Starting phenix.real_space_refine on Thu Sep 18 17:14:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e29_47446/09_2025/9e29_47446.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e29_47446/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9e29_47446/09_2025/9e29_47446.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e29_47446/09_2025/9e29_47446.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e29_47446/09_2025/9e29_47446.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e29_47446/09_2025/9e29_47446.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.043 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ASP:plan': 6, 'TYR:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 4, 'GLN:plan1': 5, 'GLU:plan': 5, 'ARG:plan': 1} 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: {'ASP:plan': 6, 'TYR:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 4, 'GLN:plan1': 5, 'GLU:plan': 5, 'ARG:plan': 1} 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: {'ASP:plan': 6, 'TYR:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 4, 'GLN:plan1': 5, 'GLU:plan': 5, 'ARG:plan': 1} 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: {'ASP:plan': 6, 'TYR:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 4, 'GLN:plan1': 5, 'GLU:plan': 5, 'ARG:plan': 1} 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: {'ASP:plan': 6, 'TYR:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 4, 'GLN:plan1': 5, 'GLU:plan': 5, 'ARG:plan': 1} 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: {'ASP:plan': 6, 'TYR:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 4, 'GLN:plan1': 5, 'GLU:plan': 5, 'ARG:plan': 1} 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: 5.24, per 1000 atoms: 0.28 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: 1.85 Conformation dependent library (CDL) restraints added in 982.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.88 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: 3.22 Time building geometry restraints manager: 2.38 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 80 through 501) selection = (chain 'B' and (resid 80 through 274 or (resid 275 and (name N or name CA or nam \ e C or name O or name CB )) or resid 276 through 501)) selection = (chain 'C' and (resid 80 through 274 or (resid 275 and (name N or name CA or nam \ e C or name O or name CB )) or resid 276 through 501)) selection = (chain 'D' and resid 80 through 501) selection = (chain 'E' and (resid 80 through 274 or (resid 275 and (name N or name CA or nam \ e C or name O or name CB )) or resid 276 through 501)) selection = (chain 'F' and (resid 80 through 274 or (resid 275 and (name N or name CA or nam \ e C or name O or name CB )) or resid 276 through 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.820 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.180 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (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 ARG 0.003 0.000 ARG D 206 TYR 0.011 0.001 TYR C 402 PHE 0.017 0.001 PHE C 364 TRP 0.004 0.001 TRP C 481 HIS 0.003 0.001 HIS D 435 Details of bonding type rmsd covalent geometry : bond 0.00448 (18732) covalent geometry : angle 0.59349 (25458) hydrogen bonds : bond 0.13277 ( 939) hydrogen bonds : angle 6.06708 ( 2733) *********************** 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 : 0.765 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: A 164 MET cc_start: 0.6322 (mtt) cc_final: 0.6003 (mpp) REVERT: A 172 PHE cc_start: 0.8072 (m-80) cc_final: 0.7484 (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: 0.7021 (mt-10) REVERT: B 241 ARG cc_start: 0.7154 (mtp180) cc_final: 0.6909 (mtp-110) REVERT: B 283 THR cc_start: 0.8178 (t) cc_final: 0.7445 (m) REVERT: B 294 MET cc_start: 0.7656 (mmm) cc_final: 0.7121 (ttp) REVERT: B 317 GLN cc_start: 0.6671 (mp-120) cc_final: 0.6351 (mm-40) REVERT: B 365 ASP cc_start: 0.7244 (m-30) cc_final: 0.6390 (m-30) REVERT: B 381 LEU cc_start: 0.6004 (tp) cc_final: 0.5468 (tt) REVERT: C 148 TYR cc_start: 0.7423 (m-80) cc_final: 0.6700 (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: 0.6001 (m110) REVERT: C 279 ILE cc_start: 0.6500 (mt) cc_final: 0.6261 (mt) REVERT: C 299 ASP cc_start: 0.8187 (t0) cc_final: 0.7903 (t0) REVERT: C 315 LEU cc_start: 0.7905 (mp) cc_final: 0.7501 (mp) REVERT: C 348 MET cc_start: 0.7150 (ptp) cc_final: 0.6385 (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: 0.7766 (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: 0.8108 (mt) REVERT: D 390 ILE cc_start: 0.7938 (mt) cc_final: 0.7647 (mt) REVERT: D 397 ILE cc_start: 0.9191 (mt) cc_final: 0.8845 (mm) REVERT: D 404 LEU cc_start: 0.8266 (mp) cc_final: 0.8036 (mp) REVERT: D 409 ILE cc_start: 0.8543 (mm) cc_final: 0.8169 (mt) REVERT: D 421 ILE cc_start: 0.8089 (mt) cc_final: 0.7869 (mt) REVERT: D 446 VAL cc_start: 0.8407 (p) cc_final: 0.7950 (t) REVERT: E 173 ILE cc_start: 0.8027 (pt) cc_final: 0.7386 (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: 0.8419 (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: 0.8561 (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: 0.8426 (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: 0.6249 (t) outliers start: 3 outliers final: 0 residues processed: 705 average time/residue: 0.1890 time to fit residues: 187.1148 Evaluate side-chains 471 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 471 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 20.0000 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 7.9990 chunk 107 optimal weight: 30.0000 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 8.9990 chunk 247 optimal weight: 30.0000 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 ASN ** B 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** E 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 435 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.086198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.068326 restraints weight = 63755.063| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 5.01 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.135 18732 Z= 0.249 Angle : 0.826 10.876 25458 Z= 0.422 Chirality : 0.052 0.300 3018 Planarity : 0.007 0.089 3366 Dihedral : 7.588 93.334 2866 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 5.19 % Allowed : 21.93 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.17), residues: 2520 helix: 1.33 (0.16), residues: 1074 sheet: -0.48 (0.25), residues: 416 loop : -0.70 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 303 TYR 0.020 0.003 TYR B 402 PHE 0.027 0.003 PHE C 364 TRP 0.019 0.004 TRP C 481 HIS 0.012 0.002 HIS C 319 Details of bonding type rmsd covalent geometry : bond 0.00572 (18732) covalent geometry : angle 0.82587 (25458) hydrogen bonds : bond 0.04388 ( 939) hydrogen bonds : angle 4.95652 ( 2733) *********************** 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 640 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 548 time to evaluate : 0.895 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: A 162 ASP cc_start: 0.4271 (p0) cc_final: 0.3967 (p0) REVERT: A 172 PHE cc_start: 0.8250 (m-80) cc_final: 0.7877 (m-80) REVERT: A 215 ASP cc_start: 0.7317 (p0) cc_final: 0.6722 (p0) REVERT: A 248 LEU cc_start: 0.6611 (OUTLIER) cc_final: 0.6409 (mt) REVERT: A 324 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.6216 (pm20) REVERT: A 343 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7739 (ttpp) REVERT: A 368 GLN cc_start: 0.7191 (mp10) cc_final: 0.6930 (mp10) REVERT: A 388 GLU cc_start: 0.7831 (tt0) cc_final: 0.7122 (tp30) REVERT: A 412 MET cc_start: 0.9197 (tpp) cc_final: 0.8831 (tmm) REVERT: A 482 ASP cc_start: 0.9280 (t0) cc_final: 0.8993 (p0) REVERT: B 164 MET cc_start: 0.6512 (mpp) cc_final: 0.6097 (mpp) REVERT: B 174 GLU cc_start: 0.7576 (tt0) cc_final: 0.7343 (tt0) REVERT: B 180 GLN cc_start: 0.8361 (mt0) cc_final: 0.8133 (mp10) REVERT: B 217 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.7019 (ttt180) REVERT: B 225 ASN cc_start: 0.7660 (t0) cc_final: 0.7077 (t0) REVERT: B 274 ARG cc_start: 0.6722 (mtt180) cc_final: 0.6476 (mmm-85) REVERT: B 450 GLN cc_start: 0.7744 (pt0) cc_final: 0.7470 (pm20) REVERT: C 148 TYR cc_start: 0.7548 (m-80) cc_final: 0.7264 (m-80) REVERT: C 223 ARG cc_start: 0.7812 (tpp80) cc_final: 0.7561 (tpp80) REVERT: C 270 ILE cc_start: 0.6760 (OUTLIER) cc_final: 0.6536 (tp) REVERT: C 299 ASP cc_start: 0.8239 (t0) cc_final: 0.7327 (t0) REVERT: C 319 HIS cc_start: 0.8046 (t-170) cc_final: 0.7702 (t-90) REVERT: C 355 VAL cc_start: 0.9044 (t) cc_final: 0.8798 (p) REVERT: C 396 MET cc_start: 0.8461 (mtm) cc_final: 0.7129 (mtt) REVERT: C 469 LYS cc_start: 0.8732 (mtmm) cc_final: 0.8245 (mtmm) REVERT: C 486 TYR cc_start: 0.8843 (t80) cc_final: 0.8621 (t80) REVERT: D 164 MET cc_start: 0.8420 (mtm) cc_final: 0.8172 (ttm) REVERT: D 243 PHE cc_start: 0.8647 (t80) cc_final: 0.8437 (t80) REVERT: D 247 LYS cc_start: 0.8896 (mmmt) cc_final: 0.8502 (mmtm) REVERT: D 324 GLU cc_start: 0.8372 (tt0) cc_final: 0.7253 (pt0) REVERT: D 343 LYS cc_start: 0.8767 (mtmm) cc_final: 0.8373 (mtmm) REVERT: D 345 CYS cc_start: 0.9055 (m) cc_final: 0.8663 (m) REVERT: D 378 MET cc_start: 0.7863 (mtm) cc_final: 0.7618 (mtm) REVERT: D 407 LYS cc_start: 0.8764 (mmmt) cc_final: 0.8550 (mmmt) REVERT: D 421 ILE cc_start: 0.8241 (mt) cc_final: 0.7986 (mt) REVERT: E 164 MET cc_start: 0.7724 (mtm) cc_final: 0.7389 (mtm) REVERT: E 173 ILE cc_start: 0.8431 (pt) cc_final: 0.8073 (pt) REVERT: E 175 VAL cc_start: 0.9179 (t) cc_final: 0.8731 (m) REVERT: E 180 GLN cc_start: 0.8671 (mt0) cc_final: 0.8429 (mp10) REVERT: E 208 ASP cc_start: 0.8984 (t0) cc_final: 0.8591 (m-30) REVERT: E 246 ASP cc_start: 0.8625 (p0) cc_final: 0.8424 (p0) REVERT: E 251 LYS cc_start: 0.9428 (mmmt) cc_final: 0.9187 (mmmt) REVERT: E 324 GLU cc_start: 0.6787 (tt0) cc_final: 0.6404 (tt0) REVERT: E 338 MET cc_start: 0.8608 (tpp) cc_final: 0.8176 (tpp) REVERT: E 341 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7908 (mm) REVERT: E 348 MET cc_start: 0.8312 (mtt) cc_final: 0.8086 (mtm) REVERT: E 437 THR cc_start: 0.7456 (OUTLIER) cc_final: 0.7134 (t) REVERT: F 164 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7750 (mtp) REVERT: F 172 PHE cc_start: 0.7957 (m-80) cc_final: 0.7649 (m-10) REVERT: F 194 ASN cc_start: 0.9693 (t0) cc_final: 0.9481 (t0) REVERT: F 202 GLN cc_start: 0.8708 (tm-30) cc_final: 0.8406 (tm-30) REVERT: F 227 ILE cc_start: 0.8177 (mm) cc_final: 0.7883 (mm) REVERT: F 345 CYS cc_start: 0.8080 (m) cc_final: 0.7779 (m) REVERT: F 388 GLU cc_start: 0.8859 (tt0) cc_final: 0.8526 (tt0) REVERT: F 399 MET cc_start: 0.8002 (ptp) cc_final: 0.7531 (ptp) REVERT: F 443 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7337 (mp0) outliers start: 92 outliers final: 41 residues processed: 590 average time/residue: 0.1619 time to fit residues: 140.6947 Evaluate side-chains 488 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 439 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 337 THR Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 217 ARG 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 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 B residue 497 LEU Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 202 GLN Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 411 GLU 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 199 ILE 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 377 SER Chi-restraints excluded: chain D residue 380 THR 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 341 LEU 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 164 MET 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 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 141 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 chunk 214 optimal weight: 3.9990 chunk 244 optimal weight: 8.9990 chunk 20 optimal weight: 30.0000 chunk 110 optimal weight: 1.9990 chunk 165 optimal weight: 40.0000 chunk 250 optimal weight: 7.9990 chunk 143 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 chunk 84 optimal weight: 90.0000 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 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN B 450 GLN C 374 HIS D 225 ASN D 368 GLN D 384 ASN ** E 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 189 ASN F 382 HIS F 435 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.084342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.066178 restraints weight = 65047.689| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 5.02 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.6030 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= 0.207 Angle : 0.781 11.949 25458 Z= 0.390 Chirality : 0.051 0.388 3018 Planarity : 0.006 0.080 3366 Dihedral : 7.430 80.375 2866 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 5.86 % Allowed : 23.56 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.17), residues: 2520 helix: 1.25 (0.16), residues: 1076 sheet: -0.90 (0.23), residues: 476 loop : -0.62 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 347 TYR 0.029 0.002 TYR D 402 PHE 0.024 0.002 PHE B 364 TRP 0.012 0.002 TRP F 481 HIS 0.009 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00460 (18732) covalent geometry : angle 0.78082 (25458) hydrogen bonds : bond 0.03881 ( 939) hydrogen bonds : angle 4.68586 ( 2733) *********************** 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 597 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 493 time to evaluate : 0.755 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: A 172 PHE cc_start: 0.8826 (m-80) cc_final: 0.8523 (m-80) REVERT: A 205 ARG cc_start: 0.8675 (ptp-110) cc_final: 0.8379 (ptp90) REVERT: A 250 MET cc_start: 0.7201 (pmm) cc_final: 0.6390 (mmm) REVERT: A 273 CYS cc_start: 0.6711 (t) cc_final: 0.6190 (p) REVERT: A 324 GLU cc_start: 0.7372 (pp20) cc_final: 0.6780 (pm20) REVERT: A 366 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8299 (tt) REVERT: A 443 GLU cc_start: 0.8963 (mp0) cc_final: 0.8759 (mp0) REVERT: B 174 GLU cc_start: 0.7760 (tt0) cc_final: 0.7325 (tt0) REVERT: B 180 GLN cc_start: 0.8589 (mt0) cc_final: 0.8335 (mp10) REVERT: B 233 LEU cc_start: 0.8869 (mt) cc_final: 0.7584 (mt) REVERT: B 270 ILE cc_start: 0.8139 (mm) cc_final: 0.7887 (mm) REVERT: B 274 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.7394 (mmm-85) REVERT: B 277 LEU cc_start: 0.6672 (OUTLIER) cc_final: 0.6432 (tt) REVERT: B 290 LEU cc_start: 0.8151 (tp) cc_final: 0.7894 (tp) REVERT: B 343 LYS cc_start: 0.8516 (mtmt) cc_final: 0.8154 (mtmt) REVERT: B 346 LEU cc_start: 0.9270 (mt) cc_final: 0.8964 (mm) REVERT: B 347 ARG cc_start: 0.8278 (mtm110) cc_final: 0.7668 (ptp-110) REVERT: B 378 MET cc_start: 0.7383 (OUTLIER) cc_final: 0.7145 (ptp) REVERT: B 410 LYS cc_start: 0.8483 (mmmt) cc_final: 0.8208 (mmmm) REVERT: B 450 GLN cc_start: 0.7717 (pt0) cc_final: 0.7339 (pm20) REVERT: C 186 PHE cc_start: 0.8059 (OUTLIER) cc_final: 0.7317 (t80) REVERT: C 225 ASN cc_start: 0.8368 (t0) cc_final: 0.7999 (t0) REVERT: C 239 THR cc_start: 0.8135 (p) cc_final: 0.7869 (p) REVERT: C 243 PHE cc_start: 0.7918 (t80) cc_final: 0.7689 (t80) REVERT: C 299 ASP cc_start: 0.8722 (t0) cc_final: 0.8397 (t0) REVERT: C 308 GLU cc_start: 0.8217 (pm20) cc_final: 0.7394 (pm20) REVERT: C 351 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8116 (mm-30) REVERT: C 355 VAL cc_start: 0.9461 (t) cc_final: 0.9259 (p) REVERT: C 396 MET cc_start: 0.8096 (mtm) cc_final: 0.7143 (mtm) REVERT: C 407 LYS cc_start: 0.8963 (mmmt) cc_final: 0.7866 (tppt) REVERT: C 411 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8647 (mp0) REVERT: C 445 ASP cc_start: 0.7901 (m-30) cc_final: 0.7588 (m-30) REVERT: D 164 MET cc_start: 0.8698 (mtm) cc_final: 0.8120 (ttm) REVERT: D 247 LYS cc_start: 0.9225 (mmmt) cc_final: 0.8927 (mmtm) REVERT: D 251 LYS cc_start: 0.9424 (ptmm) cc_final: 0.9178 (tmmt) REVERT: D 324 GLU cc_start: 0.8371 (tt0) cc_final: 0.7817 (tm-30) REVERT: D 345 CYS cc_start: 0.9220 (m) cc_final: 0.8826 (m) REVERT: D 351 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8096 (mm-30) REVERT: D 396 MET cc_start: 0.9145 (mtt) cc_final: 0.8738 (mmm) REVERT: D 421 ILE cc_start: 0.8766 (mt) cc_final: 0.8524 (mt) REVERT: E 158 ASP cc_start: 0.9013 (t0) cc_final: 0.8812 (t0) REVERT: E 164 MET cc_start: 0.8402 (mtm) cc_final: 0.7706 (mtm) REVERT: E 173 ILE cc_start: 0.8680 (pt) cc_final: 0.8346 (pt) REVERT: E 175 VAL cc_start: 0.9321 (t) cc_final: 0.8861 (m) REVERT: E 178 LYS cc_start: 0.8945 (mmmt) cc_final: 0.8433 (mmmt) REVERT: E 208 ASP cc_start: 0.8966 (t0) cc_final: 0.8491 (m-30) REVERT: E 256 PHE cc_start: 0.8607 (m-10) cc_final: 0.8338 (m-10) REVERT: E 324 GLU cc_start: 0.7089 (tt0) cc_final: 0.6675 (tt0) REVERT: E 338 MET cc_start: 0.8794 (tpp) cc_final: 0.8470 (tpp) REVERT: E 341 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8148 (mm) REVERT: E 348 MET cc_start: 0.8648 (mtt) cc_final: 0.8257 (mtp) REVERT: E 399 MET cc_start: 0.8861 (ttp) cc_final: 0.8595 (tmm) REVERT: E 410 LYS cc_start: 0.9241 (mttt) cc_final: 0.8852 (mttm) REVERT: E 492 GLU cc_start: 0.9203 (mm-30) cc_final: 0.8940 (tp30) REVERT: F 202 GLN cc_start: 0.8980 (tm-30) cc_final: 0.8676 (tm-30) REVERT: F 250 MET cc_start: 0.7584 (mmm) cc_final: 0.7355 (mmm) REVERT: F 251 LYS cc_start: 0.9241 (mppt) cc_final: 0.9008 (mtmm) REVERT: F 275 CYS cc_start: 0.8022 (m) cc_final: 0.7577 (m) REVERT: F 316 GLN cc_start: 0.7967 (pm20) cc_final: 0.7736 (pm20) REVERT: F 317 GLN cc_start: 0.6783 (mm110) cc_final: 0.6111 (mm-40) REVERT: F 399 MET cc_start: 0.8675 (ptp) cc_final: 0.8155 (ptp) REVERT: F 491 ARG cc_start: 0.9338 (ptp90) cc_final: 0.9032 (ptp90) outliers start: 104 outliers final: 49 residues processed: 544 average time/residue: 0.1345 time to fit residues: 109.3284 Evaluate side-chains 481 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 425 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 245 LYS Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 388 GLU 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 199 ILE Chi-restraints excluded: chain C residue 202 GLN Chi-restraints excluded: chain C residue 288 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 D residue 199 ILE Chi-restraints excluded: chain D residue 306 THR 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 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 D residue 472 SER Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 275 CYS Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 160 ILE Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 244 LYS Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain F residue 419 VAL 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 118 optimal weight: 5.9990 chunk 246 optimal weight: 20.0000 chunk 119 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 46 optimal weight: 30.0000 chunk 175 optimal weight: 20.0000 chunk 216 optimal weight: 50.0000 chunk 169 optimal weight: 0.0050 chunk 76 optimal weight: 30.0000 chunk 178 optimal weight: 20.0000 overall best weight: 6.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 ASN ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 GLN ** D 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 GLN ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 317 GLN F 344 ASN F 374 HIS F 435 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.082773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.064589 restraints weight = 65152.308| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 5.00 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.7138 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= 0.196 Angle : 0.752 11.723 25458 Z= 0.373 Chirality : 0.049 0.346 3018 Planarity : 0.006 0.063 3366 Dihedral : 7.189 78.204 2866 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 5.47 % Allowed : 26.55 % Favored : 67.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.17), residues: 2520 helix: 1.28 (0.16), residues: 1090 sheet: -0.76 (0.23), residues: 460 loop : -0.70 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG E 491 TYR 0.043 0.002 TYR D 402 PHE 0.021 0.002 PHE F 243 TRP 0.014 0.001 TRP C 481 HIS 0.021 0.001 HIS F 435 Details of bonding type rmsd covalent geometry : bond 0.00447 (18732) covalent geometry : angle 0.75190 (25458) hydrogen bonds : bond 0.03432 ( 939) hydrogen bonds : angle 4.54771 ( 2733) *********************** 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 534 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 437 time to evaluate : 0.711 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: A 172 PHE cc_start: 0.8911 (m-80) cc_final: 0.8690 (m-80) REVERT: A 182 THR cc_start: 0.8138 (OUTLIER) cc_final: 0.7937 (t) REVERT: A 205 ARG cc_start: 0.8708 (ptp-110) cc_final: 0.8385 (ptp90) REVERT: A 245 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8805 (mptt) REVERT: A 250 MET cc_start: 0.7460 (pmm) cc_final: 0.6685 (mmm) REVERT: A 349 ARG cc_start: 0.8042 (ptm-80) cc_final: 0.7747 (ptm-80) REVERT: A 351 GLU cc_start: 0.8497 (mp0) cc_final: 0.7734 (mp0) REVERT: A 368 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7879 (mp10) REVERT: A 388 GLU cc_start: 0.8923 (tt0) cc_final: 0.7783 (tp30) REVERT: A 443 GLU cc_start: 0.9050 (mp0) cc_final: 0.8802 (mp0) REVERT: B 174 GLU cc_start: 0.8141 (tt0) cc_final: 0.7590 (tt0) REVERT: B 180 GLN cc_start: 0.8696 (mt0) cc_final: 0.8275 (mp10) REVERT: B 202 GLN cc_start: 0.9111 (mm-40) cc_final: 0.8688 (mp10) REVERT: B 339 ARG cc_start: 0.8501 (ttp80) cc_final: 0.8051 (ttp80) REVERT: B 343 LYS cc_start: 0.8719 (mtmt) cc_final: 0.8262 (mtmm) REVERT: B 347 ARG cc_start: 0.8254 (mtm110) cc_final: 0.7939 (mtm110) REVERT: B 378 MET cc_start: 0.7524 (OUTLIER) cc_final: 0.7136 (ptp) REVERT: B 410 LYS cc_start: 0.8587 (mmmt) cc_final: 0.8309 (mmmm) REVERT: B 414 VAL cc_start: 0.8968 (t) cc_final: 0.8733 (p) REVERT: B 450 GLN cc_start: 0.7744 (pt0) cc_final: 0.7319 (pm20) REVERT: C 239 THR cc_start: 0.8555 (p) cc_final: 0.8242 (p) REVERT: C 303 ARG cc_start: 0.8981 (OUTLIER) cc_final: 0.8217 (ttt90) REVERT: C 345 CYS cc_start: 0.9365 (m) cc_final: 0.9053 (m) REVERT: C 396 MET cc_start: 0.8547 (mtm) cc_final: 0.7608 (mtm) REVERT: C 407 LYS cc_start: 0.8976 (mmmt) cc_final: 0.8239 (tppt) REVERT: C 445 ASP cc_start: 0.7956 (m-30) cc_final: 0.7550 (m-30) REVERT: D 164 MET cc_start: 0.8641 (mtm) cc_final: 0.7698 (ttm) REVERT: D 244 LYS cc_start: 0.9571 (mmmm) cc_final: 0.9354 (mmmm) REVERT: D 247 LYS cc_start: 0.9307 (mmmt) cc_final: 0.8927 (mmtm) REVERT: D 341 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8013 (mp) REVERT: D 345 CYS cc_start: 0.9282 (m) cc_final: 0.8794 (m) REVERT: D 351 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8281 (mm-30) REVERT: D 407 LYS cc_start: 0.8906 (mmmt) cc_final: 0.8575 (mmmt) REVERT: D 421 ILE cc_start: 0.8942 (mt) cc_final: 0.8689 (mt) REVERT: E 158 ASP cc_start: 0.9129 (t0) cc_final: 0.8900 (t0) REVERT: E 164 MET cc_start: 0.8630 (mtm) cc_final: 0.7845 (mtm) REVERT: E 208 ASP cc_start: 0.9011 (t0) cc_final: 0.8561 (m-30) REVERT: E 243 PHE cc_start: 0.8467 (t80) cc_final: 0.8023 (t80) REVERT: E 314 GLN cc_start: 0.8919 (tt0) cc_final: 0.8685 (tp-100) REVERT: E 324 GLU cc_start: 0.7351 (tt0) cc_final: 0.7073 (tt0) REVERT: E 338 MET cc_start: 0.8857 (tpp) cc_final: 0.8542 (tpp) REVERT: E 346 LEU cc_start: 0.9408 (tt) cc_final: 0.9110 (tp) REVERT: E 396 MET cc_start: 0.9056 (ttp) cc_final: 0.8743 (tpp) REVERT: E 399 MET cc_start: 0.8839 (ttp) cc_final: 0.8525 (tmm) REVERT: E 402 TYR cc_start: 0.7637 (m-80) cc_final: 0.7367 (m-80) REVERT: E 410 LYS cc_start: 0.9279 (mttt) cc_final: 0.8884 (mttm) REVERT: E 437 THR cc_start: 0.7645 (OUTLIER) cc_final: 0.7326 (t) REVERT: E 492 GLU cc_start: 0.9244 (mm-30) cc_final: 0.8746 (tp30) REVERT: F 202 GLN cc_start: 0.9070 (tm-30) cc_final: 0.8767 (tm-30) REVERT: F 251 LYS cc_start: 0.9308 (mppt) cc_final: 0.9101 (mtmm) REVERT: F 275 CYS cc_start: 0.8525 (m) cc_final: 0.7870 (m) REVERT: F 343 LYS cc_start: 0.8920 (ttpt) cc_final: 0.8615 (ttpt) REVERT: F 365 ASP cc_start: 0.9193 (t70) cc_final: 0.8645 (t0) REVERT: F 399 MET cc_start: 0.8871 (ptp) cc_final: 0.8314 (ptp) REVERT: F 451 ASP cc_start: 0.7869 (m-30) cc_final: 0.6670 (t0) outliers start: 97 outliers final: 58 residues processed: 485 average time/residue: 0.1336 time to fit residues: 98.1101 Evaluate side-chains 468 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 403 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 200 VAL 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 248 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 368 GLN Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 202 GLN 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 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 171 VAL Chi-restraints excluded: chain D residue 196 CYS Chi-restraints excluded: chain D residue 199 ILE 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 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 367 LEU Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 393 ILE Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain F residue 160 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 293 THR Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 397 ILE Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain F residue 448 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 95 optimal weight: 20.0000 chunk 39 optimal weight: 7.9990 chunk 127 optimal weight: 7.9990 chunk 159 optimal weight: 0.9980 chunk 220 optimal weight: 20.0000 chunk 219 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 140 optimal weight: 7.9990 chunk 65 optimal weight: 20.0000 chunk 108 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 470 HIS ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 GLN D 368 GLN ** D 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** 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 = 0.3632 r_free = 0.3632 target = 0.082280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.064481 restraints weight = 64321.353| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 4.95 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.8072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 18732 Z= 0.185 Angle : 0.728 9.717 25458 Z= 0.359 Chirality : 0.049 0.338 3018 Planarity : 0.005 0.043 3366 Dihedral : 6.974 69.778 2866 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 5.41 % Allowed : 26.72 % Favored : 67.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.17), residues: 2520 helix: 1.27 (0.16), residues: 1094 sheet: -0.76 (0.24), residues: 446 loop : -0.77 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 265 TYR 0.030 0.002 TYR D 402 PHE 0.017 0.002 PHE D 243 TRP 0.007 0.001 TRP C 481 HIS 0.008 0.001 HIS F 435 Details of bonding type rmsd covalent geometry : bond 0.00436 (18732) covalent geometry : angle 0.72835 (25458) hydrogen bonds : bond 0.03355 ( 939) hydrogen bonds : angle 4.52427 ( 2733) *********************** 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 523 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 427 time to evaluate : 0.754 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: A 172 PHE cc_start: 0.9049 (m-80) cc_final: 0.8818 (m-80) REVERT: A 193 MET cc_start: 0.8659 (tpt) cc_final: 0.7888 (tpp) REVERT: A 250 MET cc_start: 0.7604 (pmm) cc_final: 0.7151 (mmm) REVERT: A 349 ARG cc_start: 0.8456 (ptm-80) cc_final: 0.8227 (ptm-80) REVERT: A 351 GLU cc_start: 0.8689 (mp0) cc_final: 0.8122 (mp0) REVERT: A 384 ASN cc_start: 0.8922 (m-40) cc_final: 0.8647 (m-40) REVERT: A 387 ARG cc_start: 0.8660 (mmm160) cc_final: 0.8369 (mmm160) REVERT: B 174 GLU cc_start: 0.8377 (tt0) cc_final: 0.7741 (tt0) REVERT: B 180 GLN cc_start: 0.8841 (mt0) cc_final: 0.8492 (mp10) REVERT: B 239 THR cc_start: 0.9119 (m) cc_final: 0.8715 (p) REVERT: B 278 VAL cc_start: 0.8109 (t) cc_final: 0.7790 (t) REVERT: B 324 GLU cc_start: 0.8046 (tt0) cc_final: 0.7690 (tp30) REVERT: B 347 ARG cc_start: 0.8307 (mtm110) cc_final: 0.7555 (mtm110) REVERT: B 381 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7779 (tp) REVERT: B 410 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8340 (mmmm) REVERT: B 417 VAL cc_start: 0.7410 (OUTLIER) cc_final: 0.7109 (p) REVERT: B 420 ILE cc_start: 0.8469 (mt) cc_final: 0.8192 (tp) REVERT: B 450 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7722 (pm20) REVERT: B 479 ARG cc_start: 0.7744 (ptm160) cc_final: 0.7262 (ttt180) REVERT: C 345 CYS cc_start: 0.9373 (m) cc_final: 0.9022 (m) REVERT: C 370 MET cc_start: 0.9361 (mtt) cc_final: 0.8664 (mtt) REVERT: C 396 MET cc_start: 0.8870 (mtm) cc_final: 0.8094 (mtm) REVERT: C 407 LYS cc_start: 0.9005 (mmmt) cc_final: 0.7927 (tppt) REVERT: C 411 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8669 (mp0) REVERT: C 477 ARG cc_start: 0.8555 (mmm-85) cc_final: 0.8208 (mmm-85) REVERT: D 205 ARG cc_start: 0.9145 (mtp-110) cc_final: 0.8919 (mtp-110) REVERT: D 243 PHE cc_start: 0.8812 (t80) cc_final: 0.8605 (t80) REVERT: D 247 LYS cc_start: 0.9344 (mmmt) cc_final: 0.9055 (mmtm) REVERT: D 351 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8345 (mm-30) REVERT: D 368 GLN cc_start: 0.9131 (OUTLIER) cc_final: 0.8597 (mp10) REVERT: D 396 MET cc_start: 0.9301 (mtt) cc_final: 0.8937 (mtt) REVERT: D 407 LYS cc_start: 0.8937 (mmmt) cc_final: 0.8670 (tppt) REVERT: D 421 ILE cc_start: 0.9010 (mt) cc_final: 0.8783 (mt) REVERT: D 426 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8591 (mm) REVERT: D 450 GLN cc_start: 0.8414 (pm20) cc_final: 0.7997 (pm20) REVERT: E 164 MET cc_start: 0.8731 (mtm) cc_final: 0.7814 (mtm) REVERT: E 208 ASP cc_start: 0.9058 (t0) cc_final: 0.8553 (m-30) REVERT: E 314 GLN cc_start: 0.8993 (tt0) cc_final: 0.8743 (tp-100) REVERT: E 348 MET cc_start: 0.9056 (mtp) cc_final: 0.8282 (mpp) REVERT: E 396 MET cc_start: 0.9046 (ttp) cc_final: 0.8678 (tpp) REVERT: E 399 MET cc_start: 0.8981 (ttp) cc_final: 0.8545 (tmm) REVERT: E 437 THR cc_start: 0.7763 (OUTLIER) cc_final: 0.7500 (t) REVERT: E 492 GLU cc_start: 0.9209 (mm-30) cc_final: 0.8763 (tp30) REVERT: F 148 TYR cc_start: 0.8497 (m-80) cc_final: 0.8203 (m-80) REVERT: F 202 GLN cc_start: 0.9109 (tm-30) cc_final: 0.8772 (tm-30) REVERT: F 246 ASP cc_start: 0.9251 (m-30) cc_final: 0.8815 (t0) REVERT: F 250 MET cc_start: 0.8079 (mmm) cc_final: 0.7776 (mmm) REVERT: F 251 LYS cc_start: 0.9354 (mppt) cc_final: 0.8712 (mtmm) REVERT: F 275 CYS cc_start: 0.8748 (m) cc_final: 0.8332 (m) REVERT: F 343 LYS cc_start: 0.9106 (ttpt) cc_final: 0.8824 (ttpt) REVERT: F 365 ASP cc_start: 0.9178 (t70) cc_final: 0.8527 (t0) REVERT: F 368 GLN cc_start: 0.8667 (tp40) cc_final: 0.8449 (tp40) REVERT: F 399 MET cc_start: 0.8930 (ptp) cc_final: 0.8351 (ptp) REVERT: F 451 ASP cc_start: 0.8111 (m-30) cc_final: 0.6714 (t0) outliers start: 96 outliers final: 51 residues processed: 483 average time/residue: 0.1347 time to fit residues: 99.4652 Evaluate side-chains 429 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 370 time to evaluate : 0.732 ------------------------------------------------------------------------------- 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 199 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain B residue 266 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 410 LYS Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 450 GLN 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 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 171 VAL Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 196 CYS Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 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 426 LEU 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 295 THR Chi-restraints excluded: chain E residue 307 CYS Chi-restraints excluded: chain E residue 367 LEU 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 160 ILE Chi-restraints excluded: chain F residue 180 GLN Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 397 ILE Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain F residue 434 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 233 optimal weight: 20.0000 chunk 167 optimal weight: 5.9990 chunk 222 optimal weight: 0.5980 chunk 31 optimal weight: 8.9990 chunk 42 optimal weight: 100.0000 chunk 147 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 166 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 234 optimal weight: 10.0000 chunk 196 optimal weight: 8.9990 overall best weight: 5.7188 ------------------------------------------------------------------------------- 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** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 ASN D 368 GLN ** D 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 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 = 0.3615 r_free = 0.3615 target = 0.081154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.063467 restraints weight = 64406.411| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 4.93 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.8747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 18732 Z= 0.181 Angle : 0.712 11.330 25458 Z= 0.350 Chirality : 0.048 0.313 3018 Planarity : 0.005 0.059 3366 Dihedral : 6.783 69.331 2866 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.79 % Allowed : 28.07 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.17), residues: 2520 helix: 1.31 (0.16), residues: 1092 sheet: -0.68 (0.24), residues: 444 loop : -0.77 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 339 TYR 0.014 0.002 TYR C 402 PHE 0.022 0.002 PHE F 243 TRP 0.007 0.001 TRP C 481 HIS 0.005 0.001 HIS F 382 Details of bonding type rmsd covalent geometry : bond 0.00427 (18732) covalent geometry : angle 0.71214 (25458) hydrogen bonds : bond 0.03220 ( 939) hydrogen bonds : angle 4.47705 ( 2733) *********************** 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 471 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 386 time to evaluate : 0.749 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: A 193 MET cc_start: 0.8808 (tpt) cc_final: 0.8061 (tpp) REVERT: A 250 MET cc_start: 0.7619 (pmm) cc_final: 0.7271 (tmm) REVERT: A 351 GLU cc_start: 0.8729 (mp0) cc_final: 0.8370 (mp0) REVERT: B 174 GLU cc_start: 0.8439 (tt0) cc_final: 0.7716 (tp30) REVERT: B 180 GLN cc_start: 0.8888 (mt0) cc_final: 0.8487 (mp10) REVERT: B 202 GLN cc_start: 0.9415 (OUTLIER) cc_final: 0.9151 (mp10) REVERT: B 238 LEU cc_start: 0.9113 (tp) cc_final: 0.8642 (mp) REVERT: B 247 LYS cc_start: 0.8079 (mmtm) cc_final: 0.7521 (mmmt) REVERT: B 278 VAL cc_start: 0.8349 (t) cc_final: 0.8006 (t) REVERT: B 290 LEU cc_start: 0.8794 (tp) cc_final: 0.8551 (tp) REVERT: B 323 LEU cc_start: 0.9120 (mp) cc_final: 0.8916 (mp) REVERT: B 324 GLU cc_start: 0.8256 (tt0) cc_final: 0.7941 (tp30) REVERT: B 343 LYS cc_start: 0.8843 (mtpt) cc_final: 0.7880 (mtmm) REVERT: B 347 ARG cc_start: 0.8358 (mtm110) cc_final: 0.7554 (mtm-85) REVERT: B 377 SER cc_start: 0.8391 (t) cc_final: 0.7601 (p) REVERT: B 410 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.7696 (mmmm) REVERT: B 420 ILE cc_start: 0.8581 (mt) cc_final: 0.8362 (tp) REVERT: B 437 THR cc_start: 0.8636 (p) cc_final: 0.8166 (t) REVERT: B 450 GLN cc_start: 0.8111 (pt0) cc_final: 0.7832 (pm20) REVERT: C 315 LEU cc_start: 0.8962 (mt) cc_final: 0.8569 (mt) REVERT: C 345 CYS cc_start: 0.9333 (m) cc_final: 0.8949 (m) REVERT: C 370 MET cc_start: 0.9372 (mtt) cc_final: 0.8655 (mtt) REVERT: C 396 MET cc_start: 0.9015 (mtm) cc_final: 0.8493 (mtm) REVERT: D 351 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8010 (mp0) REVERT: D 364 PHE cc_start: 0.8939 (t80) cc_final: 0.8157 (t80) REVERT: D 368 GLN cc_start: 0.9036 (OUTLIER) cc_final: 0.8350 (mp10) REVERT: D 378 MET cc_start: 0.8390 (mtt) cc_final: 0.8164 (mtt) REVERT: D 407 LYS cc_start: 0.9161 (mmmt) cc_final: 0.8625 (tppt) REVERT: D 411 GLU cc_start: 0.9219 (mt-10) cc_final: 0.8870 (mp0) REVERT: D 421 ILE cc_start: 0.9040 (mt) cc_final: 0.8774 (mt) REVERT: D 450 GLN cc_start: 0.8430 (pm20) cc_final: 0.8144 (pm20) REVERT: E 164 MET cc_start: 0.8810 (mtm) cc_final: 0.7884 (mtm) REVERT: E 208 ASP cc_start: 0.9061 (t0) cc_final: 0.8505 (m-30) REVERT: E 314 GLN cc_start: 0.9094 (tt0) cc_final: 0.8791 (tp-100) REVERT: E 396 MET cc_start: 0.9012 (ttp) cc_final: 0.8717 (tpp) REVERT: E 399 MET cc_start: 0.8994 (ttp) cc_final: 0.8675 (tmm) REVERT: E 437 THR cc_start: 0.7764 (OUTLIER) cc_final: 0.7504 (t) REVERT: E 452 LEU cc_start: 0.9243 (tp) cc_final: 0.9002 (mp) REVERT: E 492 GLU cc_start: 0.9227 (mm-30) cc_final: 0.8776 (tp30) REVERT: F 148 TYR cc_start: 0.8517 (m-80) cc_final: 0.8258 (m-80) REVERT: F 202 GLN cc_start: 0.9145 (tm-30) cc_final: 0.8803 (tm-30) REVERT: F 220 ASP cc_start: 0.9031 (m-30) cc_final: 0.8771 (t0) REVERT: F 246 ASP cc_start: 0.9108 (m-30) cc_final: 0.8834 (t0) REVERT: F 275 CYS cc_start: 0.8931 (m) cc_final: 0.8633 (m) REVERT: F 343 LYS cc_start: 0.9235 (ttpt) cc_final: 0.8975 (ttpt) REVERT: F 365 ASP cc_start: 0.9196 (t70) cc_final: 0.8561 (t0) REVERT: F 396 MET cc_start: 0.7689 (ttt) cc_final: 0.7178 (ttt) REVERT: F 399 MET cc_start: 0.9028 (ptp) cc_final: 0.8455 (ptp) REVERT: F 410 LYS cc_start: 0.8449 (mttp) cc_final: 0.8152 (mtpt) outliers start: 85 outliers final: 57 residues processed: 442 average time/residue: 0.1473 time to fit residues: 98.8140 Evaluate side-chains 417 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 356 time to evaluate : 0.727 ------------------------------------------------------------------------------- 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 200 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 454 VAL 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 410 LYS Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain C residue 199 ILE 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 378 MET 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 469 LYS Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 196 CYS Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 320 VAL 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 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 295 THR Chi-restraints excluded: chain E residue 307 CYS Chi-restraints excluded: chain E residue 367 LEU 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 239 THR Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 307 CYS Chi-restraints excluded: chain F residue 397 ILE Chi-restraints excluded: chain F residue 398 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 57 optimal weight: 7.9990 chunk 216 optimal weight: 3.9990 chunk 220 optimal weight: 4.9990 chunk 205 optimal weight: 20.0000 chunk 107 optimal weight: 30.0000 chunk 43 optimal weight: 50.0000 chunk 251 optimal weight: 7.9990 chunk 120 optimal weight: 4.9990 chunk 204 optimal weight: 20.0000 chunk 134 optimal weight: 7.9990 chunk 96 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 319 HIS ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN D 292 ASN D 314 GLN ** D 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.079297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.061080 restraints weight = 65315.419| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 4.95 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.9497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 18732 Z= 0.182 Angle : 0.728 13.480 25458 Z= 0.358 Chirality : 0.048 0.292 3018 Planarity : 0.005 0.059 3366 Dihedral : 6.643 65.897 2866 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.45 % Allowed : 28.69 % Favored : 66.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.17), residues: 2520 helix: 1.24 (0.16), residues: 1098 sheet: -0.68 (0.23), residues: 458 loop : -0.76 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 491 TYR 0.012 0.002 TYR B 486 PHE 0.028 0.002 PHE A 172 TRP 0.004 0.001 TRP C 481 HIS 0.006 0.001 HIS A 382 Details of bonding type rmsd covalent geometry : bond 0.00426 (18732) covalent geometry : angle 0.72804 (25458) hydrogen bonds : bond 0.03314 ( 939) hydrogen bonds : angle 4.49836 ( 2733) *********************** 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 454 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 375 time to evaluate : 0.792 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: A 193 MET cc_start: 0.8911 (tpt) cc_final: 0.8237 (tpp) REVERT: A 351 GLU cc_start: 0.8753 (mp0) cc_final: 0.8311 (mp0) REVERT: A 384 ASN cc_start: 0.9354 (m-40) cc_final: 0.9105 (m-40) REVERT: B 174 GLU cc_start: 0.8427 (tt0) cc_final: 0.7857 (tp30) REVERT: B 178 LYS cc_start: 0.8904 (ptmm) cc_final: 0.7987 (ptmm) REVERT: B 202 GLN cc_start: 0.9363 (OUTLIER) cc_final: 0.9003 (mp10) REVERT: B 238 LEU cc_start: 0.9250 (tp) cc_final: 0.8796 (mp) REVERT: B 247 LYS cc_start: 0.8311 (mmtm) cc_final: 0.7771 (mmmt) REVERT: B 290 LEU cc_start: 0.8913 (tp) cc_final: 0.8707 (tp) REVERT: B 314 GLN cc_start: 0.8891 (tt0) cc_final: 0.8538 (tm-30) REVERT: B 339 ARG cc_start: 0.8734 (ttp80) cc_final: 0.8357 (ptm-80) REVERT: B 347 ARG cc_start: 0.8382 (mtm110) cc_final: 0.7576 (mtm-85) REVERT: B 371 ASN cc_start: 0.8576 (t0) cc_final: 0.8330 (t0) REVERT: B 410 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.8161 (mmmm) REVERT: B 420 ILE cc_start: 0.8449 (mt) cc_final: 0.8222 (tp) REVERT: B 450 GLN cc_start: 0.8240 (pt0) cc_final: 0.7783 (pm20) REVERT: C 345 CYS cc_start: 0.9322 (m) cc_final: 0.8924 (m) REVERT: C 370 MET cc_start: 0.9398 (mtt) cc_final: 0.8678 (mtt) REVERT: C 396 MET cc_start: 0.9117 (mtm) cc_final: 0.8875 (mtm) REVERT: C 450 GLN cc_start: 0.7620 (tm-30) cc_final: 0.7015 (tm-30) REVERT: D 164 MET cc_start: 0.8978 (mtm) cc_final: 0.8401 (mtm) REVERT: D 243 PHE cc_start: 0.8881 (t80) cc_final: 0.8513 (t80) REVERT: D 244 LYS cc_start: 0.9592 (mmmm) cc_final: 0.9366 (mmmm) REVERT: D 306 THR cc_start: 0.8979 (OUTLIER) cc_final: 0.8771 (t) REVERT: D 351 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8108 (mp0) REVERT: D 370 MET cc_start: 0.8083 (mtp) cc_final: 0.7517 (mtp) REVERT: D 407 LYS cc_start: 0.9233 (mmmt) cc_final: 0.9031 (tppt) REVERT: D 450 GLN cc_start: 0.8575 (pm20) cc_final: 0.8323 (pm20) REVERT: E 164 MET cc_start: 0.8840 (mtm) cc_final: 0.7944 (mtm) REVERT: E 206 ARG cc_start: 0.7737 (ptm160) cc_final: 0.6954 (ttp80) REVERT: E 314 GLN cc_start: 0.9129 (tt0) cc_final: 0.8879 (tp-100) REVERT: E 324 GLU cc_start: 0.8270 (tt0) cc_final: 0.7782 (tp30) REVERT: E 348 MET cc_start: 0.9126 (mtp) cc_final: 0.8705 (mtm) REVERT: E 396 MET cc_start: 0.9071 (ttp) cc_final: 0.8652 (tpp) REVERT: E 399 MET cc_start: 0.9093 (ttp) cc_final: 0.8737 (tmm) REVERT: E 437 THR cc_start: 0.7879 (OUTLIER) cc_final: 0.7633 (t) REVERT: E 452 LEU cc_start: 0.9278 (tp) cc_final: 0.9036 (mp) REVERT: E 492 GLU cc_start: 0.9235 (mm-30) cc_final: 0.8769 (tp30) REVERT: F 202 GLN cc_start: 0.9167 (tm-30) cc_final: 0.8817 (tm-30) REVERT: F 242 LYS cc_start: 0.9180 (mtpt) cc_final: 0.8624 (mtmm) REVERT: F 246 ASP cc_start: 0.9170 (m-30) cc_final: 0.8908 (t0) REVERT: F 275 CYS cc_start: 0.9008 (m) cc_final: 0.8771 (m) REVERT: F 299 ASP cc_start: 0.8785 (t0) cc_final: 0.8396 (t0) REVERT: F 343 LYS cc_start: 0.9311 (ttpt) cc_final: 0.9025 (ttpt) REVERT: F 357 GLU cc_start: 0.8184 (tt0) cc_final: 0.7516 (tp30) REVERT: F 365 ASP cc_start: 0.9157 (t70) cc_final: 0.8547 (t0) REVERT: F 396 MET cc_start: 0.7828 (ttt) cc_final: 0.7119 (ttt) REVERT: F 399 MET cc_start: 0.9019 (ptp) cc_final: 0.8443 (ptp) outliers start: 79 outliers final: 60 residues processed: 423 average time/residue: 0.1477 time to fit residues: 94.4410 Evaluate side-chains 404 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 340 time to evaluate : 0.771 ------------------------------------------------------------------------------- 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 200 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 368 GLN Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 497 LEU 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 368 GLN Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 463 HIS Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 378 MET 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 190 LEU Chi-restraints excluded: chain D residue 196 CYS Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 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 393 ILE 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 239 THR Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 397 ILE Chi-restraints excluded: chain F residue 398 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 38 optimal weight: 10.0000 chunk 213 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 177 optimal weight: 5.9990 chunk 118 optimal weight: 30.0000 chunk 69 optimal weight: 0.0170 chunk 179 optimal weight: 8.9990 chunk 86 optimal weight: 3.9990 chunk 249 optimal weight: 4.9990 overall best weight: 3.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN ** C 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN D 292 ASN D 368 GLN E 202 GLN ** E 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.080757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.062589 restraints weight = 64904.187| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 4.95 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.9787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 18732 Z= 0.151 Angle : 0.729 13.489 25458 Z= 0.359 Chirality : 0.048 0.280 3018 Planarity : 0.005 0.051 3366 Dihedral : 6.471 64.039 2866 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.83 % Allowed : 29.76 % Favored : 66.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.17), residues: 2520 helix: 1.25 (0.16), residues: 1096 sheet: -0.54 (0.24), residues: 436 loop : -0.84 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 205 TYR 0.013 0.001 TYR A 402 PHE 0.044 0.002 PHE A 364 TRP 0.006 0.001 TRP C 481 HIS 0.005 0.001 HIS F 382 Details of bonding type rmsd covalent geometry : bond 0.00361 (18732) covalent geometry : angle 0.72915 (25458) hydrogen bonds : bond 0.03170 ( 939) hydrogen bonds : angle 4.47104 ( 2733) *********************** 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 444 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 376 time to evaluate : 0.710 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: 0.8913 (tpt) cc_final: 0.8258 (tpp) REVERT: A 351 GLU cc_start: 0.8750 (mp0) cc_final: 0.8346 (mp0) REVERT: B 174 GLU cc_start: 0.8484 (tt0) cc_final: 0.7909 (tp30) REVERT: B 178 LYS cc_start: 0.8669 (ptmm) cc_final: 0.8215 (pptt) REVERT: B 202 GLN cc_start: 0.9348 (OUTLIER) cc_final: 0.8983 (mp10) REVERT: B 217 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7835 (tpt-90) REVERT: B 238 LEU cc_start: 0.9282 (tp) cc_final: 0.8817 (mp) REVERT: B 247 LYS cc_start: 0.8378 (mmtm) cc_final: 0.7786 (mmmt) REVERT: B 314 GLN cc_start: 0.8927 (tt0) cc_final: 0.8550 (tm-30) REVERT: B 339 ARG cc_start: 0.8762 (ttp80) cc_final: 0.8409 (ptm-80) REVERT: B 347 ARG cc_start: 0.8367 (mtm110) cc_final: 0.7408 (mtm-85) REVERT: B 351 GLU cc_start: 0.8645 (mp0) cc_final: 0.8288 (mp0) REVERT: B 377 SER cc_start: 0.8542 (t) cc_final: 0.8057 (p) REVERT: B 410 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8218 (mmmm) REVERT: B 450 GLN cc_start: 0.8283 (pt0) cc_final: 0.7827 (pm20) REVERT: C 245 LYS cc_start: 0.9204 (mmtm) cc_final: 0.9003 (mmmt) REVERT: C 251 LYS cc_start: 0.9364 (ttpp) cc_final: 0.9076 (pttm) REVERT: D 164 MET cc_start: 0.8985 (mtm) cc_final: 0.8687 (mtm) REVERT: D 180 GLN cc_start: 0.8137 (tm-30) cc_final: 0.7741 (tm-30) REVERT: D 306 THR cc_start: 0.8992 (m) cc_final: 0.8777 (t) REVERT: D 351 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8077 (mp0) REVERT: D 368 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8317 (mp10) REVERT: D 396 MET cc_start: 0.9370 (mtt) cc_final: 0.8882 (mmm) REVERT: D 399 MET cc_start: 0.8898 (tmm) cc_final: 0.8584 (ppp) REVERT: D 407 LYS cc_start: 0.9241 (mmmt) cc_final: 0.9013 (tppt) REVERT: D 440 VAL cc_start: 0.7795 (OUTLIER) cc_final: 0.7581 (m) REVERT: E 164 MET cc_start: 0.8774 (mtm) cc_final: 0.7937 (mtm) REVERT: E 202 GLN cc_start: 0.9401 (OUTLIER) cc_final: 0.9151 (pp30) REVERT: E 314 GLN cc_start: 0.9156 (tt0) cc_final: 0.8912 (tp-100) REVERT: E 324 GLU cc_start: 0.8198 (tt0) cc_final: 0.7700 (tp30) REVERT: E 347 ARG cc_start: 0.9366 (tpp80) cc_final: 0.9034 (tpp80) REVERT: E 348 MET cc_start: 0.9121 (mtp) cc_final: 0.8685 (mtm) REVERT: E 399 MET cc_start: 0.9080 (ttp) cc_final: 0.8846 (tmm) REVERT: E 450 GLN cc_start: 0.8696 (pt0) cc_final: 0.8485 (mp10) REVERT: E 492 GLU cc_start: 0.9222 (mm-30) cc_final: 0.8760 (tp30) REVERT: F 148 TYR cc_start: 0.8293 (m-80) cc_final: 0.7846 (m-80) REVERT: F 202 GLN cc_start: 0.9176 (tm-30) cc_final: 0.8788 (tm-30) REVERT: F 242 LYS cc_start: 0.9178 (mtpt) cc_final: 0.8655 (mtmm) REVERT: F 245 LYS cc_start: 0.9654 (mmmm) cc_final: 0.9311 (mmtt) REVERT: F 246 ASP cc_start: 0.9252 (m-30) cc_final: 0.8951 (t0) REVERT: F 299 ASP cc_start: 0.8751 (t0) cc_final: 0.8355 (t0) REVERT: F 357 GLU cc_start: 0.8217 (tt0) cc_final: 0.7595 (tp30) REVERT: F 396 MET cc_start: 0.7945 (ttt) cc_final: 0.7266 (ttt) REVERT: F 399 MET cc_start: 0.9005 (ptp) cc_final: 0.8554 (ptp) outliers start: 68 outliers final: 49 residues processed: 417 average time/residue: 0.1320 time to fit residues: 83.6841 Evaluate side-chains 390 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 335 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 180 GLN 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 248 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 304 VAL 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 B residue 202 GLN Chi-restraints excluded: chain B residue 217 ARG Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 378 MET 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 196 CYS Chi-restraints excluded: chain D residue 259 ILE 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 440 VAL 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 202 GLN 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 439 VAL Chi-restraints excluded: chain F residue 190 LEU 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 307 CYS Chi-restraints excluded: chain F residue 397 ILE Chi-restraints excluded: chain F residue 398 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 132 optimal weight: 30.0000 chunk 245 optimal weight: 20.0000 chunk 88 optimal weight: 5.9990 chunk 84 optimal weight: 110.0000 chunk 143 optimal weight: 5.9990 chunk 166 optimal weight: 8.9990 chunk 120 optimal weight: 20.0000 chunk 8 optimal weight: 5.9990 chunk 230 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 19 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 ASN C 450 GLN D 225 ASN D 368 GLN D 384 ASN ** E 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.079312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.061152 restraints weight = 65468.992| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 4.91 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 1.0189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 18732 Z= 0.183 Angle : 0.748 13.524 25458 Z= 0.369 Chirality : 0.048 0.307 3018 Planarity : 0.005 0.048 3366 Dihedral : 6.416 62.116 2866 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.33 % Favored : 96.63 % Rotamer: Outliers : 4.00 % Allowed : 30.44 % Favored : 65.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.17), residues: 2520 helix: 1.29 (0.16), residues: 1096 sheet: -0.63 (0.24), residues: 422 loop : -0.80 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 205 TYR 0.023 0.002 TYR C 402 PHE 0.034 0.002 PHE B 364 TRP 0.005 0.001 TRP C 481 HIS 0.005 0.001 HIS F 382 Details of bonding type rmsd covalent geometry : bond 0.00431 (18732) covalent geometry : angle 0.74820 (25458) hydrogen bonds : bond 0.03269 ( 939) hydrogen bonds : angle 4.45909 ( 2733) *********************** 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 406 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 335 time to evaluate : 0.754 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: 0.8945 (tpt) cc_final: 0.8528 (tpp) REVERT: A 205 ARG cc_start: 0.8409 (ptp90) cc_final: 0.8116 (ptp90) REVERT: A 351 GLU cc_start: 0.8781 (mp0) cc_final: 0.8463 (mp0) REVERT: A 370 MET cc_start: 0.8970 (mmt) cc_final: 0.8297 (mmm) REVERT: B 174 GLU cc_start: 0.8641 (tt0) cc_final: 0.8019 (tp30) REVERT: B 202 GLN cc_start: 0.9307 (OUTLIER) cc_final: 0.8925 (mp10) REVERT: B 238 LEU cc_start: 0.9353 (tp) cc_final: 0.8878 (mp) REVERT: B 306 THR cc_start: 0.9405 (m) cc_final: 0.9150 (p) REVERT: B 314 GLN cc_start: 0.8988 (tt0) cc_final: 0.8573 (tm-30) REVERT: B 339 ARG cc_start: 0.8825 (ttp80) cc_final: 0.8512 (ptm-80) REVERT: B 351 GLU cc_start: 0.8658 (mp0) cc_final: 0.8297 (mp0) REVERT: B 359 ARG cc_start: 0.8938 (mtp85) cc_final: 0.8714 (mtt-85) REVERT: B 377 SER cc_start: 0.8701 (t) cc_final: 0.8278 (p) REVERT: B 407 LYS cc_start: 0.9016 (tppt) cc_final: 0.8678 (tppt) REVERT: B 411 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8345 (mp0) REVERT: B 412 MET cc_start: 0.9529 (tmm) cc_final: 0.9072 (tmm) REVERT: B 450 GLN cc_start: 0.8368 (pt0) cc_final: 0.7878 (pm20) REVERT: C 370 MET cc_start: 0.9335 (mtt) cc_final: 0.8700 (mtt) REVERT: C 396 MET cc_start: 0.8901 (ttm) cc_final: 0.8583 (mtm) REVERT: C 477 ARG cc_start: 0.8767 (tpp80) cc_final: 0.8527 (mmm-85) REVERT: D 164 MET cc_start: 0.9042 (mtm) cc_final: 0.8707 (mtm) REVERT: D 351 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8129 (mp0) REVERT: D 370 MET cc_start: 0.8048 (mtp) cc_final: 0.7632 (mtp) REVERT: D 402 TYR cc_start: 0.8604 (m-10) cc_final: 0.8336 (m-10) REVERT: D 407 LYS cc_start: 0.9266 (mmmt) cc_final: 0.9040 (tppt) REVERT: D 450 GLN cc_start: 0.8625 (pm20) cc_final: 0.8382 (pm20) REVERT: E 164 MET cc_start: 0.8795 (mtm) cc_final: 0.7973 (mtm) REVERT: E 245 LYS cc_start: 0.9443 (mmmt) cc_final: 0.9192 (mmtt) REVERT: E 324 GLU cc_start: 0.8205 (tt0) cc_final: 0.7723 (tp30) REVERT: E 347 ARG cc_start: 0.9370 (tpp80) cc_final: 0.9022 (tpp80) REVERT: E 437 THR cc_start: 0.7895 (OUTLIER) cc_final: 0.7637 (t) REVERT: E 492 GLU cc_start: 0.9246 (mm-30) cc_final: 0.8763 (tp30) REVERT: F 148 TYR cc_start: 0.8309 (m-80) cc_final: 0.7915 (m-80) REVERT: F 202 GLN cc_start: 0.9230 (tm-30) cc_final: 0.8836 (tm-30) REVERT: F 242 LYS cc_start: 0.9242 (mtpt) cc_final: 0.8529 (mtmm) REVERT: F 245 LYS cc_start: 0.9654 (mmmm) cc_final: 0.9331 (mmtt) REVERT: F 246 ASP cc_start: 0.9274 (m-30) cc_final: 0.9024 (t0) REVERT: F 251 LYS cc_start: 0.9344 (mtmm) cc_final: 0.8896 (pttm) REVERT: F 299 ASP cc_start: 0.8797 (t0) cc_final: 0.8409 (t0) REVERT: F 357 GLU cc_start: 0.8261 (tt0) cc_final: 0.7666 (tp30) REVERT: F 399 MET cc_start: 0.9081 (ptp) cc_final: 0.8619 (ptp) outliers start: 71 outliers final: 61 residues processed: 378 average time/residue: 0.1291 time to fit residues: 75.4003 Evaluate side-chains 378 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 315 time to evaluate : 0.666 ------------------------------------------------------------------------------- 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 248 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 307 CYS Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 463 HIS Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 378 MET 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 196 CYS Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 259 ILE 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 393 ILE 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 200 VAL 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 397 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 239 THR Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 307 CYS Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 397 ILE Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain F residue 469 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 214 optimal weight: 50.0000 chunk 137 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 203 optimal weight: 20.0000 chunk 4 optimal weight: 120.0000 chunk 87 optimal weight: 50.0000 chunk 164 optimal weight: 8.9990 chunk 209 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 88 optimal weight: 50.0000 chunk 111 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN ** E 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 368 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 = 0.3573 r_free = 0.3573 target = 0.079100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.060735 restraints weight = 65347.951| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 4.89 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 1.0776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 18732 Z= 0.202 Angle : 0.775 13.158 25458 Z= 0.382 Chirality : 0.048 0.279 3018 Planarity : 0.006 0.127 3366 Dihedral : 6.466 59.478 2866 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.09 % Favored : 95.87 % Rotamer: Outliers : 3.78 % Allowed : 30.61 % Favored : 65.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.17), residues: 2520 helix: 1.25 (0.16), residues: 1096 sheet: -0.65 (0.24), residues: 430 loop : -0.89 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 205 TYR 0.025 0.002 TYR C 402 PHE 0.038 0.002 PHE B 364 TRP 0.004 0.001 TRP E 481 HIS 0.005 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00472 (18732) covalent geometry : angle 0.77450 (25458) hydrogen bonds : bond 0.03286 ( 939) hydrogen bonds : angle 4.50742 ( 2733) ********************** 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 390 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 323 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.9264 (mtm) cc_final: 0.8911 (mtm) REVERT: A 193 MET cc_start: 0.9196 (tpt) cc_final: 0.8539 (tpp) REVERT: A 205 ARG cc_start: 0.8362 (ptp90) cc_final: 0.8115 (ptp90) REVERT: A 351 GLU cc_start: 0.8817 (mp0) cc_final: 0.8576 (mp0) REVERT: A 370 MET cc_start: 0.9014 (mmt) cc_final: 0.8365 (mmm) REVERT: A 398 THR cc_start: 0.9486 (m) cc_final: 0.9280 (p) REVERT: B 174 GLU cc_start: 0.8666 (tt0) cc_final: 0.8286 (tp30) REVERT: B 197 GLN cc_start: 0.9304 (tt0) cc_final: 0.8942 (mt0) REVERT: B 202 GLN cc_start: 0.9279 (OUTLIER) cc_final: 0.8897 (mp10) REVERT: B 306 THR cc_start: 0.9446 (m) cc_final: 0.9134 (p) REVERT: B 314 GLN cc_start: 0.9048 (tt0) cc_final: 0.8640 (tm-30) REVERT: B 339 ARG cc_start: 0.8873 (ttp80) cc_final: 0.8582 (ptm-80) REVERT: B 347 ARG cc_start: 0.8398 (mtm110) cc_final: 0.7518 (mtm-85) REVERT: B 351 GLU cc_start: 0.8617 (mp0) cc_final: 0.8240 (mp0) REVERT: B 359 ARG cc_start: 0.8985 (mtp85) cc_final: 0.8739 (mtt-85) REVERT: B 370 MET cc_start: 0.8294 (mmt) cc_final: 0.8040 (tpp) REVERT: B 377 SER cc_start: 0.8650 (t) cc_final: 0.8444 (p) REVERT: B 407 LYS cc_start: 0.8970 (tppt) cc_final: 0.8625 (tppt) REVERT: B 411 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8401 (mp0) REVERT: B 412 MET cc_start: 0.9527 (tmm) cc_final: 0.9075 (tmm) REVERT: B 450 GLN cc_start: 0.8418 (pt0) cc_final: 0.7839 (pm20) REVERT: B 479 ARG cc_start: 0.7797 (ptm160) cc_final: 0.7266 (ttt180) REVERT: D 164 MET cc_start: 0.9101 (mtm) cc_final: 0.8815 (mtm) REVERT: D 351 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8069 (mp0) REVERT: D 370 MET cc_start: 0.8070 (mtp) cc_final: 0.7869 (mtp) REVERT: D 396 MET cc_start: 0.9281 (mtt) cc_final: 0.8652 (mmm) REVERT: D 399 MET cc_start: 0.9145 (tmm) cc_final: 0.8788 (ppp) REVERT: D 407 LYS cc_start: 0.9273 (mmmt) cc_final: 0.9059 (tppt) REVERT: D 450 GLN cc_start: 0.8680 (pm20) cc_final: 0.8428 (pm20) REVERT: E 164 MET cc_start: 0.8813 (mtm) cc_final: 0.7999 (mtm) REVERT: E 202 GLN cc_start: 0.9541 (OUTLIER) cc_final: 0.9281 (pp30) REVERT: E 324 GLU cc_start: 0.8224 (tt0) cc_final: 0.7652 (mm-30) REVERT: E 437 THR cc_start: 0.7966 (OUTLIER) cc_final: 0.7723 (t) REVERT: F 148 TYR cc_start: 0.8397 (m-80) cc_final: 0.8060 (m-80) REVERT: F 202 GLN cc_start: 0.9281 (tm-30) cc_final: 0.8889 (tm-30) REVERT: F 242 LYS cc_start: 0.9262 (mtpt) cc_final: 0.8603 (mtmm) REVERT: F 245 LYS cc_start: 0.9624 (mmmm) cc_final: 0.9327 (mmtt) REVERT: F 251 LYS cc_start: 0.9379 (mtmm) cc_final: 0.8951 (pttm) REVERT: F 299 ASP cc_start: 0.8854 (t0) cc_final: 0.8481 (t0) REVERT: F 357 GLU cc_start: 0.8389 (tt0) cc_final: 0.7688 (tp30) outliers start: 67 outliers final: 54 residues processed: 364 average time/residue: 0.1284 time to fit residues: 72.6959 Evaluate side-chains 357 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 300 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 307 CYS Chi-restraints excluded: chain A residue 368 GLN Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 497 LEU 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 368 GLN Chi-restraints excluded: chain B residue 402 TYR Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 463 HIS Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 421 ILE Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 196 CYS Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 259 ILE 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 202 GLN 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 417 VAL Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain F residue 180 GLN 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 307 CYS Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 397 ILE Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 451 ASP Chi-restraints excluded: chain F residue 469 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 80.0000 chunk 38 optimal weight: 0.4980 chunk 138 optimal weight: 50.0000 chunk 121 optimal weight: 20.0000 chunk 241 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 172 optimal weight: 20.0000 chunk 102 optimal weight: 50.0000 chunk 223 optimal weight: 20.0000 chunk 207 optimal weight: 20.0000 chunk 27 optimal weight: 0.0070 overall best weight: 6.7006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN ** E 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 368 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 = 0.3568 r_free = 0.3568 target = 0.078454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.060130 restraints weight = 65529.810| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 4.88 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 1.0775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.124 18732 Z= 0.243 Angle : 0.904 59.198 25458 Z= 0.486 Chirality : 0.053 1.171 3018 Planarity : 0.006 0.119 3366 Dihedral : 6.468 59.488 2866 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.13 % Favored : 95.83 % Rotamer: Outliers : 3.49 % Allowed : 31.45 % Favored : 65.05 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.17), residues: 2520 helix: 1.24 (0.16), residues: 1096 sheet: -0.65 (0.24), residues: 430 loop : -0.90 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG F 479 TYR 0.022 0.002 TYR C 402 PHE 0.032 0.002 PHE B 364 TRP 0.005 0.001 TRP C 481 HIS 0.004 0.001 HIS C 319 Details of bonding type rmsd covalent geometry : bond 0.00558 (18732) covalent geometry : angle 0.90438 (25458) hydrogen bonds : bond 0.03289 ( 939) hydrogen bonds : angle 4.51279 ( 2733) =============================================================================== Job complete usr+sys time: 3698.02 seconds wall clock time: 64 minutes 28.84 seconds (3868.84 seconds total)