Starting phenix.real_space_refine on Thu Feb 5 08:04:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zpx_74536/02_2026/9zpx_74536.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zpx_74536/02_2026/9zpx_74536.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zpx_74536/02_2026/9zpx_74536.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zpx_74536/02_2026/9zpx_74536.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zpx_74536/02_2026/9zpx_74536.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zpx_74536/02_2026/9zpx_74536.map" } resolution = 2.64 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 K 2 8.98 5 P 19 5.49 5 S 76 5.16 5 C 10297 2.51 5 N 2400 2.21 5 O 2833 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15627 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3688 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3688 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 3688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3688 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 3687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3687 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 222 Unusual residues: {' K': 2, 'CLR': 1, 'PCG': 1, 'PCW': 5} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 94 Planarities with less than four sites: {'PCW:plan-2': 3, 'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 217 Unusual residues: {'CLR': 1, 'PCG': 1, 'PCW': 5} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 96 Planarities with less than four sites: {'PCW:plan-2': 3, 'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 217 Unusual residues: {'CLR': 1, 'PCG': 1, 'PCW': 5} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 97 Planarities with less than four sites: {'PCW:plan-4': 3, 'PCW:plan-2': 2} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 220 Unusual residues: {'CLR': 1, 'PCG': 1, 'PCW': 5} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 94 Planarities with less than four sites: {'PCW:plan-4': 3, 'PCW:plan-2': 2} Unresolved non-hydrogen planarities: 16 Time building chain proxies: 2.92, per 1000 atoms: 0.19 Number of scatterers: 15627 At special positions: 0 Unit cell: (99.9, 99.9, 116.1, 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) K 2 19.00 S 76 16.00 P 19 15.00 O 2833 8.00 N 2400 7.00 C 10297 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 Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.45 Conformation dependent library (CDL) restraints added in 574.6 milliseconds 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3406 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 12 sheets defined 70.6% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 162 through 189 removed outlier: 3.573A pdb=" N TYR A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) Proline residue: A 175 - end of helix removed outlier: 5.177A pdb=" N ILE A 184 " --> pdb=" O TRP A 180 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 removed outlier: 3.590A pdb=" N GLN A 193 " --> pdb=" O PHE A 189 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 220 Processing helix chain 'A' and resid 232 through 242 Processing helix chain 'A' and resid 243 through 253 removed outlier: 3.951A pdb=" N LYS A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 258 Processing helix chain 'A' and resid 259 through 264 Processing helix chain 'A' and resid 267 through 276 removed outlier: 3.756A pdb=" N ILE A 270 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASN A 273 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 292 removed outlier: 3.938A pdb=" N MET A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 326 Processing helix chain 'A' and resid 344 through 361 Processing helix chain 'A' and resid 371 through 404 removed outlier: 3.605A pdb=" N ALA A 390 " --> pdb=" O VAL A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 424 Processing helix chain 'A' and resid 427 through 444 Processing helix chain 'A' and resid 449 through 455 Processing helix chain 'A' and resid 458 through 470 Processing helix chain 'A' and resid 471 through 476 removed outlier: 3.513A pdb=" N LYS A 476 " --> pdb=" O ASP A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 483 removed outlier: 3.632A pdb=" N ALA A 481 " --> pdb=" O VAL A 477 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP A 482 " --> pdb=" O ARG A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 492 removed outlier: 4.345A pdb=" N LEU A 488 " --> pdb=" O GLU A 484 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 495 No H-bonds generated for 'chain 'A' and resid 493 through 495' Processing helix chain 'A' and resid 545 through 551 removed outlier: 4.220A pdb=" N ILE A 549 " --> pdb=" O GLY A 545 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN A 551 " --> pdb=" O ILE A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 588 removed outlier: 3.628A pdb=" N GLU A 587 " --> pdb=" O GLU A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 605 Processing helix chain 'B' and resid 162 through 189 removed outlier: 3.577A pdb=" N TYR B 166 " --> pdb=" O GLY B 162 " (cutoff:3.500A) Proline residue: B 175 - end of helix removed outlier: 5.205A pdb=" N ILE B 184 " --> pdb=" O TRP B 180 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ALA B 185 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 196 removed outlier: 3.592A pdb=" N GLN B 193 " --> pdb=" O PHE B 189 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 220 Processing helix chain 'B' and resid 232 through 242 Processing helix chain 'B' and resid 243 through 253 removed outlier: 3.950A pdb=" N LYS B 247 " --> pdb=" O ASN B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 258 Processing helix chain 'B' and resid 259 through 264 Processing helix chain 'B' and resid 267 through 276 removed outlier: 3.735A pdb=" N ILE B 270 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASN B 273 " --> pdb=" O ILE B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 292 removed outlier: 3.940A pdb=" N MET B 281 " --> pdb=" O ARG B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 326 Processing helix chain 'B' and resid 344 through 361 Processing helix chain 'B' and resid 371 through 404 removed outlier: 3.598A pdb=" N ALA B 390 " --> pdb=" O VAL B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 424 Processing helix chain 'B' and resid 427 through 444 Processing helix chain 'B' and resid 449 through 455 Processing helix chain 'B' and resid 458 through 470 Processing helix chain 'B' and resid 471 through 476 removed outlier: 3.524A pdb=" N LYS B 476 " --> pdb=" O ASP B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 483 removed outlier: 3.636A pdb=" N ALA B 481 " --> pdb=" O VAL B 477 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP B 482 " --> pdb=" O ARG B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 492 Processing helix chain 'B' and resid 545 through 551 removed outlier: 4.244A pdb=" N ILE B 549 " --> pdb=" O GLY B 545 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN B 551 " --> pdb=" O ILE B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 588 Processing helix chain 'B' and resid 591 through 605 Processing helix chain 'C' and resid 162 through 189 removed outlier: 3.572A pdb=" N TYR C 166 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Proline residue: C 175 - end of helix removed outlier: 5.210A pdb=" N ILE C 184 " --> pdb=" O TRP C 180 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ALA C 185 " --> pdb=" O THR C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 196 removed outlier: 3.584A pdb=" N GLN C 193 " --> pdb=" O PHE C 189 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR C 196 " --> pdb=" O LEU C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 220 Processing helix chain 'C' and resid 232 through 242 Processing helix chain 'C' and resid 243 through 253 removed outlier: 3.950A pdb=" N LYS C 247 " --> pdb=" O ASN C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 258 Processing helix chain 'C' and resid 259 through 264 Processing helix chain 'C' and resid 267 through 276 removed outlier: 3.732A pdb=" N ILE C 270 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASN C 273 " --> pdb=" O ILE C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 292 removed outlier: 3.941A pdb=" N MET C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 326 Processing helix chain 'C' and resid 344 through 361 Processing helix chain 'C' and resid 371 through 404 removed outlier: 3.616A pdb=" N ALA C 390 " --> pdb=" O VAL C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 424 Processing helix chain 'C' and resid 427 through 444 Processing helix chain 'C' and resid 449 through 455 Processing helix chain 'C' and resid 458 through 470 Processing helix chain 'C' and resid 471 through 476 removed outlier: 3.544A pdb=" N LYS C 476 " --> pdb=" O ASP C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 483 removed outlier: 3.604A pdb=" N ALA C 481 " --> pdb=" O VAL C 477 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP C 482 " --> pdb=" O ARG C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 492 removed outlier: 4.201A pdb=" N VAL C 489 " --> pdb=" O ALA C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 551 removed outlier: 4.226A pdb=" N ILE C 549 " --> pdb=" O GLY C 545 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN C 551 " --> pdb=" O ILE C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 588 Processing helix chain 'C' and resid 591 through 605 Processing helix chain 'D' and resid 162 through 182 removed outlier: 3.572A pdb=" N TYR D 166 " --> pdb=" O GLY D 162 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 183 through 189 Processing helix chain 'D' and resid 189 through 196 removed outlier: 3.613A pdb=" N GLN D 193 " --> pdb=" O PHE D 189 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR D 196 " --> pdb=" O LEU D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 220 Processing helix chain 'D' and resid 232 through 242 Processing helix chain 'D' and resid 243 through 253 removed outlier: 3.948A pdb=" N LYS D 247 " --> pdb=" O ASN D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 258 Processing helix chain 'D' and resid 259 through 264 Processing helix chain 'D' and resid 267 through 276 removed outlier: 3.735A pdb=" N ILE D 270 " --> pdb=" O TYR D 267 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ASN D 273 " --> pdb=" O ILE D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 292 removed outlier: 3.940A pdb=" N MET D 281 " --> pdb=" O ARG D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 326 Processing helix chain 'D' and resid 344 through 361 Processing helix chain 'D' and resid 371 through 404 removed outlier: 3.577A pdb=" N ALA D 390 " --> pdb=" O VAL D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 424 Processing helix chain 'D' and resid 427 through 444 Processing helix chain 'D' and resid 449 through 455 Processing helix chain 'D' and resid 458 through 470 Processing helix chain 'D' and resid 471 through 476 removed outlier: 3.557A pdb=" N LYS D 476 " --> pdb=" O ASP D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 483 removed outlier: 3.700A pdb=" N ALA D 481 " --> pdb=" O VAL D 477 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP D 482 " --> pdb=" O ARG D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 492 Processing helix chain 'D' and resid 545 through 551 removed outlier: 4.230A pdb=" N ILE D 549 " --> pdb=" O GLY D 545 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN D 551 " --> pdb=" O ILE D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 588 Processing helix chain 'D' and resid 591 through 605 Processing sheet with id=AA1, first strand: chain 'A' and resid 224 through 225 Processing sheet with id=AA2, first strand: chain 'A' and resid 496 through 500 removed outlier: 6.154A pdb=" N PHE A 574 " --> pdb=" O ILE A 519 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ILE A 519 " --> pdb=" O PHE A 574 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU A 576 " --> pdb=" O TYR A 517 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N TYR A 517 " --> pdb=" O LEU A 576 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 534 through 538 removed outlier: 3.981A pdb=" N VAL A 536 " --> pdb=" O VAL A 526 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASN A 564 " --> pdb=" O VAL A 527 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 224 through 225 Processing sheet with id=AA5, first strand: chain 'B' and resid 496 through 500 removed outlier: 6.167A pdb=" N PHE B 574 " --> pdb=" O ILE B 519 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ILE B 519 " --> pdb=" O PHE B 574 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU B 576 " --> pdb=" O TYR B 517 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N TYR B 517 " --> pdb=" O LEU B 576 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 534 through 538 removed outlier: 3.978A pdb=" N VAL B 536 " --> pdb=" O VAL B 526 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASN B 564 " --> pdb=" O VAL B 527 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 224 through 225 Processing sheet with id=AA8, first strand: chain 'C' and resid 496 through 500 removed outlier: 6.187A pdb=" N PHE C 574 " --> pdb=" O ILE C 519 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ILE C 519 " --> pdb=" O PHE C 574 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU C 576 " --> pdb=" O TYR C 517 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N TYR C 517 " --> pdb=" O LEU C 576 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 505 through 507 removed outlier: 6.521A pdb=" N TYR C 505 " --> pdb=" O SER C 567 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N SER C 567 " --> pdb=" O TYR C 505 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS C 507 " --> pdb=" O ILE C 565 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASN C 564 " --> pdb=" O VAL C 527 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL C 536 " --> pdb=" O VAL C 526 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 224 through 225 Processing sheet with id=AB2, first strand: chain 'D' and resid 496 through 500 removed outlier: 6.771A pdb=" N ASP D 572 " --> pdb=" O LYS D 520 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 534 through 538 removed outlier: 3.988A pdb=" N VAL D 536 " --> pdb=" O VAL D 526 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN D 564 " --> pdb=" O VAL D 527 " (cutoff:3.500A) 921 hydrogen bonds defined for protein. 2643 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: 1.86 Time building geometry restraints manager: 1.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2416 1.31 - 1.44: 4302 1.44 - 1.57: 9068 1.57 - 1.70: 42 1.70 - 1.82: 140 Bond restraints: 15968 Sorted by residual: bond pdb=" C2' PCG C 701 " pdb=" C3' PCG C 701 " ideal model delta sigma weight residual 1.514 1.194 0.320 2.00e-02 2.50e+03 2.55e+02 bond pdb=" C2' PCG D 702 " pdb=" C3' PCG D 702 " ideal model delta sigma weight residual 1.514 1.195 0.319 2.00e-02 2.50e+03 2.55e+02 bond pdb=" C2' PCG A 701 " pdb=" C3' PCG A 701 " ideal model delta sigma weight residual 1.514 1.195 0.319 2.00e-02 2.50e+03 2.54e+02 bond pdb=" C2' PCG B 701 " pdb=" C3' PCG B 701 " ideal model delta sigma weight residual 1.514 1.195 0.319 2.00e-02 2.50e+03 2.54e+02 bond pdb=" C3' PCG C 701 " pdb=" C4' PCG C 701 " ideal model delta sigma weight residual 1.519 1.813 -0.294 2.00e-02 2.50e+03 2.16e+02 ... (remaining 15963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 21316 2.30 - 4.61: 127 4.61 - 6.91: 53 6.91 - 9.21: 30 9.21 - 11.52: 16 Bond angle restraints: 21542 Sorted by residual: angle pdb=" CB MET B 582 " pdb=" CG MET B 582 " pdb=" SD MET B 582 " ideal model delta sigma weight residual 112.70 124.22 -11.52 3.00e+00 1.11e-01 1.47e+01 angle pdb=" CB MET D 582 " pdb=" CG MET D 582 " pdb=" SD MET D 582 " ideal model delta sigma weight residual 112.70 124.21 -11.51 3.00e+00 1.11e-01 1.47e+01 angle pdb=" CB MET C 582 " pdb=" CG MET C 582 " pdb=" SD MET C 582 " ideal model delta sigma weight residual 112.70 124.11 -11.41 3.00e+00 1.11e-01 1.45e+01 angle pdb=" CB MET A 582 " pdb=" CG MET A 582 " pdb=" SD MET A 582 " ideal model delta sigma weight residual 112.70 124.11 -11.41 3.00e+00 1.11e-01 1.45e+01 angle pdb=" CB ARG D 478 " pdb=" CG ARG D 478 " pdb=" CD ARG D 478 " ideal model delta sigma weight residual 111.30 119.83 -8.53 2.30e+00 1.89e-01 1.38e+01 ... (remaining 21537 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.33: 9049 27.33 - 54.66: 763 54.66 - 81.99: 71 81.99 - 109.32: 13 109.32 - 136.65: 3 Dihedral angle restraints: 9899 sinusoidal: 4585 harmonic: 5314 Sorted by residual: dihedral pdb=" N PCW C 704 " pdb=" C4 PCW C 704 " pdb=" C5 PCW C 704 " pdb=" O4P PCW C 704 " ideal model delta sinusoidal sigma weight residual 293.34 156.69 136.65 1 3.00e+01 1.11e-03 1.84e+01 dihedral pdb=" N PCW B 705 " pdb=" C4 PCW B 705 " pdb=" C5 PCW B 705 " pdb=" O4P PCW B 705 " ideal model delta sinusoidal sigma weight residual -66.66 58.00 -124.66 1 3.00e+01 1.11e-03 1.67e+01 dihedral pdb=" N PCW D 705 " pdb=" C4 PCW D 705 " pdb=" C5 PCW D 705 " pdb=" O4P PCW D 705 " ideal model delta sinusoidal sigma weight residual -66.66 55.63 -122.29 1 3.00e+01 1.11e-03 1.64e+01 ... (remaining 9896 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 2314 0.104 - 0.209: 36 0.209 - 0.313: 0 0.313 - 0.418: 8 0.418 - 0.522: 4 Chirality restraints: 2362 Sorted by residual: chirality pdb=" PA PCG C 701 " pdb=" O2A PCG C 701 " pdb=" O3' PCG C 701 " pdb=" O5' PCG C 701 " both_signs ideal model delta sigma weight residual True 2.70 3.22 -0.52 2.00e-01 2.50e+01 6.81e+00 chirality pdb=" PA PCG B 701 " pdb=" O2A PCG B 701 " pdb=" O3' PCG B 701 " pdb=" O5' PCG B 701 " both_signs ideal model delta sigma weight residual True 2.70 3.22 -0.52 2.00e-01 2.50e+01 6.79e+00 chirality pdb=" PA PCG D 702 " pdb=" O2A PCG D 702 " pdb=" O3' PCG D 702 " pdb=" O5' PCG D 702 " both_signs ideal model delta sigma weight residual True 2.70 3.22 -0.52 2.00e-01 2.50e+01 6.79e+00 ... (remaining 2359 not shown) Planarity restraints: 2600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 478 " -0.111 9.50e-02 1.11e+02 5.01e-02 2.01e+00 pdb=" NE ARG D 478 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG D 478 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG D 478 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG D 478 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 334 " -0.020 5.00e-02 4.00e+02 3.07e-02 1.51e+00 pdb=" N PRO A 335 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 335 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 335 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 334 " 0.020 5.00e-02 4.00e+02 3.03e-02 1.47e+00 pdb=" N PRO C 335 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO C 335 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 335 " 0.017 5.00e-02 4.00e+02 ... (remaining 2597 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.77: 2870 2.77 - 3.36: 17849 3.36 - 3.95: 30958 3.95 - 4.55: 43355 4.55 - 5.14: 63542 Nonbonded interactions: 158574 Sorted by model distance: nonbonded pdb=" O THR C 357 " pdb=" OG1 THR C 361 " model vdw 2.174 3.040 nonbonded pdb=" O THR A 357 " pdb=" OG1 THR A 361 " model vdw 2.175 3.040 nonbonded pdb=" OG SER D 427 " pdb=" OD1 ASP D 429 " model vdw 2.177 3.040 nonbonded pdb=" OG SER C 427 " pdb=" OD1 ASP C 429 " model vdw 2.178 3.040 nonbonded pdb=" OG SER A 427 " pdb=" OD1 ASP A 429 " model vdw 2.198 3.040 ... (remaining 158569 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 156 through 344 or (resid 345 and (name N or name CA or na \ me C or name O or name CG or name CD1 or name CD2)) or resid 346 through 605 or \ (resid 704 and (name C1 or name C11 or name C12 or name C13 or name C14 or name \ C2 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or nam \ e C36 or name C37)) or (resid 705 and (name C1 or name C11 or name C12 or name C \ 13 or name C14 or name C15 or name C16 or name C2 or name C3 or name C31 or name \ C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or \ name O11 or name O2 or name O3 or name O31 or name O3P)) or (resid 706 and (name \ C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or n \ ame C17 or name C18 or name C2 or name C3 or name C31 or name C32 or name O3 or \ name O31 or name O3P)) or (resid 707 and (name C1 or name C11 or name C12 or nam \ e C13 or name C2 or name C3 or name C31 or name C32 or name C33 or name C34 or n \ ame C35 or name C36 or name C37 or name C38 or name O11 or name O1P or name O2 o \ r name O2P or name O3 or name O31 or name O3P or name O4P or name P )))) selection = (chain 'B' and (resid 156 through 344 or (resid 345 and (name N or name CA or na \ me C or name O or name CG or name CD1 or name CD2)) or resid 346 through 605 or \ (resid 704 and (name C1 or name C11 or name C12 or name C13 or name C14 or name \ C2 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or nam \ e C36 or name C37)) or (resid 705 and (name C1 or name C11 or name C12 or name C \ 13 or name C14 or name C15 or name C16 or name C2 or name C3 or name C31 or name \ C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or \ name O11 or name O2 or name O3 or name O31 or name O3P)) or (resid 706 and (name \ C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or n \ ame C17 or name C18 or name C2 or name C3 or name C31 or name C32 or name O3 or \ name O31 or name O3P)) or (resid 707 and (name C1 or name C11 or name C12 or nam \ e C13 or name C2 or name C3 or name C31 or name C32 or name C33 or name C34 or n \ ame C35 or name C36 or name C37 or name C38 or name O11 or name O1P or name O2 o \ r name O2P or name O3 or name O31 or name O3P or name O4P or name P )))) selection = (chain 'C' and (resid 156 through 344 or (resid 345 and (name N or name CA or na \ me C or name O or name CG or name CD1 or name CD2)) or resid 346 through 605 or \ (resid 704 and (name C1 or name C11 or name C12 or name C13 or name C14 or name \ C2 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or nam \ e C36 or name C37)) or (resid 705 and (name C1 or name C11 or name C12 or name C \ 13 or name C14 or name C15 or name C16 or name C2 or name C3 or name C31 or name \ C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or \ name O11 or name O2 or name O3 or name O31 or name O3P)) or (resid 706 and (name \ C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or n \ ame C17 or name C18 or name C2 or name C3 or name C31 or name C32 or name O3 or \ name O31 or name O3P)) or (resid 707 and (name C1 or name C11 or name C12 or nam \ e C13 or name C2 or name C3 or name C31 or name C32 or name C33 or name C34 or n \ ame C35 or name C36 or name C37 or name C38 or name O11 or name O1P or name O2 o \ r name O2P or name O3 or name O31 or name O3P or name O4P or name P )))) selection = (chain 'D' and (resid 156 through 605 or (resid 704 and (name C1 or name C11 or \ name C12 or name C13 or name C14 or name C2 or name C3 or name C31 or name C32 o \ r name C33 or name C34 or name C35 or name C36 or name C37)) or (resid 705 and ( \ name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 \ or name C2 or name C3 or name C31 or name C32 or name C33 or name C34 or name C3 \ 5 or name C36 or name C37 or name C38 or name O11 or name O2 or name O3 or name \ O31 or name O3P)) or (resid 706 and (name C1 or name C11 or name C12 or name C13 \ or name C14 or name C15 or name C16 or name C17 or name C18 or name C2 or name \ C3 or name C31 or name C32 or name O3 or name O31 or name O3P)) or (resid 707 an \ d (name C1 or name C11 or name C12 or name C13 or name C2 or name C3 or name C31 \ or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name O11 or name O1P or name O2 or name O2P or name O3 or name O31 or na \ me O3P or name O4P or name P )))) } 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: 2.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 12.650 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.020 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:5.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 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 : 0.011 0.320 15968 Z= 0.541 Angle : 0.657 11.516 21542 Z= 0.282 Chirality : 0.048 0.522 2362 Planarity : 0.003 0.050 2600 Dihedral : 18.214 136.655 6493 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.29 % Allowed : 27.12 % Favored : 70.60 % 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 are not related in a simple way. whole: 3.38 (0.20), residues: 1792 helix: 3.00 (0.15), residues: 1084 sheet: 0.83 (0.50), residues: 68 loop : 1.18 (0.27), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 478 TYR 0.009 0.001 TYR A 375 PHE 0.006 0.001 PHE B 438 TRP 0.016 0.001 TRP B 168 HIS 0.004 0.001 HIS D 312 Details of bonding type rmsd covalent geometry : bond 0.01087 (15968) covalent geometry : angle 0.65681 (21542) hydrogen bonds : bond 0.10256 ( 921) hydrogen bonds : angle 3.91127 ( 2643) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 111 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 384 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8461 (mp) REVERT: A 399 MET cc_start: 0.6631 (mtp) cc_final: 0.6419 (mtp) REVERT: A 464 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8301 (tm-30) REVERT: A 496 GLN cc_start: 0.8355 (mm-40) cc_final: 0.7915 (mm-40) REVERT: A 498 GLN cc_start: 0.8501 (mt0) cc_final: 0.8123 (mt0) REVERT: A 579 ASP cc_start: 0.9472 (OUTLIER) cc_final: 0.9197 (p0) REVERT: B 384 ILE cc_start: 0.9035 (OUTLIER) cc_final: 0.8474 (mp) REVERT: B 404 ASN cc_start: 0.7814 (OUTLIER) cc_final: 0.7152 (t0) REVERT: B 452 GLU cc_start: 0.8428 (tm-30) cc_final: 0.8213 (tm-30) REVERT: B 494 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.9056 (mmmm) REVERT: B 496 GLN cc_start: 0.8911 (mt0) cc_final: 0.8547 (mm-40) REVERT: B 601 GLN cc_start: 0.9078 (tm-30) cc_final: 0.8717 (tm-30) REVERT: C 384 ILE cc_start: 0.9029 (OUTLIER) cc_final: 0.8468 (mp) REVERT: C 494 LYS cc_start: 0.9311 (OUTLIER) cc_final: 0.9047 (mmmm) REVERT: C 496 GLN cc_start: 0.8850 (mt0) cc_final: 0.8412 (mm-40) REVERT: C 498 GLN cc_start: 0.8588 (mt0) cc_final: 0.8142 (mt0) REVERT: C 514 ARG cc_start: 0.8824 (pmm-80) cc_final: 0.8580 (pmm-80) REVERT: C 579 ASP cc_start: 0.9473 (OUTLIER) cc_final: 0.8992 (p0) REVERT: C 588 TYR cc_start: 0.7503 (m-10) cc_final: 0.7086 (m-10) REVERT: C 601 GLN cc_start: 0.9103 (tm-30) cc_final: 0.8742 (tm-30) REVERT: D 384 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8488 (mp) REVERT: D 399 MET cc_start: 0.6534 (mtp) cc_final: 0.6322 (mtp) REVERT: D 496 GLN cc_start: 0.8817 (mt0) cc_final: 0.8461 (mm-40) REVERT: D 514 ARG cc_start: 0.8786 (pmm-80) cc_final: 0.8151 (pmm-80) REVERT: D 579 ASP cc_start: 0.9493 (OUTLIER) cc_final: 0.9140 (p0) REVERT: D 594 MET cc_start: 0.8674 (tpp) cc_final: 0.8148 (tpt) REVERT: D 601 GLN cc_start: 0.9092 (tm-30) cc_final: 0.8720 (tm-30) outliers start: 37 outliers final: 21 residues processed: 144 average time/residue: 0.5719 time to fit residues: 91.2017 Evaluate side-chains 138 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 107 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 404 ASN Chi-restraints excluded: chain B residue 494 LYS Chi-restraints excluded: chain B residue 575 CYS Chi-restraints excluded: chain B residue 579 ASP Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 381 ASP Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 494 LYS Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain D residue 329 ASN Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 575 CYS Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 579 ASP Chi-restraints excluded: chain D residue 590 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 534 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.089543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.062045 restraints weight = 30831.223| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.42 r_work: 0.2752 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.0667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15968 Z= 0.191 Angle : 0.480 5.912 21542 Z= 0.248 Chirality : 0.040 0.191 2362 Planarity : 0.003 0.036 2600 Dihedral : 12.811 137.061 2981 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 4.76 % Allowed : 22.85 % Favored : 72.39 % 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 are not related in a simple way. whole: 2.77 (0.20), residues: 1792 helix: 2.39 (0.15), residues: 1156 sheet: 1.36 (0.49), residues: 48 loop : 0.86 (0.27), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 514 TYR 0.011 0.001 TYR B 354 PHE 0.010 0.001 PHE B 298 TRP 0.016 0.001 TRP A 168 HIS 0.005 0.001 HIS D 312 Details of bonding type rmsd covalent geometry : bond 0.00446 (15968) covalent geometry : angle 0.48044 (21542) hydrogen bonds : bond 0.03926 ( 921) hydrogen bonds : angle 3.65047 ( 2643) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 117 time to evaluate : 0.631 Fit side-chains REVERT: A 384 ILE cc_start: 0.9054 (OUTLIER) cc_final: 0.8491 (mp) REVERT: A 398 SER cc_start: 0.7841 (OUTLIER) cc_final: 0.7622 (p) REVERT: A 399 MET cc_start: 0.6629 (mtp) cc_final: 0.6372 (mtp) REVERT: A 464 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8320 (tm-30) REVERT: A 496 GLN cc_start: 0.8461 (mm-40) cc_final: 0.8019 (mm-40) REVERT: A 498 GLN cc_start: 0.8511 (mt0) cc_final: 0.8239 (mt0) REVERT: A 572 ASP cc_start: 0.8550 (t70) cc_final: 0.8313 (t70) REVERT: B 384 ILE cc_start: 0.9067 (OUTLIER) cc_final: 0.8511 (mp) REVERT: B 399 MET cc_start: 0.6547 (mtp) cc_final: 0.6301 (mtp) REVERT: B 452 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8223 (tm-30) REVERT: B 494 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.9018 (mmmm) REVERT: B 496 GLN cc_start: 0.8893 (mt0) cc_final: 0.8495 (mm-40) REVERT: B 572 ASP cc_start: 0.8543 (t70) cc_final: 0.8234 (t70) REVERT: B 601 GLN cc_start: 0.9106 (tm-30) cc_final: 0.8718 (tm-30) REVERT: C 384 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8512 (mp) REVERT: C 399 MET cc_start: 0.6606 (mtp) cc_final: 0.6385 (mtp) REVERT: C 403 MET cc_start: 0.8286 (ttp) cc_final: 0.8068 (ttt) REVERT: C 494 LYS cc_start: 0.9295 (OUTLIER) cc_final: 0.8988 (mmmm) REVERT: C 496 GLN cc_start: 0.8829 (mt0) cc_final: 0.8329 (mm-40) REVERT: C 498 GLN cc_start: 0.8562 (mt0) cc_final: 0.8272 (mt0) REVERT: C 572 ASP cc_start: 0.8553 (t70) cc_final: 0.8270 (t70) REVERT: C 588 TYR cc_start: 0.7594 (m-10) cc_final: 0.7385 (m-10) REVERT: C 601 GLN cc_start: 0.9114 (tm-30) cc_final: 0.8745 (tm-30) REVERT: D 384 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8523 (mp) REVERT: D 494 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8452 (mtmm) REVERT: D 496 GLN cc_start: 0.8851 (mt0) cc_final: 0.8499 (mm-40) REVERT: D 514 ARG cc_start: 0.8801 (pmm-80) cc_final: 0.8516 (pmm-80) REVERT: D 594 MET cc_start: 0.8450 (tpp) cc_final: 0.8219 (tpt) REVERT: D 601 GLN cc_start: 0.9113 (tm-30) cc_final: 0.8738 (tm-30) outliers start: 77 outliers final: 30 residues processed: 185 average time/residue: 0.5023 time to fit residues: 103.7762 Evaluate side-chains 151 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 113 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 494 LYS Chi-restraints excluded: chain B residue 575 CYS Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 381 ASP Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 494 LYS Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain D residue 260 TYR Chi-restraints excluded: chain D residue 302 ASN Chi-restraints excluded: chain D residue 329 ASN Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain D residue 404 ASN Chi-restraints excluded: chain D residue 494 LYS Chi-restraints excluded: chain D residue 575 CYS Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 581 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 74 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 133 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 118 optimal weight: 0.8980 chunk 85 optimal weight: 9.9990 chunk 105 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.090256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.062861 restraints weight = 30878.034| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.43 r_work: 0.2771 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.0737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15968 Z= 0.130 Angle : 0.453 6.269 21542 Z= 0.232 Chirality : 0.038 0.192 2362 Planarity : 0.003 0.032 2600 Dihedral : 12.542 136.937 2957 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.89 % Allowed : 23.59 % Favored : 72.51 % 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 are not related in a simple way. whole: 2.74 (0.20), residues: 1792 helix: 2.38 (0.15), residues: 1184 sheet: 1.49 (0.51), residues: 48 loop : 0.73 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 514 TYR 0.015 0.001 TYR A 588 PHE 0.007 0.001 PHE A 389 TRP 0.016 0.001 TRP C 168 HIS 0.004 0.001 HIS D 312 Details of bonding type rmsd covalent geometry : bond 0.00299 (15968) covalent geometry : angle 0.45319 (21542) hydrogen bonds : bond 0.03531 ( 921) hydrogen bonds : angle 3.56909 ( 2643) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 116 time to evaluate : 0.575 Fit side-chains REVERT: A 384 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8495 (mp) REVERT: A 399 MET cc_start: 0.6623 (mtp) cc_final: 0.6379 (mtp) REVERT: A 464 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8328 (tm-30) REVERT: A 496 GLN cc_start: 0.8487 (mm-40) cc_final: 0.8008 (mm-40) REVERT: A 498 GLN cc_start: 0.8481 (mt0) cc_final: 0.8254 (mt0) REVERT: A 572 ASP cc_start: 0.8556 (t70) cc_final: 0.8284 (t70) REVERT: A 588 TYR cc_start: 0.8018 (m-80) cc_final: 0.7762 (m-80) REVERT: B 384 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8512 (mp) REVERT: B 399 MET cc_start: 0.6545 (mtp) cc_final: 0.6300 (mtp) REVERT: B 452 GLU cc_start: 0.8477 (tm-30) cc_final: 0.8240 (tm-30) REVERT: B 494 LYS cc_start: 0.9266 (OUTLIER) cc_final: 0.8995 (mmmm) REVERT: B 496 GLN cc_start: 0.8920 (mt0) cc_final: 0.8543 (mm-40) REVERT: B 572 ASP cc_start: 0.8557 (t70) cc_final: 0.8307 (t70) REVERT: B 588 TYR cc_start: 0.7428 (m-10) cc_final: 0.7170 (m-10) REVERT: B 601 GLN cc_start: 0.9106 (tm-30) cc_final: 0.8719 (tm-30) REVERT: C 384 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8503 (mp) REVERT: C 399 MET cc_start: 0.6640 (mtp) cc_final: 0.6347 (mtp) REVERT: C 494 LYS cc_start: 0.9256 (OUTLIER) cc_final: 0.8938 (mmmm) REVERT: C 496 GLN cc_start: 0.8864 (mt0) cc_final: 0.8360 (mm-40) REVERT: C 498 GLN cc_start: 0.8573 (mt0) cc_final: 0.8288 (mt0) REVERT: C 514 ARG cc_start: 0.8772 (pmm-80) cc_final: 0.8471 (pmm-80) REVERT: C 572 ASP cc_start: 0.8545 (t70) cc_final: 0.8220 (t70) REVERT: C 588 TYR cc_start: 0.7710 (m-10) cc_final: 0.7313 (m-10) REVERT: C 601 GLN cc_start: 0.9105 (tm-30) cc_final: 0.8751 (tm-30) REVERT: D 384 ILE cc_start: 0.9072 (OUTLIER) cc_final: 0.8527 (mp) REVERT: D 494 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8408 (mtmm) REVERT: D 496 GLN cc_start: 0.8838 (mt0) cc_final: 0.8512 (mm-40) REVERT: D 514 ARG cc_start: 0.8786 (pmm-80) cc_final: 0.8517 (pmm-80) REVERT: D 601 GLN cc_start: 0.9099 (tm-30) cc_final: 0.8721 (tm-30) outliers start: 63 outliers final: 25 residues processed: 168 average time/residue: 0.5889 time to fit residues: 109.3358 Evaluate side-chains 147 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 115 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 494 LYS Chi-restraints excluded: chain B residue 575 CYS Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 381 ASP Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 494 LYS Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain D residue 260 TYR Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 404 ASN Chi-restraints excluded: chain D residue 494 LYS Chi-restraints excluded: chain D residue 575 CYS Chi-restraints excluded: chain D residue 581 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 69 optimal weight: 0.9990 chunk 127 optimal weight: 0.6980 chunk 45 optimal weight: 0.1980 chunk 152 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 166 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 38 optimal weight: 0.3980 chunk 145 optimal weight: 7.9990 chunk 158 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.090867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.063190 restraints weight = 30691.474| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.48 r_work: 0.2779 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.0778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15968 Z= 0.109 Angle : 0.448 9.425 21542 Z= 0.226 Chirality : 0.038 0.192 2362 Planarity : 0.003 0.047 2600 Dihedral : 12.189 136.416 2947 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 3.95 % Allowed : 23.72 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.75 (0.20), residues: 1792 helix: 2.41 (0.15), residues: 1192 sheet: 1.73 (0.53), residues: 48 loop : 0.59 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 478 TYR 0.010 0.001 TYR B 375 PHE 0.006 0.001 PHE D 410 TRP 0.015 0.001 TRP B 168 HIS 0.003 0.001 HIS D 312 Details of bonding type rmsd covalent geometry : bond 0.00245 (15968) covalent geometry : angle 0.44765 (21542) hydrogen bonds : bond 0.03317 ( 921) hydrogen bonds : angle 3.49365 ( 2643) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 115 time to evaluate : 0.647 Fit side-chains REVERT: A 464 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8337 (tm-30) REVERT: A 496 GLN cc_start: 0.8531 (mm-40) cc_final: 0.8069 (mm-40) REVERT: A 572 ASP cc_start: 0.8558 (t70) cc_final: 0.8335 (t70) REVERT: A 575 CYS cc_start: 0.8366 (OUTLIER) cc_final: 0.8136 (t) REVERT: B 399 MET cc_start: 0.6586 (mtp) cc_final: 0.6351 (mtp) REVERT: B 452 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8240 (tm-30) REVERT: B 494 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8964 (mmmm) REVERT: B 496 GLN cc_start: 0.8976 (mt0) cc_final: 0.8575 (mm-40) REVERT: B 572 ASP cc_start: 0.8577 (t70) cc_final: 0.8322 (t70) REVERT: B 588 TYR cc_start: 0.7596 (m-10) cc_final: 0.7333 (m-10) REVERT: B 601 GLN cc_start: 0.9104 (tm-30) cc_final: 0.8747 (tm-30) REVERT: C 399 MET cc_start: 0.6603 (mtp) cc_final: 0.6392 (mtp) REVERT: C 494 LYS cc_start: 0.9216 (OUTLIER) cc_final: 0.8924 (mmmm) REVERT: C 496 GLN cc_start: 0.8889 (mt0) cc_final: 0.8388 (mm-40) REVERT: C 498 GLN cc_start: 0.8533 (mt0) cc_final: 0.8224 (mt0) REVERT: C 514 ARG cc_start: 0.8791 (pmm-80) cc_final: 0.8444 (pmm-80) REVERT: C 572 ASP cc_start: 0.8555 (t70) cc_final: 0.8300 (t70) REVERT: C 588 TYR cc_start: 0.7679 (m-10) cc_final: 0.7403 (m-10) REVERT: C 601 GLN cc_start: 0.9104 (tm-30) cc_final: 0.8746 (tm-30) REVERT: D 494 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8408 (mtmm) REVERT: D 496 GLN cc_start: 0.8843 (mt0) cc_final: 0.8506 (mm-40) REVERT: D 514 ARG cc_start: 0.8782 (pmm-80) cc_final: 0.8511 (pmm-80) REVERT: D 601 GLN cc_start: 0.9094 (tm-30) cc_final: 0.8716 (tm-30) outliers start: 64 outliers final: 26 residues processed: 171 average time/residue: 0.5393 time to fit residues: 102.5075 Evaluate side-chains 143 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 494 LYS Chi-restraints excluded: chain B residue 523 LYS Chi-restraints excluded: chain B residue 575 CYS Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 381 ASP Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 494 LYS Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain D residue 260 TYR Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain D residue 494 LYS Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 61 optimal weight: 0.4980 chunk 150 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 156 optimal weight: 0.0670 chunk 15 optimal weight: 0.5980 chunk 40 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 122 optimal weight: 8.9990 chunk 138 optimal weight: 0.9980 chunk 175 optimal weight: 10.0000 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 GLN D 498 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.091405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.064199 restraints weight = 30692.804| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 2.43 r_work: 0.2804 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15968 Z= 0.094 Angle : 0.452 9.480 21542 Z= 0.226 Chirality : 0.038 0.191 2362 Planarity : 0.003 0.031 2600 Dihedral : 11.888 135.790 2939 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 3.46 % Allowed : 24.52 % Favored : 72.02 % 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 are not related in a simple way. whole: 3.11 (0.20), residues: 1792 helix: 2.78 (0.15), residues: 1148 sheet: 1.93 (0.54), residues: 48 loop : 0.69 (0.27), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 478 TYR 0.017 0.001 TYR A 588 PHE 0.007 0.001 PHE D 410 TRP 0.014 0.001 TRP C 168 HIS 0.003 0.001 HIS D 312 Details of bonding type rmsd covalent geometry : bond 0.00207 (15968) covalent geometry : angle 0.45156 (21542) hydrogen bonds : bond 0.03122 ( 921) hydrogen bonds : angle 3.43323 ( 2643) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 113 time to evaluate : 0.639 Fit side-chains REVERT: A 384 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8410 (mp) REVERT: A 464 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8342 (tm-30) REVERT: A 496 GLN cc_start: 0.8509 (mm-40) cc_final: 0.8142 (mm-40) REVERT: A 572 ASP cc_start: 0.8531 (t70) cc_final: 0.8303 (t70) REVERT: A 575 CYS cc_start: 0.8295 (OUTLIER) cc_final: 0.8068 (t) REVERT: B 384 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8441 (mp) REVERT: B 399 MET cc_start: 0.6546 (mtp) cc_final: 0.6305 (mtp) REVERT: B 452 GLU cc_start: 0.8491 (tm-30) cc_final: 0.8239 (tm-30) REVERT: B 494 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8929 (mmmm) REVERT: B 496 GLN cc_start: 0.8997 (mt0) cc_final: 0.8585 (mm-40) REVERT: B 572 ASP cc_start: 0.8553 (t70) cc_final: 0.8319 (t70) REVERT: B 588 TYR cc_start: 0.7521 (m-10) cc_final: 0.7299 (m-10) REVERT: B 601 GLN cc_start: 0.9106 (tm-30) cc_final: 0.8753 (tm-30) REVERT: C 384 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8436 (mp) REVERT: C 399 MET cc_start: 0.6586 (mtp) cc_final: 0.6368 (mtp) REVERT: C 494 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8936 (mmmm) REVERT: C 496 GLN cc_start: 0.8937 (mt0) cc_final: 0.8432 (mm-40) REVERT: C 498 GLN cc_start: 0.8530 (mt0) cc_final: 0.8283 (mt0) REVERT: C 572 ASP cc_start: 0.8540 (t70) cc_final: 0.8275 (t70) REVERT: C 588 TYR cc_start: 0.7632 (m-10) cc_final: 0.7244 (m-10) REVERT: C 601 GLN cc_start: 0.9103 (tm-30) cc_final: 0.8752 (tm-30) REVERT: D 384 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8433 (mp) REVERT: D 399 MET cc_start: 0.6603 (mtp) cc_final: 0.6365 (mtp) REVERT: D 494 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8434 (mtmm) REVERT: D 496 GLN cc_start: 0.8835 (mt0) cc_final: 0.8469 (mm-40) REVERT: D 514 ARG cc_start: 0.8782 (pmm-80) cc_final: 0.8520 (pmm-80) REVERT: D 601 GLN cc_start: 0.9090 (tm-30) cc_final: 0.8705 (tm-30) outliers start: 56 outliers final: 22 residues processed: 164 average time/residue: 0.5437 time to fit residues: 99.2970 Evaluate side-chains 143 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 494 LYS Chi-restraints excluded: chain B residue 523 LYS Chi-restraints excluded: chain B residue 575 CYS Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 381 ASP Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 494 LYS Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain D residue 260 TYR Chi-restraints excluded: chain D residue 329 ASN Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 494 LYS Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 171 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 133 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 175 optimal weight: 0.0070 chunk 94 optimal weight: 4.9990 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.090709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.062982 restraints weight = 30756.058| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.48 r_work: 0.2776 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15968 Z= 0.129 Angle : 0.477 9.516 21542 Z= 0.238 Chirality : 0.038 0.190 2362 Planarity : 0.003 0.032 2600 Dihedral : 11.943 135.869 2939 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 3.21 % Allowed : 24.64 % Favored : 72.14 % 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 are not related in a simple way. whole: 2.82 (0.20), residues: 1792 helix: 2.46 (0.15), residues: 1188 sheet: 1.84 (0.55), residues: 48 loop : 0.66 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 514 TYR 0.013 0.001 TYR D 588 PHE 0.007 0.001 PHE C 389 TRP 0.013 0.001 TRP C 168 HIS 0.004 0.001 HIS D 312 Details of bonding type rmsd covalent geometry : bond 0.00299 (15968) covalent geometry : angle 0.47695 (21542) hydrogen bonds : bond 0.03372 ( 921) hydrogen bonds : angle 3.50617 ( 2643) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 114 time to evaluate : 0.557 Fit side-chains REVERT: A 384 ILE cc_start: 0.8979 (OUTLIER) cc_final: 0.8405 (mp) REVERT: A 464 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8328 (tm-30) REVERT: A 494 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8563 (mtmp) REVERT: A 496 GLN cc_start: 0.8474 (mm-40) cc_final: 0.8156 (mm-40) REVERT: A 514 ARG cc_start: 0.8647 (pmm-80) cc_final: 0.8398 (pmm-80) REVERT: A 572 ASP cc_start: 0.8556 (t70) cc_final: 0.8319 (t70) REVERT: A 588 TYR cc_start: 0.8012 (m-80) cc_final: 0.7791 (m-80) REVERT: B 384 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8439 (mp) REVERT: B 399 MET cc_start: 0.6541 (mtp) cc_final: 0.6321 (mtp) REVERT: B 452 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8225 (tm-30) REVERT: B 496 GLN cc_start: 0.8991 (mt0) cc_final: 0.8610 (mm-40) REVERT: B 572 ASP cc_start: 0.8564 (t70) cc_final: 0.8306 (t70) REVERT: B 588 TYR cc_start: 0.7568 (m-10) cc_final: 0.7252 (m-10) REVERT: B 601 GLN cc_start: 0.9116 (tm-30) cc_final: 0.8763 (tm-30) REVERT: C 384 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8400 (mp) REVERT: C 494 LYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8928 (mmmm) REVERT: C 496 GLN cc_start: 0.8902 (mt0) cc_final: 0.8372 (mm-40) REVERT: C 498 GLN cc_start: 0.8530 (mt0) cc_final: 0.8210 (mt0) REVERT: C 572 ASP cc_start: 0.8554 (t70) cc_final: 0.8287 (t70) REVERT: C 588 TYR cc_start: 0.7624 (m-10) cc_final: 0.7245 (m-10) REVERT: C 601 GLN cc_start: 0.9117 (tm-30) cc_final: 0.8761 (tm-30) REVERT: D 384 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8444 (mp) REVERT: D 399 MET cc_start: 0.6545 (mtp) cc_final: 0.6294 (mtp) REVERT: D 496 GLN cc_start: 0.8723 (mt0) cc_final: 0.8454 (mm-40) REVERT: D 514 ARG cc_start: 0.8816 (pmm-80) cc_final: 0.8566 (pmm-80) REVERT: D 601 GLN cc_start: 0.9097 (tm-30) cc_final: 0.8713 (tm-30) outliers start: 52 outliers final: 37 residues processed: 162 average time/residue: 0.4915 time to fit residues: 89.1411 Evaluate side-chains 156 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 113 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 494 LYS Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 523 LYS Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 381 ASP Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 494 LYS Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain D residue 260 TYR Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 329 ASN Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 568 ILE Chi-restraints excluded: chain D residue 575 CYS Chi-restraints excluded: chain D residue 581 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 85 optimal weight: 10.0000 chunk 179 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 67 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 160 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.090586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.062924 restraints weight = 30643.704| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.44 r_work: 0.2778 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15968 Z= 0.139 Angle : 0.489 9.532 21542 Z= 0.243 Chirality : 0.039 0.191 2362 Planarity : 0.003 0.032 2600 Dihedral : 11.926 136.339 2933 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 4.01 % Allowed : 24.21 % Favored : 71.77 % 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 are not related in a simple way. whole: 2.81 (0.20), residues: 1792 helix: 2.44 (0.15), residues: 1188 sheet: 1.68 (0.56), residues: 48 loop : 0.68 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 514 TYR 0.018 0.001 TYR D 588 PHE 0.008 0.001 PHE A 298 TRP 0.014 0.001 TRP C 168 HIS 0.004 0.001 HIS D 312 Details of bonding type rmsd covalent geometry : bond 0.00326 (15968) covalent geometry : angle 0.48851 (21542) hydrogen bonds : bond 0.03457 ( 921) hydrogen bonds : angle 3.52635 ( 2643) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 113 time to evaluate : 0.382 Fit side-chains REVERT: A 384 ILE cc_start: 0.8971 (OUTLIER) cc_final: 0.8412 (mp) REVERT: A 464 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8323 (tm-30) REVERT: A 494 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8477 (mtmp) REVERT: A 496 GLN cc_start: 0.8506 (mm-40) cc_final: 0.8127 (mm-40) REVERT: A 572 ASP cc_start: 0.8549 (t70) cc_final: 0.8309 (t70) REVERT: B 384 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8453 (mp) REVERT: B 399 MET cc_start: 0.6533 (mtp) cc_final: 0.6333 (mtp) REVERT: B 452 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8217 (tm-30) REVERT: B 496 GLN cc_start: 0.9014 (mt0) cc_final: 0.8595 (mm-40) REVERT: B 572 ASP cc_start: 0.8574 (t70) cc_final: 0.8312 (t70) REVERT: B 588 TYR cc_start: 0.7593 (m-10) cc_final: 0.7329 (m-10) REVERT: B 601 GLN cc_start: 0.9114 (tm-30) cc_final: 0.8764 (tm-30) REVERT: C 384 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8426 (mp) REVERT: C 496 GLN cc_start: 0.8884 (mt0) cc_final: 0.8339 (mm-40) REVERT: C 498 GLN cc_start: 0.8511 (mt0) cc_final: 0.8183 (mt0) REVERT: C 572 ASP cc_start: 0.8555 (t70) cc_final: 0.8281 (t70) REVERT: C 588 TYR cc_start: 0.7632 (m-10) cc_final: 0.7252 (m-10) REVERT: C 601 GLN cc_start: 0.9120 (tm-30) cc_final: 0.8771 (tm-30) REVERT: D 384 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8438 (mp) REVERT: D 399 MET cc_start: 0.6552 (mtp) cc_final: 0.6306 (mtp) REVERT: D 496 GLN cc_start: 0.8714 (mt0) cc_final: 0.8444 (mm-40) REVERT: D 514 ARG cc_start: 0.8818 (pmm-80) cc_final: 0.8573 (pmm-80) REVERT: D 601 GLN cc_start: 0.9091 (tm-30) cc_final: 0.8718 (tm-30) outliers start: 65 outliers final: 41 residues processed: 170 average time/residue: 0.4690 time to fit residues: 89.4351 Evaluate side-chains 158 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 112 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 494 LYS Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 523 LYS Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 381 ASP Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain D residue 260 TYR Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 302 ASN Chi-restraints excluded: chain D residue 329 ASN Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 401 SER Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain D residue 568 ILE Chi-restraints excluded: chain D residue 575 CYS Chi-restraints excluded: chain D residue 581 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 21 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 99 optimal weight: 0.0980 chunk 72 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 141 optimal weight: 0.5980 chunk 44 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.091349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.063996 restraints weight = 30668.217| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.43 r_work: 0.2799 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15968 Z= 0.100 Angle : 0.472 10.308 21542 Z= 0.231 Chirality : 0.038 0.191 2362 Planarity : 0.003 0.031 2600 Dihedral : 11.715 136.119 2929 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 2.84 % Allowed : 25.45 % Favored : 71.71 % 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 are not related in a simple way. whole: 2.89 (0.20), residues: 1792 helix: 2.48 (0.15), residues: 1192 sheet: 1.83 (0.58), residues: 48 loop : 0.75 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 514 TYR 0.019 0.001 TYR D 588 PHE 0.007 0.001 PHE C 410 TRP 0.015 0.001 TRP C 168 HIS 0.003 0.001 HIS D 312 Details of bonding type rmsd covalent geometry : bond 0.00225 (15968) covalent geometry : angle 0.47204 (21542) hydrogen bonds : bond 0.03175 ( 921) hydrogen bonds : angle 3.47960 ( 2643) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 112 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 384 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8444 (mp) REVERT: A 399 MET cc_start: 0.6613 (mtp) cc_final: 0.6316 (mtp) REVERT: A 464 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8336 (tm-30) REVERT: A 494 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8466 (mtmp) REVERT: A 496 GLN cc_start: 0.8528 (mm-40) cc_final: 0.8157 (mm-40) REVERT: A 572 ASP cc_start: 0.8520 (t70) cc_final: 0.8276 (t70) REVERT: B 384 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8462 (mp) REVERT: B 399 MET cc_start: 0.6520 (mtp) cc_final: 0.6308 (mtp) REVERT: B 452 GLU cc_start: 0.8505 (tm-30) cc_final: 0.8246 (tm-30) REVERT: B 496 GLN cc_start: 0.9029 (mt0) cc_final: 0.8592 (mm-40) REVERT: B 572 ASP cc_start: 0.8573 (t70) cc_final: 0.8333 (t70) REVERT: B 588 TYR cc_start: 0.7622 (m-10) cc_final: 0.7296 (m-10) REVERT: B 601 GLN cc_start: 0.9111 (tm-30) cc_final: 0.8762 (tm-30) REVERT: C 384 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8429 (mp) REVERT: C 496 GLN cc_start: 0.8905 (mt0) cc_final: 0.8368 (mm-40) REVERT: C 498 GLN cc_start: 0.8532 (mt0) cc_final: 0.8278 (mt0) REVERT: C 572 ASP cc_start: 0.8541 (t70) cc_final: 0.8267 (t70) REVERT: C 601 GLN cc_start: 0.9105 (tm-30) cc_final: 0.8753 (tm-30) REVERT: D 384 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8473 (mp) REVERT: D 399 MET cc_start: 0.6547 (mtp) cc_final: 0.6298 (mtp) REVERT: D 496 GLN cc_start: 0.8748 (mt0) cc_final: 0.8514 (mm-40) REVERT: D 514 ARG cc_start: 0.8802 (pmm-80) cc_final: 0.8557 (pmm-80) REVERT: D 601 GLN cc_start: 0.9084 (tm-30) cc_final: 0.8698 (tm-30) outliers start: 46 outliers final: 33 residues processed: 157 average time/residue: 0.5043 time to fit residues: 88.5066 Evaluate side-chains 150 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 112 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 494 LYS Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 523 LYS Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 381 ASP Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 401 SER Chi-restraints excluded: chain D residue 260 TYR Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 329 ASN Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 401 SER Chi-restraints excluded: chain D residue 575 CYS Chi-restraints excluded: chain D residue 581 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 125 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 124 optimal weight: 0.0470 chunk 7 optimal weight: 0.0070 chunk 94 optimal weight: 0.5980 chunk 33 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 chunk 66 optimal weight: 0.0570 chunk 51 optimal weight: 1.9990 overall best weight: 0.5416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.092038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.064627 restraints weight = 30587.351| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.43 r_work: 0.2815 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15968 Z= 0.094 Angle : 0.495 10.728 21542 Z= 0.242 Chirality : 0.038 0.191 2362 Planarity : 0.003 0.031 2600 Dihedral : 11.541 135.360 2928 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 3.03 % Allowed : 25.63 % Favored : 71.34 % 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 are not related in a simple way. whole: 3.18 (0.20), residues: 1792 helix: 2.81 (0.15), residues: 1148 sheet: 2.01 (0.60), residues: 48 loop : 0.77 (0.27), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 514 TYR 0.044 0.001 TYR D 588 PHE 0.007 0.001 PHE C 410 TRP 0.014 0.001 TRP C 168 HIS 0.002 0.001 HIS D 312 Details of bonding type rmsd covalent geometry : bond 0.00209 (15968) covalent geometry : angle 0.49507 (21542) hydrogen bonds : bond 0.03069 ( 921) hydrogen bonds : angle 3.44660 ( 2643) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 110 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: A 384 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8403 (mp) REVERT: A 399 MET cc_start: 0.6489 (mtp) cc_final: 0.6195 (mtp) REVERT: A 464 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8350 (tm-30) REVERT: A 494 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8452 (mtmp) REVERT: A 496 GLN cc_start: 0.8517 (mm-40) cc_final: 0.8144 (mm-40) REVERT: A 572 ASP cc_start: 0.8520 (t0) cc_final: 0.8276 (t70) REVERT: B 384 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8434 (mp) REVERT: B 399 MET cc_start: 0.6491 (mtp) cc_final: 0.6284 (mtp) REVERT: B 452 GLU cc_start: 0.8496 (tm-30) cc_final: 0.8235 (tm-30) REVERT: B 496 GLN cc_start: 0.9028 (mt0) cc_final: 0.8579 (mm-40) REVERT: B 572 ASP cc_start: 0.8566 (t70) cc_final: 0.8308 (t70) REVERT: B 588 TYR cc_start: 0.7607 (m-10) cc_final: 0.7295 (m-10) REVERT: B 601 GLN cc_start: 0.9113 (tm-30) cc_final: 0.8762 (tm-30) REVERT: C 384 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8425 (mp) REVERT: C 399 MET cc_start: 0.6422 (mtp) cc_final: 0.6143 (mtp) REVERT: C 496 GLN cc_start: 0.8911 (mt0) cc_final: 0.8385 (mm-40) REVERT: C 498 GLN cc_start: 0.8511 (mt0) cc_final: 0.8251 (mt0) REVERT: C 572 ASP cc_start: 0.8536 (t70) cc_final: 0.8260 (t0) REVERT: C 601 GLN cc_start: 0.9111 (tm-30) cc_final: 0.8765 (tm-30) REVERT: D 384 ILE cc_start: 0.9003 (OUTLIER) cc_final: 0.8434 (mp) REVERT: D 399 MET cc_start: 0.6524 (mtp) cc_final: 0.6280 (mtp) REVERT: D 494 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8370 (mtmm) REVERT: D 496 GLN cc_start: 0.8745 (mt0) cc_final: 0.8520 (mm-40) REVERT: D 514 ARG cc_start: 0.8798 (pmm-80) cc_final: 0.8555 (pmm-80) REVERT: D 601 GLN cc_start: 0.9075 (tm-30) cc_final: 0.8692 (tm-30) outliers start: 49 outliers final: 31 residues processed: 155 average time/residue: 0.5152 time to fit residues: 89.3579 Evaluate side-chains 146 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 109 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 494 LYS Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 523 LYS Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 381 ASP Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 401 SER Chi-restraints excluded: chain D residue 260 TYR Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 329 ASN Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 401 SER Chi-restraints excluded: chain D residue 494 LYS Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 44 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 chunk 177 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 153 optimal weight: 0.6980 chunk 164 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.091576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.064166 restraints weight = 30319.339| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.42 r_work: 0.2803 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 15968 Z= 0.109 Angle : 0.501 11.279 21542 Z= 0.244 Chirality : 0.038 0.190 2362 Planarity : 0.003 0.031 2600 Dihedral : 11.564 135.238 2928 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.59 % Allowed : 26.07 % Favored : 71.34 % 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 are not related in a simple way. whole: 2.92 (0.20), residues: 1792 helix: 2.48 (0.15), residues: 1192 sheet: 1.99 (0.59), residues: 48 loop : 0.80 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 514 TYR 0.009 0.001 TYR D 375 PHE 0.006 0.001 PHE D 410 TRP 0.013 0.001 TRP C 168 HIS 0.003 0.001 HIS D 312 Details of bonding type rmsd covalent geometry : bond 0.00249 (15968) covalent geometry : angle 0.50122 (21542) hydrogen bonds : bond 0.03199 ( 921) hydrogen bonds : angle 3.46957 ( 2643) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 108 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: A 384 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8372 (mp) REVERT: A 399 MET cc_start: 0.6530 (mtp) cc_final: 0.6230 (mtp) REVERT: A 464 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8338 (tm-30) REVERT: A 494 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8448 (mtmp) REVERT: A 496 GLN cc_start: 0.8513 (mm-40) cc_final: 0.8139 (mm-40) REVERT: A 572 ASP cc_start: 0.8544 (t0) cc_final: 0.8290 (t70) REVERT: B 384 ILE cc_start: 0.9010 (OUTLIER) cc_final: 0.8415 (mp) REVERT: B 452 GLU cc_start: 0.8516 (tm-30) cc_final: 0.8246 (tm-30) REVERT: B 496 GLN cc_start: 0.9031 (mt0) cc_final: 0.8588 (mm-40) REVERT: B 572 ASP cc_start: 0.8566 (t70) cc_final: 0.8306 (t70) REVERT: B 588 TYR cc_start: 0.7578 (m-10) cc_final: 0.7269 (m-10) REVERT: B 601 GLN cc_start: 0.9145 (tm-30) cc_final: 0.8778 (tm-30) REVERT: C 384 ILE cc_start: 0.8994 (OUTLIER) cc_final: 0.8400 (mp) REVERT: C 399 MET cc_start: 0.6464 (mtp) cc_final: 0.6166 (mtp) REVERT: C 496 GLN cc_start: 0.8909 (mt0) cc_final: 0.8344 (mm-40) REVERT: C 498 GLN cc_start: 0.8540 (mt0) cc_final: 0.8267 (mt0) REVERT: C 572 ASP cc_start: 0.8543 (t70) cc_final: 0.8273 (t0) REVERT: C 601 GLN cc_start: 0.9106 (tm-30) cc_final: 0.8756 (tm-30) REVERT: D 384 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8411 (mp) REVERT: D 399 MET cc_start: 0.6551 (mtp) cc_final: 0.6305 (mtp) REVERT: D 494 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8637 (mmmm) REVERT: D 496 GLN cc_start: 0.8720 (mt0) cc_final: 0.8439 (mm-40) REVERT: D 601 GLN cc_start: 0.9083 (tm-30) cc_final: 0.8698 (tm-30) outliers start: 42 outliers final: 31 residues processed: 149 average time/residue: 0.4864 time to fit residues: 81.4786 Evaluate side-chains 144 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 107 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 494 LYS Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 523 LYS Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 381 ASP Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 401 SER Chi-restraints excluded: chain C residue 568 ILE Chi-restraints excluded: chain D residue 260 TYR Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 329 ASN Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 401 SER Chi-restraints excluded: chain D residue 494 LYS Chi-restraints excluded: chain D residue 501 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 78 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 18 optimal weight: 0.0470 chunk 125 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 168 optimal weight: 0.0270 chunk 26 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.091840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.064383 restraints weight = 30351.703| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.43 r_work: 0.2808 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 15968 Z= 0.104 Angle : 0.507 11.306 21542 Z= 0.247 Chirality : 0.038 0.190 2362 Planarity : 0.003 0.031 2600 Dihedral : 11.504 134.943 2927 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.47 % Allowed : 26.13 % Favored : 71.40 % 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 are not related in a simple way. whole: 2.93 (0.20), residues: 1792 helix: 2.48 (0.15), residues: 1192 sheet: 2.11 (0.60), residues: 48 loop : 0.80 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 514 TYR 0.031 0.001 TYR D 588 PHE 0.006 0.001 PHE D 410 TRP 0.013 0.001 TRP C 168 HIS 0.003 0.001 HIS D 312 Details of bonding type rmsd covalent geometry : bond 0.00238 (15968) covalent geometry : angle 0.50690 (21542) hydrogen bonds : bond 0.03143 ( 921) hydrogen bonds : angle 3.45699 ( 2643) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4062.69 seconds wall clock time: 70 minutes 22.18 seconds (4222.18 seconds total)