 (mmm) REVERT: A 324 GLU cc_start: 0.7940 (pp20) cc_final: 0.7682 (pm20) REVERT: A 343 LYS cc_start: 0.9065 (ptmm) cc_final: 0.8440 (ptmt) REVERT: A 351 GLU cc_start: 0.8563 (mp0) cc_final: 0.7915 (mp0) REVERT: A 384 ASN cc_start: 0.9204 (m-40) cc_final: 0.8928 (m-40) REVERT: A 412 MET cc_start: 0.9168 (tmm) cc_final: 0.8840 (tmm) REVERT: B 174 GLU cc_start: 0.8264 (tt0) cc_final: 0.7491 (tp30) REVERT: B 179 VAL cc_start: 0.9086 (t) cc_final: 0.8804 (p) REVERT: B 202 GLN cc_start: 0.9393 (OUTLIER) cc_final: 0.9085 (mp10) REVERT: B 239 THR cc_start: 0.9186 (m) cc_final: 0.8863 (p) REVERT: B 247 LYS cc_start: 0.7886 (mmtm) cc_final: 0.7382 (mmmt) REVERT: B 339 ARG cc_start: 0.8625 (ttp80) cc_final: 0.8226 (ttp80) REVERT: B 343 LYS cc_start: 0.9085 (mtmt) cc_final: 0.8662 (mtmm) REVERT: B 347 ARG cc_start: 0.8710 (ptp-110) cc_final: 0.8486 (ptp-110) REVERT: B 377 SER cc_start: 0.8339 (t) cc_final: 0.7953 (p) REVERT: B 378 MET cc_start: 0.7737 (ptm) cc_final: 0.7348 (ptm) REVERT: B 410 LYS cc_start: 0.8787 (mmmt) cc_final: 0.8496 (mmmm) REVERT: B 412 MET cc_start: 0.9224 (tmm) cc_final: 0.8902 (tmm) REVERT: B 420 ILE cc_start: 0.8375 (mt) cc_final: 0.8115 (tp) REVERT: B 450 GLN cc_start: 0.8189 (pt0) cc_final: 0.7721 (pm20) REVERT: B 473 THR cc_start: 0.8875 (OUTLIER) cc_final: 0.8642 (p) REVERT: B 479 ARG cc_start: 0.8012 (ptm160) cc_final: 0.7690 (ptm160) REVERT: C 193 MET cc_start: 0.8511 (ppp) cc_final: 0.8305 (ppp) REVERT: C 270 ILE cc_start: 0.8691 (mt) cc_final: 0.8217 (tt) REVERT: C 299 ASP cc_start: 0.8859 (t0) cc_final: 0.8440 (t0) REVERT: C 343 LYS cc_start: 0.9094 (mtpp) cc_final: 0.8617 (mtmm) REVERT: C 345 CYS cc_start: 0.9343 (m) cc_final: 0.9069 (m) REVERT: C 370 MET cc_start: 0.9313 (mtt) cc_final: 0.8622 (mtt) REVERT: C 407 LYS cc_start: 0.8759 (mmmt) cc_final: 0.7858 (tppt) REVERT: C 411 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8597 (mp0) REVERT: D 205 ARG cc_start: 0.9078 (mtp-110) cc_final: 0.8725 (mtp-110) REVERT: D 351 GLU cc_start: 0.8587 (mm-30) cc_final: 0.7925 (mp0) REVERT: D 407 LYS cc_start: 0.8952 (mmmt) cc_final: 0.8396 (tppt) REVERT: D 411 GLU cc_start: 0.9094 (mt-10) cc_final: 0.8704 (mt-10) REVERT: D 450 GLN cc_start: 0.7544 (pt0) cc_final: 0.7056 (pm20) REVERT: E 164 MET cc_start: 0.8538 (mtm) cc_final: 0.7660 (mtm) REVERT: E 173 ILE cc_start: 0.9065 (pt) cc_final: 0.8776 (pt) REVERT: E 175 VAL cc_start: 0.9327 (t) cc_final: 0.8714 (m) REVERT: E 178 LYS cc_start: 0.9197 (mmmt) cc_final: 0.8651 (mmmt) REVERT: E 180 GLN cc_start: 0.8941 (mt0) cc_final: 0.8570 (mp10) REVERT: E 314 GLN cc_start: 0.9062 (tt0) cc_final: 0.8779 (tp-100) REVERT: E 324 GLU cc_start: 0.7597 (tt0) cc_final: 0.7395 (tt0) REVERT: E 399 MET cc_start: 0.8888 (tmm) cc_final: 0.8645 (tmm) REVERT: E 410 LYS cc_start: 0.9358 (mttt) cc_final: 0.8952 (mttm) REVERT: E 437 THR cc_start: 0.7720 (OUTLIER) cc_final: 0.7452 (t) REVERT: E 452 LEU cc_start: 0.9261 (tp) cc_final: 0.9016 (mp) REVERT: E 492 GLU cc_start: 0.9273 (mm-30) cc_final: 0.8898 (tp30) REVERT: F 148 TYR cc_start: 0.8477 (m-80) cc_final: 0.8043 (m-80) REVERT: F 202 GLN cc_start: 0.9151 (tm-30) cc_final: 0.8789 (tm-30) REVERT: F 220 ASP cc_start: 0.9007 (m-30) cc_final: 0.8793 (p0) REVERT: F 245 LYS cc_start: 0.9619 (mmmm) cc_final: 0.9340 (mmtt) REVERT: F 246 ASP cc_start: 0.9155 (m-30) cc_final: 0.8799 (t0) REVERT: F 275 CYS cc_start: 0.8668 (m) cc_final: 0.8353 (m) REVERT: F 343 LYS cc_start: 0.9158 (tptm) cc_final: 0.8947 (ttpt) REVERT: F 354 ILE cc_start: 0.8517 (mt) cc_final: 0.8287 (mm) REVERT: F 365 ASP cc_start: 0.9174 (t70) cc_final: 0.8635 (t0) REVERT: F 368 GLN cc_start: 0.8820 (tp40) cc_final: 0.8458 (tp40) REVERT: F 396 MET cc_start: 0.7281 (ttt) cc_final: 0.6494 (ttt) REVERT: F 399 MET cc_start: 0.8898 (ptp) cc_final: 0.8339 (ptp) outliers start: 82 outliers final: 55 residues processed: 434 average time/residue: 0.3016 time to fit residues: 198.1593 Evaluate side-chains 427 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 367 time to evaluate : 2.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 245 LYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 338 MET Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 421 ILE Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 259 ILE 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 348 MET Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 463 HIS Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 307 CYS Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 393 ILE Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain F residue 180 GLN Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 442 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 40 optimal weight: 6.9990 chunk 130 optimal weight: 0.4980 chunk 96 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 137 optimal weight: 8.9990 chunk 223 optimal weight: 20.0000 chunk 230 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 166 optimal weight: 9.9990 chunk 188 optimal weight: 7.9990 chunk 201 optimal weight: 7.9990 overall best weight: 4.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 169 HIS D 225 ASN ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.082090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.064423 restraints weight = 64735.897| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 4.95 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.9157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 18732 Z= 0.167 Angle : 0.728 11.662 25458 Z= 0.355 Chirality : 0.048 0.306 3018 Planarity : 0.005 0.059 3366 Dihedral : 6.465 63.271 2866 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.00 % Allowed : 28.80 % Favored : 67.19 % 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: 0.24 (0.17), residues: 2520 helix: 1.31 (0.16), residues: 1098 sheet: -0.48 (0.24), residues: 454 loop : -0.78 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 481 HIS 0.019 0.001 HIS F 435 PHE 0.025 0.002 PHE F 243 TYR 0.012 0.001 TYR D 402 ARG 0.013 0.001 ARG B 205 Details of bonding type rmsd hydrogen bonds : bond 0.03229 ( 939) hydrogen bonds : angle 4.43133 ( 2733) covalent geometry : bond 0.00397 (18732) covalent geometry : angle 0.72815 (25458) *********************** REFINEMENT MACRO_CYCLE 8 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 454 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 383 time to evaluate : 2.456 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: A 193 MET cc_start: 0.8848 (tpt) cc_final: 0.8208 (tpp) REVERT: A 197 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.8191 (mm-40) REVERT: A 343 LYS cc_start: 0.9162 (ptmm) cc_final: 0.8562 (ptmt) REVERT: A 384 ASN cc_start: 0.9184 (m-40) cc_final: 0.8771 (m-40) REVERT: B 174 GLU cc_start: 0.8163 (tt0) cc_final: 0.7629 (tp30) REVERT: B 178 LYS cc_start: 0.9145 (ptmm) cc_final: 0.8550 (ptmm) REVERT: B 196 CYS cc_start: 0.8908 (m) cc_final: 0.8241 (m) REVERT: B 202 GLN cc_start: 0.9313 (OUTLIER) cc_final: 0.8974 (mp10) REVERT: B 238 LEU cc_start: 0.9199 (tp) cc_final: 0.8699 (mp) REVERT: B 247 LYS cc_start: 0.8212 (mmtm) cc_final: 0.7742 (mmmt) REVERT: B 343 LYS cc_start: 0.9227 (mtmt) cc_final: 0.8776 (mtmm) REVERT: B 347 ARG cc_start: 0.8805 (ptp-110) cc_final: 0.8575 (ptp-110) REVERT: B 359 ARG cc_start: 0.8952 (mtp85) cc_final: 0.8744 (mtt-85) REVERT: B 377 SER cc_start: 0.8650 (t) cc_final: 0.7631 (p) REVERT: B 407 LYS cc_start: 0.9258 (ttpp) cc_final: 0.8646 (tppt) REVERT: B 410 LYS cc_start: 0.8830 (mmmt) cc_final: 0.8097 (mmmm) REVERT: B 412 MET cc_start: 0.9240 (tmm) cc_final: 0.9011 (tmm) REVERT: B 420 ILE cc_start: 0.8448 (mt) cc_final: 0.8190 (tp) REVERT: B 450 GLN cc_start: 0.8319 (pt0) cc_final: 0.7865 (pm20) REVERT: B 473 THR cc_start: 0.8954 (OUTLIER) cc_final: 0.8735 (p) REVERT: B 479 ARG cc_start: 0.8294 (ptm160) cc_final: 0.7661 (ttt180) REVERT: C 215 ASP cc_start: 0.8735 (OUTLIER) cc_final: 0.8258 (t0) REVERT: C 308 GLU cc_start: 0.7978 (pt0) cc_final: 0.7612 (pt0) REVERT: C 345 CYS cc_start: 0.9189 (m) cc_final: 0.8970 (m) REVERT: C 364 PHE cc_start: 0.8672 (t80) cc_final: 0.8424 (t80) REVERT: C 370 MET cc_start: 0.9306 (mtt) cc_final: 0.8584 (mtt) REVERT: C 396 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.8130 (mtt) REVERT: C 407 LYS cc_start: 0.8861 (mmmt) cc_final: 0.8080 (tppt) REVERT: C 411 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8634 (mp0) REVERT: C 477 ARG cc_start: 0.8501 (mmm-85) cc_final: 0.8102 (mmm-85) REVERT: D 164 MET cc_start: 0.8953 (mtm) cc_final: 0.8665 (ttm) REVERT: D 351 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8010 (mp0) REVERT: D 396 MET cc_start: 0.9331 (mtt) cc_final: 0.9075 (mmm) REVERT: D 407 LYS cc_start: 0.8993 (mmmt) cc_final: 0.8429 (tppt) REVERT: D 411 GLU cc_start: 0.9174 (mt-10) cc_final: 0.8737 (mt-10) REVERT: E 164 MET cc_start: 0.8636 (mtm) cc_final: 0.7686 (mtm) REVERT: E 173 ILE cc_start: 0.9190 (pt) cc_final: 0.8868 (pt) REVERT: E 175 VAL cc_start: 0.9293 (t) cc_final: 0.8614 (m) REVERT: E 178 LYS cc_start: 0.9188 (mmmt) cc_final: 0.8696 (mmmt) REVERT: E 180 GLN cc_start: 0.9014 (mt0) cc_final: 0.8676 (mp10) REVERT: E 206 ARG cc_start: 0.7655 (ttp80) cc_final: 0.7336 (ttp80) REVERT: E 314 GLN cc_start: 0.9126 (tt0) cc_final: 0.8892 (tp-100) REVERT: E 324 GLU cc_start: 0.7686 (tt0) cc_final: 0.7419 (tt0) REVERT: E 346 LEU cc_start: 0.9535 (tt) cc_final: 0.9301 (tp) REVERT: E 347 ARG cc_start: 0.9365 (tpp80) cc_final: 0.8982 (tpp80) REVERT: E 348 MET cc_start: 0.8897 (mtp) cc_final: 0.8587 (mtm) REVERT: E 399 MET cc_start: 0.8948 (tmm) cc_final: 0.8688 (tmm) REVERT: E 410 LYS cc_start: 0.9412 (mttt) cc_final: 0.9100 (mttm) REVERT: E 437 THR cc_start: 0.7756 (OUTLIER) cc_final: 0.7485 (t) REVERT: E 492 GLU cc_start: 0.9275 (mm-30) cc_final: 0.8848 (tp30) REVERT: F 148 TYR cc_start: 0.8582 (m-80) cc_final: 0.8152 (m-80) REVERT: F 202 GLN cc_start: 0.9212 (tm-30) cc_final: 0.8827 (tm-30) REVERT: F 245 LYS cc_start: 0.9664 (mmmm) cc_final: 0.9393 (mmtt) REVERT: F 246 ASP cc_start: 0.9102 (m-30) cc_final: 0.8871 (t0) REVERT: F 250 MET cc_start: 0.8432 (mmm) cc_final: 0.8188 (mmm) REVERT: F 354 ILE cc_start: 0.8747 (mt) cc_final: 0.8379 (mm) REVERT: F 365 ASP cc_start: 0.9120 (t70) cc_final: 0.8475 (t0) REVERT: F 368 GLN cc_start: 0.8882 (tp40) cc_final: 0.8558 (tp40) REVERT: F 378 MET cc_start: 0.8701 (mpp) cc_final: 0.8427 (mtt) REVERT: F 396 MET cc_start: 0.7580 (ttt) cc_final: 0.6917 (ttt) REVERT: F 399 MET cc_start: 0.9097 (ptp) cc_final: 0.8663 (ptp) REVERT: F 451 ASP cc_start: 0.8149 (m-30) cc_final: 0.7316 (t0) REVERT: F 479 ARG cc_start: 0.8183 (ttm170) cc_final: 0.7966 (ttm170) outliers start: 71 outliers final: 49 residues processed: 428 average time/residue: 0.3350 time to fit residues: 213.5941 Evaluate side-chains 400 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 344 time to evaluate : 2.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 421 ILE Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 320 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 D residue 463 HIS Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 307 CYS Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain F residue 180 GLN Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain F residue 442 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 51 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 212 optimal weight: 90.0000 chunk 24 optimal weight: 9.9990 chunk 209 optimal weight: 5.9990 chunk 190 optimal weight: 9.9990 chunk 81 optimal weight: 8.9990 chunk 225 optimal weight: 9.9990 chunk 173 optimal weight: 50.0000 chunk 55 optimal weight: 6.9990 chunk 136 optimal weight: 7.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 HIS ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.079635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.061333 restraints weight = 65732.248| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 4.86 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 1.0033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 18732 Z= 0.231 Angle : 0.788 13.155 25458 Z= 0.391 Chirality : 0.049 0.287 3018 Planarity : 0.006 0.079 3366 Dihedral : 6.534 60.428 2866 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.11 % Allowed : 29.31 % Favored : 66.57 % 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: 0.11 (0.17), residues: 2520 helix: 1.26 (0.16), residues: 1096 sheet: -0.55 (0.24), residues: 450 loop : -0.91 (0.19), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 481 HIS 0.005 0.001 HIS C 319 PHE 0.036 0.002 PHE A 172 TYR 0.018 0.002 TYR D 402 ARG 0.013 0.001 ARG B 205 Details of bonding type rmsd hydrogen bonds : bond 0.03461 ( 939) hydrogen bonds : angle 4.54826 ( 2733) covalent geometry : bond 0.00523 (18732) covalent geometry : angle 0.78772 (25458) *********************** REFINEMENT MACRO_CYCLE 9 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 427 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 354 time to evaluate : 2.382 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: A 178 LYS cc_start: 0.8918 (pptt) cc_final: 0.8634 (pptt) REVERT: A 193 MET cc_start: 0.8903 (tpt) cc_final: 0.8309 (tpp) REVERT: A 205 ARG cc_start: 0.8519 (ptp90) cc_final: 0.8311 (ptp90) REVERT: A 343 LYS cc_start: 0.9166 (ptmm) cc_final: 0.8630 (ptmt) REVERT: A 351 GLU cc_start: 0.8687 (mp0) cc_final: 0.8240 (mp0) REVERT: A 364 PHE cc_start: 0.9170 (t80) cc_final: 0.8779 (t80) REVERT: A 365 ASP cc_start: 0.8494 (p0) cc_final: 0.8247 (p0) REVERT: A 368 GLN cc_start: 0.8774 (mp10) cc_final: 0.8153 (mp10) REVERT: A 465 LYS cc_start: 0.7649 (mppt) cc_final: 0.7270 (mmtt) REVERT: A 491 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.8436 (ptt-90) REVERT: B 174 GLU cc_start: 0.8291 (tt0) cc_final: 0.8025 (tp30) REVERT: B 178 LYS cc_start: 0.9193 (ptmm) cc_final: 0.8609 (ptmm) REVERT: B 197 GLN cc_start: 0.9140 (tt0) cc_final: 0.8470 (tp-100) REVERT: B 202 GLN cc_start: 0.9314 (OUTLIER) cc_final: 0.8991 (mp10) REVERT: B 233 LEU cc_start: 0.9064 (mt) cc_final: 0.8818 (mt) REVERT: B 314 GLN cc_start: 0.8739 (tt0) cc_final: 0.8288 (tm-30) REVERT: B 339 ARG cc_start: 0.8821 (ttp80) cc_final: 0.8183 (ttp80) REVERT: B 343 LYS cc_start: 0.9300 (mtmt) cc_final: 0.8914 (mtmm) REVERT: B 347 ARG cc_start: 0.8919 (ptp-110) cc_final: 0.8703 (ptp-110) REVERT: B 351 GLU cc_start: 0.8690 (mp0) cc_final: 0.8315 (mp0) REVERT: B 370 MET cc_start: 0.8178 (mmt) cc_final: 0.7918 (mmt) REVERT: B 377 SER cc_start: 0.8643 (t) cc_final: 0.7925 (p) REVERT: B 410 LYS cc_start: 0.8801 (mmmt) cc_final: 0.8358 (mmmm) REVERT: B 420 ILE cc_start: 0.8484 (mt) cc_final: 0.8272 (tp) REVERT: B 450 GLN cc_start: 0.8407 (pt0) cc_final: 0.7970 (pm20) REVERT: B 479 ARG cc_start: 0.8328 (ptm160) cc_final: 0.7768 (ttt180) REVERT: C 193 MET cc_start: 0.8661 (tpt) cc_final: 0.8341 (tmm) REVERT: C 215 ASP cc_start: 0.8737 (OUTLIER) cc_final: 0.8328 (t0) REVERT: C 345 CYS cc_start: 0.9195 (m) cc_final: 0.8924 (m) REVERT: C 370 MET cc_start: 0.9378 (mtt) cc_final: 0.8709 (mtt) REVERT: C 399 MET cc_start: 0.9021 (tmm) cc_final: 0.8729 (tmm) REVERT: C 407 LYS cc_start: 0.8861 (mmmt) cc_final: 0.8140 (tppt) REVERT: C 411 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8637 (mp0) REVERT: C 477 ARG cc_start: 0.8841 (mmm-85) cc_final: 0.8358 (mmm-85) REVERT: D 164 MET cc_start: 0.8906 (mtm) cc_final: 0.8573 (mtm) REVERT: D 180 GLN cc_start: 0.8422 (tm-30) cc_final: 0.8105 (tm-30) REVERT: D 205 ARG cc_start: 0.9226 (mtp-110) cc_final: 0.8773 (ttm110) REVERT: D 206 ARG cc_start: 0.7763 (tpp-160) cc_final: 0.7530 (tpp-160) REVERT: D 339 ARG cc_start: 0.9154 (tmm-80) cc_final: 0.8799 (ttp80) REVERT: D 351 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8155 (mp0) REVERT: D 368 GLN cc_start: 0.8652 (mt0) cc_final: 0.8417 (mp10) REVERT: D 407 LYS cc_start: 0.9102 (mmmt) cc_final: 0.8591 (tppt) REVERT: D 411 GLU cc_start: 0.9159 (mt-10) cc_final: 0.8812 (mt-10) REVERT: D 450 GLN cc_start: 0.7901 (pt0) cc_final: 0.7562 (pm20) REVERT: D 469 LYS cc_start: 0.9329 (OUTLIER) cc_final: 0.9010 (pttm) REVERT: E 164 MET cc_start: 0.8795 (mtm) cc_final: 0.7836 (mtm) REVERT: E 173 ILE cc_start: 0.9391 (pt) cc_final: 0.9091 (pt) REVERT: E 178 LYS cc_start: 0.9285 (mmmt) cc_final: 0.8971 (mmmm) REVERT: E 314 GLN cc_start: 0.9236 (tt0) cc_final: 0.9007 (tp-100) REVERT: E 324 GLU cc_start: 0.7769 (tt0) cc_final: 0.7549 (tt0) REVERT: E 368 GLN cc_start: 0.9182 (tp40) cc_final: 0.8954 (tp40) REVERT: E 410 LYS cc_start: 0.9424 (mttt) cc_final: 0.9091 (mttm) REVERT: E 437 THR cc_start: 0.8003 (OUTLIER) cc_final: 0.7728 (t) REVERT: E 492 GLU cc_start: 0.9233 (mm-30) cc_final: 0.8756 (tp30) REVERT: F 148 TYR cc_start: 0.8539 (m-80) cc_final: 0.8146 (m-80) REVERT: F 194 ASN cc_start: 0.9665 (t0) cc_final: 0.9416 (t0) REVERT: F 202 GLN cc_start: 0.9278 (tm-30) cc_final: 0.8894 (tm-30) REVERT: F 246 ASP cc_start: 0.9232 (m-30) cc_final: 0.9000 (t0) REVERT: F 299 ASP cc_start: 0.8971 (t0) cc_final: 0.8547 (t0) REVERT: F 354 ILE cc_start: 0.8936 (mt) cc_final: 0.8494 (mm) REVERT: F 357 GLU cc_start: 0.8236 (tt0) cc_final: 0.7646 (tp30) REVERT: F 365 ASP cc_start: 0.9120 (t70) cc_final: 0.8511 (t0) REVERT: F 378 MET cc_start: 0.8620 (mpp) cc_final: 0.8112 (mtt) REVERT: F 396 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.7637 (ttt) REVERT: F 451 ASP cc_start: 0.8376 (m-30) cc_final: 0.8055 (t0) outliers start: 73 outliers final: 56 residues processed: 397 average time/residue: 0.3495 time to fit residues: 204.8882 Evaluate side-chains 386 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 323 time to evaluate : 2.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 408 THR 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 199 ILE Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 421 ILE Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 320 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 D residue 463 HIS Chi-restraints excluded: chain D residue 469 LYS Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 307 CYS Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 393 ILE Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain F residue 180 GLN Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 396 MET Chi-restraints excluded: chain F residue 397 ILE Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain F residue 442 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 30.0000 chunk 79 optimal weight: 20.0000 chunk 197 optimal weight: 20.0000 chunk 18 optimal weight: 6.9990 chunk 223 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 chunk 239 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 23 optimal weight: 30.0000 chunk 183 optimal weight: 1.9990 chunk 121 optimal weight: 20.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 ASN ** F 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.080105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.062504 restraints weight = 65517.520| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 4.79 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 1.0400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 18732 Z= 0.171 Angle : 0.773 12.644 25458 Z= 0.378 Chirality : 0.048 0.226 3018 Planarity : 0.005 0.064 3366 Dihedral : 6.450 59.788 2866 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.44 % Allowed : 31.23 % Favored : 65.33 % 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: 0.12 (0.17), residues: 2520 helix: 1.26 (0.16), residues: 1102 sheet: -0.60 (0.23), residues: 470 loop : -0.90 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 481 HIS 0.005 0.001 HIS F 382 PHE 0.027 0.002 PHE D 243 TYR 0.016 0.001 TYR B 486 ARG 0.013 0.001 ARG B 205 Details of bonding type rmsd hydrogen bonds : bond 0.03367 ( 939) hydrogen bonds : angle 4.55585 ( 2733) covalent geometry : bond 0.00408 (18732) covalent geometry : angle 0.77286 (25458) ********************** REFINEMENT MACRO_CYCLE 10 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 402 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 341 time to evaluate : 2.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.8948 (tpt) cc_final: 0.8437 (tpp) REVERT: A 205 ARG cc_start: 0.8475 (ptp90) cc_final: 0.8266 (ptp90) REVERT: A 343 LYS cc_start: 0.9224 (ptmm) cc_final: 0.8611 (ptmt) REVERT: A 351 GLU cc_start: 0.8742 (mp0) cc_final: 0.8267 (mp0) REVERT: A 370 MET cc_start: 0.8899 (mmt) cc_final: 0.8056 (mmt) REVERT: A 394 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8533 (mm-30) REVERT: A 491 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.8432 (ptt-90) REVERT: B 174 GLU cc_start: 0.8294 (tt0) cc_final: 0.8036 (tp30) REVERT: B 178 LYS cc_start: 0.9202 (ptmm) cc_final: 0.8516 (ptmm) REVERT: B 197 GLN cc_start: 0.9145 (tt0) cc_final: 0.8835 (mt0) REVERT: B 202 GLN cc_start: 0.9278 (OUTLIER) cc_final: 0.8923 (mp10) REVERT: B 339 ARG cc_start: 0.8801 (ttp80) cc_final: 0.8211 (ttp80) REVERT: B 343 LYS cc_start: 0.9325 (mtmt) cc_final: 0.8930 (mtmm) REVERT: B 351 GLU cc_start: 0.8635 (mp0) cc_final: 0.8345 (mp0) REVERT: B 370 MET cc_start: 0.8208 (mmt) cc_final: 0.7695 (mmt) REVERT: B 377 SER cc_start: 0.8644 (t) cc_final: 0.7974 (p) REVERT: B 410 LYS cc_start: 0.8814 (mmmt) cc_final: 0.8564 (mmmm) REVERT: B 450 GLN cc_start: 0.8377 (pt0) cc_final: 0.7924 (pm20) REVERT: B 479 ARG cc_start: 0.8318 (ptm160) cc_final: 0.7696 (ttt180) REVERT: C 193 MET cc_start: 0.8693 (tpt) cc_final: 0.8381 (tmm) REVERT: C 308 GLU cc_start: 0.8027 (pt0) cc_final: 0.7189 (pt0) REVERT: C 345 CYS cc_start: 0.9240 (m) cc_final: 0.9012 (m) REVERT: C 399 MET cc_start: 0.9129 (tmm) cc_final: 0.8877 (tmm) REVERT: C 407 LYS cc_start: 0.8870 (mmmt) cc_final: 0.8139 (tppt) REVERT: C 411 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8587 (mp0) REVERT: C 477 ARG cc_start: 0.8858 (mmm-85) cc_final: 0.8410 (mmm-85) REVERT: D 164 MET cc_start: 0.9034 (mtm) cc_final: 0.8644 (mtm) REVERT: D 205 ARG cc_start: 0.9274 (mtp-110) cc_final: 0.8803 (ttm110) REVERT: D 206 ARG cc_start: 0.7812 (tpp-160) cc_final: 0.7471 (tpp-160) REVERT: D 339 ARG cc_start: 0.9154 (tmm-80) cc_final: 0.8749 (ttp80) REVERT: D 351 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8175 (mp0) REVERT: D 370 MET cc_start: 0.7859 (mtt) cc_final: 0.7209 (mmt) REVERT: D 396 MET cc_start: 0.9254 (mtt) cc_final: 0.9050 (mmm) REVERT: D 407 LYS cc_start: 0.9128 (mmmt) cc_final: 0.8630 (tppt) REVERT: D 411 GLU cc_start: 0.9167 (mt-10) cc_final: 0.8823 (mt-10) REVERT: D 450 GLN cc_start: 0.7966 (pt0) cc_final: 0.7651 (pm20) REVERT: E 164 MET cc_start: 0.8765 (mtm) cc_final: 0.7818 (mtm) REVERT: E 196 CYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8630 (p) REVERT: E 314 GLN cc_start: 0.9237 (tt0) cc_final: 0.9032 (tp-100) REVERT: E 347 ARG cc_start: 0.9354 (tpp80) cc_final: 0.8939 (tpp80) REVERT: E 410 LYS cc_start: 0.9420 (mttt) cc_final: 0.9095 (mttm) REVERT: E 437 THR cc_start: 0.7914 (OUTLIER) cc_final: 0.7686 (t) REVERT: E 492 GLU cc_start: 0.9235 (mm-30) cc_final: 0.8730 (tp30) REVERT: F 148 TYR cc_start: 0.8562 (m-80) cc_final: 0.8127 (m-80) REVERT: F 194 ASN cc_start: 0.9678 (t0) cc_final: 0.9412 (t0) REVERT: F 202 GLN cc_start: 0.9291 (tm-30) cc_final: 0.8903 (tm-30) REVERT: F 299 ASP cc_start: 0.8968 (t0) cc_final: 0.8542 (t0) REVERT: F 357 GLU cc_start: 0.8254 (tt0) cc_final: 0.7743 (tp30) REVERT: F 378 MET cc_start: 0.8499 (mpp) cc_final: 0.8231 (mtt) REVERT: F 451 ASP cc_start: 0.8519 (m-30) cc_final: 0.8174 (t0) outliers start: 61 outliers final: 43 residues processed: 378 average time/residue: 0.3196 time to fit residues: 180.4758 Evaluate side-chains 362 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 314 time to evaluate : 2.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 408 THR 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 199 ILE Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 421 ILE Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 320 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 D residue 463 HIS Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 307 CYS Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 393 ILE Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain F residue 180 GLN Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 442 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 30.0000 chunk 117 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 144 optimal weight: 5.9990 chunk 172 optimal weight: 40.0000 chunk 232 optimal weight: 0.9990 chunk 139 optimal weight: 5.9990 chunk 240 optimal weight: 5.9990 chunk 241 optimal weight: 8.9990 chunk 94 optimal weight: 20.0000 chunk 55 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN D 314 GLN ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.079904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.062737 restraints weight = 64953.853| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 4.55 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 1.0773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 18732 Z= 0.183 Angle : 0.785 12.421 25458 Z= 0.384 Chirality : 0.049 0.235 3018 Planarity : 0.005 0.067 3366 Dihedral : 6.395 58.436 2866 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.49 % Allowed : 31.00 % Favored : 65.50 % 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: 0.07 (0.17), residues: 2520 helix: 1.24 (0.16), residues: 1102 sheet: -0.66 (0.23), residues: 474 loop : -0.91 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 481 HIS 0.006 0.001 HIS A 382 PHE 0.058 0.002 PHE A 364 TYR 0.018 0.002 TYR E 148 ARG 0.012 0.001 ARG B 205 Details of bonding type rmsd hydrogen bonds : bond 0.03370 ( 939) hydrogen bonds : angle 4.55079 ( 2733) covalent geometry : bond 0.00437 (18732) covalent geometry : angle 0.78542 (25458) =============================================================================== Job complete usr+sys time: 8265.78 seconds wall clock time: 145 minutes 6.85 seconds (8706.85 seconds total)