Starting phenix.real_space_refine on Fri Feb 16 08:11:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lfw_23307/02_2024/7lfw_23307_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lfw_23307/02_2024/7lfw_23307.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lfw_23307/02_2024/7lfw_23307_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lfw_23307/02_2024/7lfw_23307_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lfw_23307/02_2024/7lfw_23307_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lfw_23307/02_2024/7lfw_23307.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lfw_23307/02_2024/7lfw_23307.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lfw_23307/02_2024/7lfw_23307_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lfw_23307/02_2024/7lfw_23307_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.001 sd= 0.005 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 Ca 2 9.91 5 P 4 5.49 5 S 76 5.16 5 C 9684 2.51 5 N 2396 2.21 5 O 2684 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 186": "NH1" <-> "NH2" Residue "A ARG 218": "NH1" <-> "NH2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A ARG 280": "NH1" <-> "NH2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A ARG 287": "NH1" <-> "NH2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A GLU 341": "OE1" <-> "OE2" Residue "A ARG 344": "NH1" <-> "NH2" Residue "A ARG 407": "NH1" <-> "NH2" Residue "A GLU 409": "OE1" <-> "OE2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "A ARG 462": "NH1" <-> "NH2" Residue "A ARG 514": "NH1" <-> "NH2" Residue "A ARG 560": "NH1" <-> "NH2" Residue "A ARG 561": "NH1" <-> "NH2" Residue "B ARG 186": "NH1" <-> "NH2" Residue "B ARG 218": "NH1" <-> "NH2" Residue "B ARG 220": "NH1" <-> "NH2" Residue "B ARG 280": "NH1" <-> "NH2" Residue "B GLU 283": "OE1" <-> "OE2" Residue "B ARG 287": "NH1" <-> "NH2" Residue "B GLU 289": "OE1" <-> "OE2" Residue "B GLU 341": "OE1" <-> "OE2" Residue "B ARG 344": "NH1" <-> "NH2" Residue "B ARG 407": "NH1" <-> "NH2" Residue "B GLU 409": "OE1" <-> "OE2" Residue "B GLU 431": "OE1" <-> "OE2" Residue "B ARG 462": "NH1" <-> "NH2" Residue "B ARG 514": "NH1" <-> "NH2" Residue "B ARG 560": "NH1" <-> "NH2" Residue "B ARG 561": "NH1" <-> "NH2" Residue "C ARG 186": "NH1" <-> "NH2" Residue "C ARG 218": "NH1" <-> "NH2" Residue "C ARG 220": "NH1" <-> "NH2" Residue "C ARG 280": "NH1" <-> "NH2" Residue "C GLU 283": "OE1" <-> "OE2" Residue "C ARG 287": "NH1" <-> "NH2" Residue "C GLU 289": "OE1" <-> "OE2" Residue "C ARG 344": "NH1" <-> "NH2" Residue "C ARG 407": "NH1" <-> "NH2" Residue "C GLU 409": "OE1" <-> "OE2" Residue "C GLU 431": "OE1" <-> "OE2" Residue "C ARG 462": "NH1" <-> "NH2" Residue "C ARG 514": "NH1" <-> "NH2" Residue "C ARG 560": "NH1" <-> "NH2" Residue "C ARG 561": "NH1" <-> "NH2" Residue "D ARG 186": "NH1" <-> "NH2" Residue "D ARG 218": "NH1" <-> "NH2" Residue "D ARG 220": "NH1" <-> "NH2" Residue "D ARG 280": "NH1" <-> "NH2" Residue "D GLU 283": "OE1" <-> "OE2" Residue "D ARG 287": "NH1" <-> "NH2" Residue "D GLU 289": "OE1" <-> "OE2" Residue "D GLU 341": "OE1" <-> "OE2" Residue "D ARG 344": "NH1" <-> "NH2" Residue "D ARG 407": "NH1" <-> "NH2" Residue "D GLU 409": "OE1" <-> "OE2" Residue "D GLU 431": "OE1" <-> "OE2" Residue "D ARG 462": "NH1" <-> "NH2" Residue "D ARG 514": "NH1" <-> "NH2" Residue "D ARG 560": "NH1" <-> "NH2" Residue "D ARG 561": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14846 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: 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: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 25 Unusual residues: {' CA': 2, 'PCG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.77, per 1000 atoms: 0.52 Number of scatterers: 14846 At special positions: 0 Unit cell: (96.485, 96.485, 114.104, 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) Ca 2 19.99 S 76 16.00 P 4 15.00 O 2684 8.00 N 2396 7.00 C 9684 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.16 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 3408 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 8 sheets defined 60.4% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.79 Creating SS restraints... Processing helix chain 'A' and resid 163 through 188 Proline residue: A 175 - end of helix removed outlier: 5.259A pdb=" N ILE A 184 " --> pdb=" O TRP A 180 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 195 Processing helix chain 'A' and resid 197 through 219 removed outlier: 3.588A pdb=" N ILE A 202 " --> pdb=" O GLU A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 241 Processing helix chain 'A' and resid 244 through 252 Processing helix chain 'A' and resid 256 through 263 removed outlier: 4.343A pdb=" N LEU A 263 " --> pdb=" O TYR A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 291 removed outlier: 4.055A pdb=" N ASN A 273 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG A 277 " --> pdb=" O ARG A 274 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N SER A 279 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU A 289 " --> pdb=" O GLN A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 325 Processing helix chain 'A' and resid 345 through 360 Processing helix chain 'A' and resid 372 through 403 removed outlier: 3.519A pdb=" N GLY A 397 " --> pdb=" O VAL A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 423 Processing helix chain 'A' and resid 428 through 443 Processing helix chain 'A' and resid 450 through 456 removed outlier: 4.905A pdb=" N TYR A 456 " --> pdb=" O GLU A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 474 removed outlier: 5.039A pdb=" N GLU A 464 " --> pdb=" O LYS A 460 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ASP A 472 " --> pdb=" O ASN A 468 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N THR A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 492 removed outlier: 3.725A pdb=" N LEU A 491 " --> pdb=" O LEU A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 549 No H-bonds generated for 'chain 'A' and resid 547 through 549' Processing helix chain 'A' and resid 578 through 585 Processing helix chain 'A' and resid 592 through 604 Processing helix chain 'B' and resid 163 through 188 Proline residue: B 175 - end of helix removed outlier: 5.261A pdb=" N ILE B 184 " --> pdb=" O TRP B 180 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA B 185 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 195 Processing helix chain 'B' and resid 197 through 219 removed outlier: 3.588A pdb=" N ILE B 202 " --> pdb=" O GLU B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 241 Processing helix chain 'B' and resid 244 through 252 Processing helix chain 'B' and resid 256 through 263 removed outlier: 4.343A pdb=" N LEU B 263 " --> pdb=" O TYR B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 291 removed outlier: 4.054A pdb=" N ASN B 273 " --> pdb=" O ILE B 270 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG B 277 " --> pdb=" O ARG B 274 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N SER B 279 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLU B 289 " --> pdb=" O GLN B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 325 Processing helix chain 'B' and resid 345 through 360 Processing helix chain 'B' and resid 372 through 403 removed outlier: 3.519A pdb=" N GLY B 397 " --> pdb=" O VAL B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 423 Processing helix chain 'B' and resid 428 through 443 Processing helix chain 'B' and resid 450 through 456 removed outlier: 4.905A pdb=" N TYR B 456 " --> pdb=" O GLU B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 474 removed outlier: 5.040A pdb=" N GLU B 464 " --> pdb=" O LYS B 460 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ASP B 472 " --> pdb=" O ASN B 468 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N THR B 473 " --> pdb=" O VAL B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 492 removed outlier: 3.726A pdb=" N LEU B 491 " --> pdb=" O LEU B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 549 No H-bonds generated for 'chain 'B' and resid 547 through 549' Processing helix chain 'B' and resid 578 through 585 Processing helix chain 'B' and resid 592 through 604 Processing helix chain 'C' and resid 163 through 188 Proline residue: C 175 - end of helix removed outlier: 5.253A pdb=" N ILE C 184 " --> pdb=" O TRP C 180 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA C 185 " --> pdb=" O THR C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 195 Processing helix chain 'C' and resid 197 through 219 removed outlier: 3.588A pdb=" N ILE C 202 " --> pdb=" O GLU C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 241 Processing helix chain 'C' and resid 244 through 252 Processing helix chain 'C' and resid 256 through 263 removed outlier: 4.343A pdb=" N LEU C 263 " --> pdb=" O TYR C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 291 removed outlier: 4.055A pdb=" N ASN C 273 " --> pdb=" O ILE C 270 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG C 277 " --> pdb=" O ARG C 274 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N SER C 279 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU C 289 " --> pdb=" O GLN C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 325 Processing helix chain 'C' and resid 345 through 360 Processing helix chain 'C' and resid 372 through 403 removed outlier: 3.519A pdb=" N GLY C 397 " --> pdb=" O VAL C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 423 Processing helix chain 'C' and resid 428 through 443 Processing helix chain 'C' and resid 450 through 456 removed outlier: 4.905A pdb=" N TYR C 456 " --> pdb=" O GLU C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 474 removed outlier: 5.040A pdb=" N GLU C 464 " --> pdb=" O LYS C 460 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ASP C 472 " --> pdb=" O ASN C 468 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N THR C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 492 removed outlier: 3.726A pdb=" N LEU C 491 " --> pdb=" O LEU C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 549 No H-bonds generated for 'chain 'C' and resid 547 through 549' Processing helix chain 'C' and resid 578 through 585 Processing helix chain 'C' and resid 592 through 604 Processing helix chain 'D' and resid 163 through 188 Proline residue: D 175 - end of helix removed outlier: 5.253A pdb=" N ILE D 184 " --> pdb=" O TRP D 180 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA D 185 " --> pdb=" O THR D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 195 Processing helix chain 'D' and resid 197 through 219 removed outlier: 3.588A pdb=" N ILE D 202 " --> pdb=" O GLU D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 241 Processing helix chain 'D' and resid 244 through 252 Processing helix chain 'D' and resid 256 through 263 removed outlier: 4.343A pdb=" N LEU D 263 " --> pdb=" O TYR D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 291 removed outlier: 4.056A pdb=" N ASN D 273 " --> pdb=" O ILE D 270 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG D 277 " --> pdb=" O ARG D 274 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N SER D 279 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLU D 289 " --> pdb=" O GLN D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 325 Processing helix chain 'D' and resid 345 through 360 Processing helix chain 'D' and resid 372 through 403 removed outlier: 3.519A pdb=" N GLY D 397 " --> pdb=" O VAL D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 423 Processing helix chain 'D' and resid 428 through 443 Processing helix chain 'D' and resid 450 through 456 removed outlier: 4.905A pdb=" N TYR D 456 " --> pdb=" O GLU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 474 removed outlier: 5.040A pdb=" N GLU D 464 " --> pdb=" O LYS D 460 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ASP D 472 " --> pdb=" O ASN D 468 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N THR D 473 " --> pdb=" O VAL D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 492 removed outlier: 3.725A pdb=" N LEU D 491 " --> pdb=" O LEU D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 549 No H-bonds generated for 'chain 'D' and resid 547 through 549' Processing helix chain 'D' and resid 578 through 585 Processing helix chain 'D' and resid 592 through 604 Processing sheet with id= A, first strand: chain 'A' and resid 496 through 500 removed outlier: 6.562A pdb=" N PHE A 574 " --> pdb=" O ILE A 519 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ILE A 519 " --> pdb=" O PHE A 574 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU A 576 " --> pdb=" O TYR A 517 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N TYR A 517 " --> pdb=" O LEU A 576 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 564 through 568 removed outlier: 4.435A pdb=" N ASN A 564 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS A 523 " --> pdb=" O ILE A 568 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 496 through 500 removed outlier: 6.563A pdb=" N PHE B 574 " --> pdb=" O ILE B 519 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ILE B 519 " --> pdb=" O PHE B 574 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU B 576 " --> pdb=" O TYR B 517 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N TYR B 517 " --> pdb=" O LEU B 576 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 564 through 568 removed outlier: 4.434A pdb=" N ASN B 564 " --> pdb=" O VAL B 527 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS B 523 " --> pdb=" O ILE B 568 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 496 through 500 removed outlier: 6.562A pdb=" N PHE C 574 " --> pdb=" O ILE C 519 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ILE C 519 " --> pdb=" O PHE C 574 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU C 576 " --> pdb=" O TYR C 517 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N TYR C 517 " --> pdb=" O LEU C 576 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 564 through 568 removed outlier: 4.433A pdb=" N ASN C 564 " --> pdb=" O VAL C 527 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS C 523 " --> pdb=" O ILE C 568 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 496 through 500 removed outlier: 6.562A pdb=" N PHE D 574 " --> pdb=" O ILE D 519 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ILE D 519 " --> pdb=" O PHE D 574 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU D 576 " --> pdb=" O TYR D 517 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N TYR D 517 " --> pdb=" O LEU D 576 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 564 through 568 removed outlier: 4.434A pdb=" N ASN D 564 " --> pdb=" O VAL D 527 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS D 523 " --> pdb=" O ILE D 568 " (cutoff:3.500A) 808 hydrogen bonds defined for protein. 2148 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: 4.46 Time building geometry restraints manager: 6.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4358 1.34 - 1.45: 2369 1.45 - 1.57: 8333 1.57 - 1.69: 8 1.69 - 1.81: 128 Bond restraints: 15196 Sorted by residual: bond pdb=" C3' PCG A 701 " pdb=" C4' PCG A 701 " ideal model delta sigma weight residual 1.808 1.494 0.314 2.00e-02 2.50e+03 2.46e+02 bond pdb=" C3' PCG B 701 " pdb=" C4' PCG B 701 " ideal model delta sigma weight residual 1.808 1.495 0.313 2.00e-02 2.50e+03 2.45e+02 bond pdb=" C3' PCG C 701 " pdb=" C4' PCG C 701 " ideal model delta sigma weight residual 1.808 1.495 0.313 2.00e-02 2.50e+03 2.45e+02 bond pdb=" C3' PCG D 701 " pdb=" C4' PCG D 701 " ideal model delta sigma weight residual 1.808 1.495 0.313 2.00e-02 2.50e+03 2.45e+02 bond pdb=" C2' PCG C 701 " pdb=" C3' PCG C 701 " ideal model delta sigma weight residual 1.200 1.509 -0.309 2.00e-02 2.50e+03 2.38e+02 ... (remaining 15191 not shown) Histogram of bond angle deviations from ideal: 100.40 - 107.14: 363 107.14 - 113.88: 8581 113.88 - 120.62: 6172 120.62 - 127.36: 5361 127.36 - 134.10: 131 Bond angle restraints: 20608 Sorted by residual: angle pdb=" N ARG C 291 " pdb=" CA ARG C 291 " pdb=" C ARG C 291 " ideal model delta sigma weight residual 112.89 119.24 -6.35 1.24e+00 6.50e-01 2.62e+01 angle pdb=" N ARG D 291 " pdb=" CA ARG D 291 " pdb=" C ARG D 291 " ideal model delta sigma weight residual 112.89 119.21 -6.32 1.24e+00 6.50e-01 2.60e+01 angle pdb=" N ARG B 291 " pdb=" CA ARG B 291 " pdb=" C ARG B 291 " ideal model delta sigma weight residual 112.89 119.18 -6.29 1.24e+00 6.50e-01 2.57e+01 angle pdb=" N ARG A 291 " pdb=" CA ARG A 291 " pdb=" C ARG A 291 " ideal model delta sigma weight residual 112.89 119.16 -6.27 1.24e+00 6.50e-01 2.56e+01 angle pdb=" O3' PCG B 701 " pdb=" PA PCG B 701 " pdb=" O5' PCG B 701 " ideal model delta sigma weight residual 111.92 101.71 10.21 3.00e+00 1.11e-01 1.16e+01 ... (remaining 20603 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.65: 8043 16.65 - 33.29: 821 33.29 - 49.94: 120 49.94 - 66.59: 28 66.59 - 83.24: 4 Dihedral angle restraints: 9016 sinusoidal: 3700 harmonic: 5316 Sorted by residual: dihedral pdb=" CA GLU B 596 " pdb=" C GLU B 596 " pdb=" N GLU B 597 " pdb=" CA GLU B 597 " ideal model delta harmonic sigma weight residual 180.00 158.84 21.16 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA GLU A 596 " pdb=" C GLU A 596 " pdb=" N GLU A 597 " pdb=" CA GLU A 597 " ideal model delta harmonic sigma weight residual 180.00 158.88 21.12 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA GLU C 596 " pdb=" C GLU C 596 " pdb=" N GLU C 597 " pdb=" CA GLU C 597 " ideal model delta harmonic sigma weight residual 180.00 158.88 21.12 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 9013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 2193 0.088 - 0.175: 99 0.175 - 0.263: 8 0.263 - 0.351: 4 0.351 - 0.439: 8 Chirality restraints: 2312 Sorted by residual: chirality pdb=" C3' PCG C 701 " pdb=" C2' PCG C 701 " pdb=" C4' PCG C 701 " pdb=" O3' PCG C 701 " both_signs ideal model delta sigma weight residual False -2.10 -2.54 0.44 2.00e-01 2.50e+01 4.81e+00 chirality pdb=" C3' PCG D 701 " pdb=" C2' PCG D 701 " pdb=" C4' PCG D 701 " pdb=" O3' PCG D 701 " both_signs ideal model delta sigma weight residual False -2.10 -2.54 0.44 2.00e-01 2.50e+01 4.78e+00 chirality pdb=" C3' PCG A 701 " pdb=" C2' PCG A 701 " pdb=" C4' PCG A 701 " pdb=" O3' PCG A 701 " both_signs ideal model delta sigma weight residual False -2.10 -2.54 0.44 2.00e-01 2.50e+01 4.76e+00 ... (remaining 2309 not shown) Planarity restraints: 2540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 526 " -0.008 2.00e-02 2.50e+03 1.54e-02 2.37e+00 pdb=" C VAL D 526 " 0.027 2.00e-02 2.50e+03 pdb=" O VAL D 526 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL D 527 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 526 " -0.008 2.00e-02 2.50e+03 1.54e-02 2.36e+00 pdb=" C VAL C 526 " 0.027 2.00e-02 2.50e+03 pdb=" O VAL C 526 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL C 527 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 526 " -0.007 2.00e-02 2.50e+03 1.51e-02 2.29e+00 pdb=" C VAL B 526 " 0.026 2.00e-02 2.50e+03 pdb=" O VAL B 526 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL B 527 " -0.009 2.00e-02 2.50e+03 ... (remaining 2537 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2696 2.76 - 3.30: 15712 3.30 - 3.83: 27003 3.83 - 4.37: 32679 4.37 - 4.90: 53437 Nonbonded interactions: 131527 Sorted by model distance: nonbonded pdb=" O PHE B 216 " pdb=" OG1 THR B 219 " model vdw 2.226 2.440 nonbonded pdb=" O PHE A 216 " pdb=" OG1 THR A 219 " model vdw 2.226 2.440 nonbonded pdb=" O PHE C 216 " pdb=" OG1 THR C 219 " model vdw 2.226 2.440 nonbonded pdb=" O PHE D 216 " pdb=" OG1 THR D 219 " model vdw 2.227 2.440 nonbonded pdb=" O THR A 357 " pdb=" OG1 THR A 361 " model vdw 2.319 2.440 ... (remaining 131522 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 156 through 605 or resid 701)) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 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: 5.820 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 41.800 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 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 : 0.012 0.314 15196 Z= 0.745 Angle : 0.644 10.214 20608 Z= 0.359 Chirality : 0.050 0.439 2312 Planarity : 0.003 0.028 2540 Dihedral : 13.108 83.236 5608 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.25 % Allowed : 2.72 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.19), residues: 1792 helix: -0.53 (0.14), residues: 1080 sheet: -1.26 (0.82), residues: 56 loop : -0.92 (0.27), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 168 HIS 0.003 0.001 HIS C 312 PHE 0.014 0.002 PHE C 389 TYR 0.014 0.001 TYR C 349 ARG 0.003 0.000 ARG D 561 *********************** 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 267 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 263 time to evaluate : 1.538 Fit side-chains REVERT: A 266 ASN cc_start: 0.7431 (t0) cc_final: 0.7210 (t0) REVERT: A 428 LYS cc_start: 0.7731 (mtpt) cc_final: 0.7404 (mptp) REVERT: A 450 GLU cc_start: 0.6476 (pt0) cc_final: 0.6117 (pp20) REVERT: A 496 GLN cc_start: 0.7368 (mm-40) cc_final: 0.7093 (mt0) REVERT: A 605 LYS cc_start: 0.6438 (ptmt) cc_final: 0.6228 (mptp) REVERT: B 266 ASN cc_start: 0.7432 (t0) cc_final: 0.7216 (t0) REVERT: B 428 LYS cc_start: 0.7729 (mtpt) cc_final: 0.7399 (mptp) REVERT: B 450 GLU cc_start: 0.6477 (pt0) cc_final: 0.6120 (pp20) REVERT: B 496 GLN cc_start: 0.7384 (mm-40) cc_final: 0.7107 (mt0) REVERT: B 605 LYS cc_start: 0.6441 (ptmt) cc_final: 0.6225 (mptp) REVERT: C 266 ASN cc_start: 0.7427 (t0) cc_final: 0.7206 (t0) REVERT: C 428 LYS cc_start: 0.7740 (mtpt) cc_final: 0.7416 (mptp) REVERT: C 450 GLU cc_start: 0.6478 (pt0) cc_final: 0.6130 (pp20) REVERT: C 496 GLN cc_start: 0.7431 (mm-40) cc_final: 0.7142 (mt0) REVERT: C 605 LYS cc_start: 0.6438 (ptmt) cc_final: 0.6226 (mptp) REVERT: D 266 ASN cc_start: 0.7421 (t0) cc_final: 0.7181 (t0) REVERT: D 428 LYS cc_start: 0.7728 (mtpt) cc_final: 0.7399 (mptp) REVERT: D 450 GLU cc_start: 0.6475 (pt0) cc_final: 0.6119 (pp20) REVERT: D 496 GLN cc_start: 0.7373 (mm-40) cc_final: 0.7088 (mt0) REVERT: D 605 LYS cc_start: 0.6449 (ptmt) cc_final: 0.6219 (mptp) outliers start: 4 outliers final: 4 residues processed: 267 average time/residue: 1.4769 time to fit residues: 427.7830 Evaluate side-chains 174 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 170 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain B residue 291 ARG Chi-restraints excluded: chain C residue 291 ARG Chi-restraints excluded: chain D residue 291 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 0.8980 chunk 136 optimal weight: 0.8980 chunk 75 optimal weight: 0.1980 chunk 46 optimal weight: 0.9980 chunk 92 optimal weight: 0.0870 chunk 72 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 85 optimal weight: 8.9990 chunk 105 optimal weight: 0.9990 chunk 163 optimal weight: 4.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN A 302 ASN A 395 ASN A 402 ASN A 468 ASN A 534 GLN B 238 ASN B 302 ASN B 395 ASN B 402 ASN B 468 ASN B 534 GLN C 238 ASN C 302 ASN C 395 ASN C 402 ASN C 468 ASN C 534 GLN D 238 ASN D 302 ASN D 395 ASN D 402 ASN D 468 ASN D 534 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15196 Z= 0.155 Angle : 0.491 7.881 20608 Z= 0.253 Chirality : 0.039 0.148 2312 Planarity : 0.003 0.025 2540 Dihedral : 4.754 24.140 2048 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.60 % Allowed : 10.19 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.21), residues: 1792 helix: 0.66 (0.16), residues: 1088 sheet: -0.59 (0.89), residues: 48 loop : -0.41 (0.28), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 168 HIS 0.001 0.000 HIS D 312 PHE 0.011 0.001 PHE D 389 TYR 0.010 0.001 TYR A 349 ARG 0.002 0.000 ARG D 478 *********************** 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 234 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 208 time to evaluate : 1.620 Fit side-chains REVERT: A 266 ASN cc_start: 0.7478 (t0) cc_final: 0.7238 (t0) REVERT: A 428 LYS cc_start: 0.7692 (mtpt) cc_final: 0.7368 (mptp) REVERT: A 430 MET cc_start: 0.7289 (tpp) cc_final: 0.7060 (tpt) REVERT: A 450 GLU cc_start: 0.6554 (pt0) cc_final: 0.6206 (pp20) REVERT: A 496 GLN cc_start: 0.7466 (mm-40) cc_final: 0.7155 (mt0) REVERT: B 266 ASN cc_start: 0.7472 (t0) cc_final: 0.7238 (t0) REVERT: B 428 LYS cc_start: 0.7685 (mtpt) cc_final: 0.7361 (mptp) REVERT: B 430 MET cc_start: 0.7287 (tpp) cc_final: 0.7061 (tpt) REVERT: B 450 GLU cc_start: 0.6518 (pt0) cc_final: 0.6167 (pp20) REVERT: B 496 GLN cc_start: 0.7472 (mm-40) cc_final: 0.7144 (mt0) REVERT: C 266 ASN cc_start: 0.7460 (t0) cc_final: 0.7226 (t0) REVERT: C 428 LYS cc_start: 0.7694 (mtpt) cc_final: 0.7370 (mptp) REVERT: C 430 MET cc_start: 0.7291 (tpp) cc_final: 0.7062 (tpt) REVERT: C 450 GLU cc_start: 0.6528 (pt0) cc_final: 0.6180 (pp20) REVERT: C 496 GLN cc_start: 0.7481 (mm-40) cc_final: 0.7153 (mt0) REVERT: D 266 ASN cc_start: 0.7456 (t0) cc_final: 0.7223 (t0) REVERT: D 428 LYS cc_start: 0.7690 (mtpt) cc_final: 0.7367 (mptp) REVERT: D 430 MET cc_start: 0.7294 (tpp) cc_final: 0.7061 (tpt) REVERT: D 450 GLU cc_start: 0.6552 (pt0) cc_final: 0.6201 (pp20) REVERT: D 496 GLN cc_start: 0.7476 (mm-40) cc_final: 0.7154 (mt0) outliers start: 26 outliers final: 7 residues processed: 220 average time/residue: 1.3237 time to fit residues: 319.4227 Evaluate side-chains 187 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 180 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 540 ASP Chi-restraints excluded: chain D residue 540 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 8.9990 chunk 50 optimal weight: 0.9990 chunk 136 optimal weight: 0.5980 chunk 111 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 163 optimal weight: 5.9990 chunk 176 optimal weight: 9.9990 chunk 145 optimal weight: 0.6980 chunk 162 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 131 optimal weight: 9.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN A 419 GLN B 395 ASN B 419 GLN C 395 ASN C 419 GLN D 395 ASN D 419 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15196 Z= 0.162 Angle : 0.473 8.152 20608 Z= 0.244 Chirality : 0.039 0.146 2312 Planarity : 0.003 0.024 2540 Dihedral : 4.477 25.072 2032 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.42 % Allowed : 13.33 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.21), residues: 1792 helix: 0.94 (0.16), residues: 1096 sheet: -0.36 (0.84), residues: 48 loop : -0.30 (0.27), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 168 HIS 0.001 0.001 HIS C 312 PHE 0.012 0.001 PHE A 389 TYR 0.013 0.001 TYR B 349 ARG 0.002 0.000 ARG B 407 *********************** 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 206 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 183 time to evaluate : 1.836 Fit side-chains REVERT: A 266 ASN cc_start: 0.7499 (t0) cc_final: 0.7274 (t0) REVERT: A 428 LYS cc_start: 0.7716 (mtpt) cc_final: 0.7455 (mptp) REVERT: A 450 GLU cc_start: 0.6555 (pt0) cc_final: 0.6231 (pp20) REVERT: A 451 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7652 (ttpp) REVERT: B 228 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8143 (mm) REVERT: B 266 ASN cc_start: 0.7500 (t0) cc_final: 0.7296 (t0) REVERT: B 428 LYS cc_start: 0.7710 (mtpt) cc_final: 0.7451 (mptp) REVERT: B 450 GLU cc_start: 0.6559 (pt0) cc_final: 0.6229 (pp20) REVERT: B 451 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7657 (ttpp) REVERT: C 228 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8096 (mm) REVERT: C 266 ASN cc_start: 0.7498 (t0) cc_final: 0.7270 (t0) REVERT: C 428 LYS cc_start: 0.7715 (mtpt) cc_final: 0.7458 (mptp) REVERT: C 450 GLU cc_start: 0.6553 (pt0) cc_final: 0.6231 (pp20) REVERT: C 451 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7608 (ttpp) REVERT: D 228 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8141 (mm) REVERT: D 266 ASN cc_start: 0.7451 (t0) cc_final: 0.7180 (t0) REVERT: D 428 LYS cc_start: 0.7713 (mtpt) cc_final: 0.7455 (mptp) REVERT: D 450 GLU cc_start: 0.6557 (pt0) cc_final: 0.6230 (pp20) REVERT: D 451 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7610 (ttpp) outliers start: 23 outliers final: 8 residues processed: 194 average time/residue: 1.3271 time to fit residues: 282.6835 Evaluate side-chains 175 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 160 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 594 MET Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 540 ASP Chi-restraints excluded: chain C residue 594 MET Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 451 LYS Chi-restraints excluded: chain D residue 540 ASP Chi-restraints excluded: chain D residue 594 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 0.8980 chunk 123 optimal weight: 0.9980 chunk 84 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 109 optimal weight: 0.6980 chunk 164 optimal weight: 3.9990 chunk 173 optimal weight: 9.9990 chunk 85 optimal weight: 4.9990 chunk 155 optimal weight: 0.0060 chunk 46 optimal weight: 0.9980 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 395 ASN A 419 GLN ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 GLN ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 395 ASN C 419 GLN ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 395 ASN D 419 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15196 Z= 0.149 Angle : 0.461 8.420 20608 Z= 0.236 Chirality : 0.039 0.145 2312 Planarity : 0.003 0.025 2540 Dihedral : 4.347 24.050 2032 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.74 % Allowed : 14.38 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.21), residues: 1792 helix: 1.12 (0.16), residues: 1092 sheet: -0.38 (0.82), residues: 48 loop : -0.17 (0.27), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 168 HIS 0.001 0.000 HIS A 312 PHE 0.012 0.001 PHE B 535 TYR 0.011 0.001 TYR C 349 ARG 0.002 0.000 ARG C 407 *********************** 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 201 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 189 time to evaluate : 1.735 Fit side-chains REVERT: A 266 ASN cc_start: 0.7436 (t0) cc_final: 0.7170 (t0) REVERT: A 286 GLN cc_start: 0.7573 (tm-30) cc_final: 0.7098 (mt0) REVERT: A 450 GLU cc_start: 0.6538 (pt0) cc_final: 0.6249 (pp20) REVERT: B 266 ASN cc_start: 0.7446 (t0) cc_final: 0.7181 (t0) REVERT: B 286 GLN cc_start: 0.7577 (tm-30) cc_final: 0.7096 (mt0) REVERT: B 450 GLU cc_start: 0.6538 (pt0) cc_final: 0.6233 (pp20) REVERT: C 266 ASN cc_start: 0.7426 (t0) cc_final: 0.7171 (t0) REVERT: C 286 GLN cc_start: 0.7661 (tm-30) cc_final: 0.7157 (mt0) REVERT: C 431 GLU cc_start: 0.7697 (tt0) cc_final: 0.7371 (mt-10) REVERT: C 450 GLU cc_start: 0.6536 (pt0) cc_final: 0.6247 (pp20) REVERT: D 266 ASN cc_start: 0.7391 (t0) cc_final: 0.7136 (t0) REVERT: D 286 GLN cc_start: 0.7658 (tm-30) cc_final: 0.7159 (mt0) REVERT: D 450 GLU cc_start: 0.6537 (pt0) cc_final: 0.6247 (pp20) outliers start: 12 outliers final: 4 residues processed: 197 average time/residue: 1.3321 time to fit residues: 288.1304 Evaluate side-chains 164 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 160 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain C residue 540 ASP Chi-restraints excluded: chain D residue 540 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 8.9990 chunk 98 optimal weight: 0.0980 chunk 2 optimal weight: 0.6980 chunk 129 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 0.9980 chunk 156 optimal weight: 4.9990 chunk 43 optimal weight: 0.0770 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 395 ASN A 419 GLN ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 ASN B 419 GLN ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 395 ASN C 419 GLN ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 395 ASN D 419 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15196 Z= 0.154 Angle : 0.461 8.284 20608 Z= 0.236 Chirality : 0.038 0.145 2312 Planarity : 0.003 0.025 2540 Dihedral : 4.263 23.337 2032 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.11 % Allowed : 14.14 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.21), residues: 1792 helix: 1.20 (0.16), residues: 1096 sheet: -0.64 (0.78), residues: 48 loop : -0.18 (0.27), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 168 HIS 0.001 0.000 HIS B 312 PHE 0.012 0.001 PHE D 535 TYR 0.012 0.001 TYR B 349 ARG 0.002 0.000 ARG B 413 *********************** 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 195 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 177 time to evaluate : 1.894 Fit side-chains REVERT: A 266 ASN cc_start: 0.7410 (t0) cc_final: 0.7158 (t0) REVERT: A 450 GLU cc_start: 0.6525 (pt0) cc_final: 0.6244 (pp20) REVERT: B 266 ASN cc_start: 0.7429 (t0) cc_final: 0.7178 (t0) REVERT: B 450 GLU cc_start: 0.6493 (pt0) cc_final: 0.6245 (pp20) REVERT: C 266 ASN cc_start: 0.7420 (t0) cc_final: 0.7176 (t0) REVERT: C 431 GLU cc_start: 0.7641 (tt0) cc_final: 0.7339 (mt-10) REVERT: C 450 GLU cc_start: 0.6489 (pt0) cc_final: 0.6242 (pp20) REVERT: D 266 ASN cc_start: 0.7368 (t0) cc_final: 0.7131 (t0) REVERT: D 431 GLU cc_start: 0.7643 (tt0) cc_final: 0.7330 (mt-10) REVERT: D 450 GLU cc_start: 0.6522 (pt0) cc_final: 0.6241 (pp20) outliers start: 18 outliers final: 8 residues processed: 187 average time/residue: 1.3467 time to fit residues: 276.1845 Evaluate side-chains 167 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 159 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 594 MET Chi-restraints excluded: chain C residue 540 ASP Chi-restraints excluded: chain C residue 594 MET Chi-restraints excluded: chain D residue 540 ASP Chi-restraints excluded: chain D residue 594 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 0.9980 chunk 156 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 174 optimal weight: 9.9990 chunk 144 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 GLN A 395 ASN A 419 GLN A 422 HIS ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 GLN B 395 ASN B 419 GLN B 422 HIS ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 GLN C 395 ASN C 419 GLN ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 286 GLN D 395 ASN D 419 GLN D 422 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15196 Z= 0.166 Angle : 0.480 8.010 20608 Z= 0.245 Chirality : 0.039 0.145 2312 Planarity : 0.003 0.025 2540 Dihedral : 4.255 22.949 2032 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.93 % Allowed : 15.06 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.20), residues: 1792 helix: 1.01 (0.15), residues: 1132 sheet: -0.74 (0.77), residues: 48 loop : -0.16 (0.28), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 168 HIS 0.001 0.001 HIS C 312 PHE 0.012 0.001 PHE C 535 TYR 0.013 0.001 TYR B 349 ARG 0.005 0.000 ARG C 413 *********************** 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 185 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 170 time to evaluate : 1.613 Fit side-chains REVERT: A 266 ASN cc_start: 0.7440 (t0) cc_final: 0.7200 (t0) REVERT: A 413 ARG cc_start: 0.8035 (mtm-85) cc_final: 0.7822 (mtt-85) REVERT: A 431 GLU cc_start: 0.7626 (tt0) cc_final: 0.7320 (mt-10) REVERT: A 450 GLU cc_start: 0.6491 (pt0) cc_final: 0.6255 (pp20) REVERT: B 266 ASN cc_start: 0.7453 (t0) cc_final: 0.7209 (t0) REVERT: B 431 GLU cc_start: 0.7618 (tt0) cc_final: 0.7320 (mt-10) REVERT: B 450 GLU cc_start: 0.6508 (pt0) cc_final: 0.6267 (pp20) REVERT: C 266 ASN cc_start: 0.7434 (t0) cc_final: 0.7206 (t0) REVERT: C 431 GLU cc_start: 0.7626 (tt0) cc_final: 0.7328 (mt-10) REVERT: C 450 GLU cc_start: 0.6468 (pt0) cc_final: 0.6228 (pp20) REVERT: D 266 ASN cc_start: 0.7376 (t0) cc_final: 0.7133 (t0) REVERT: D 431 GLU cc_start: 0.7626 (tt0) cc_final: 0.7318 (mt-10) REVERT: D 450 GLU cc_start: 0.6505 (pt0) cc_final: 0.6226 (pp20) outliers start: 15 outliers final: 4 residues processed: 177 average time/residue: 1.3747 time to fit residues: 266.9073 Evaluate side-chains 165 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 161 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain C residue 540 ASP Chi-restraints excluded: chain D residue 540 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 99 optimal weight: 8.9990 chunk 127 optimal weight: 0.0980 chunk 98 optimal weight: 0.5980 chunk 146 optimal weight: 0.7980 chunk 97 optimal weight: 7.9990 chunk 173 optimal weight: 0.0980 chunk 108 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 80 optimal weight: 8.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 395 ASN A 419 GLN A 422 HIS ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 ASN B 419 GLN B 422 HIS ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 395 ASN C 419 GLN ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 395 ASN D 419 GLN D 422 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15196 Z= 0.134 Angle : 0.470 9.562 20608 Z= 0.237 Chirality : 0.038 0.141 2312 Planarity : 0.003 0.026 2540 Dihedral : 4.143 21.638 2032 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.74 % Allowed : 16.36 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.21), residues: 1792 helix: 1.22 (0.16), residues: 1108 sheet: -0.78 (0.79), residues: 48 loop : -0.12 (0.27), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 168 HIS 0.001 0.000 HIS C 312 PHE 0.012 0.001 PHE B 535 TYR 0.009 0.001 TYR B 349 ARG 0.005 0.000 ARG B 413 *********************** 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 193 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 181 time to evaluate : 1.853 Fit side-chains REVERT: A 266 ASN cc_start: 0.7347 (t0) cc_final: 0.7108 (t0) REVERT: A 431 GLU cc_start: 0.7625 (tt0) cc_final: 0.7330 (mt-10) REVERT: A 450 GLU cc_start: 0.6475 (pt0) cc_final: 0.6272 (pp20) REVERT: A 543 TYR cc_start: 0.7290 (p90) cc_final: 0.6979 (p90) REVERT: A 562 THR cc_start: 0.7899 (p) cc_final: 0.7589 (p) REVERT: A 578 LYS cc_start: 0.6188 (ttpt) cc_final: 0.5651 (ptmm) REVERT: B 266 ASN cc_start: 0.7379 (t0) cc_final: 0.7135 (t0) REVERT: B 431 GLU cc_start: 0.7614 (tt0) cc_final: 0.7327 (mt-10) REVERT: B 450 GLU cc_start: 0.6478 (pt0) cc_final: 0.6275 (pp20) REVERT: B 543 TYR cc_start: 0.7286 (p90) cc_final: 0.6977 (p90) REVERT: B 562 THR cc_start: 0.7902 (p) cc_final: 0.7594 (p) REVERT: B 578 LYS cc_start: 0.6167 (ttpt) cc_final: 0.5634 (ptmm) REVERT: C 266 ASN cc_start: 0.7348 (t0) cc_final: 0.7108 (t0) REVERT: C 431 GLU cc_start: 0.7626 (tt0) cc_final: 0.7339 (mt-10) REVERT: C 450 GLU cc_start: 0.6474 (pt0) cc_final: 0.6267 (pp20) REVERT: C 543 TYR cc_start: 0.7292 (p90) cc_final: 0.6983 (p90) REVERT: C 562 THR cc_start: 0.7906 (p) cc_final: 0.7594 (p) REVERT: C 578 LYS cc_start: 0.6171 (ttpt) cc_final: 0.5640 (ptmm) REVERT: D 266 ASN cc_start: 0.7307 (t0) cc_final: 0.7077 (t0) REVERT: D 431 GLU cc_start: 0.7624 (tt0) cc_final: 0.7331 (mt-10) REVERT: D 450 GLU cc_start: 0.6476 (pt0) cc_final: 0.6268 (pp20) REVERT: D 562 THR cc_start: 0.7902 (p) cc_final: 0.7586 (p) REVERT: D 578 LYS cc_start: 0.6173 (ttpt) cc_final: 0.5645 (ptmm) outliers start: 12 outliers final: 4 residues processed: 189 average time/residue: 1.2218 time to fit residues: 256.9206 Evaluate side-chains 178 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 174 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain C residue 540 ASP Chi-restraints excluded: chain D residue 540 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 52 optimal weight: 0.0670 chunk 34 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 chunk 118 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 136 optimal weight: 0.7980 overall best weight: 0.8922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 395 ASN A 419 GLN ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 ASN B 419 GLN B 422 HIS ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 395 ASN C 419 GLN C 422 HIS ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 395 ASN D 419 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15196 Z= 0.164 Angle : 0.497 9.389 20608 Z= 0.248 Chirality : 0.039 0.133 2312 Planarity : 0.003 0.026 2540 Dihedral : 4.176 21.866 2032 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.93 % Allowed : 16.54 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.21), residues: 1792 helix: 1.09 (0.15), residues: 1132 sheet: -0.85 (0.75), residues: 48 loop : -0.09 (0.28), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 168 HIS 0.002 0.001 HIS D 312 PHE 0.013 0.001 PHE B 535 TYR 0.012 0.001 TYR B 349 ARG 0.006 0.000 ARG A 413 *********************** 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 174 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 159 time to evaluate : 1.967 Fit side-chains REVERT: A 266 ASN cc_start: 0.7413 (t0) cc_final: 0.7172 (t0) REVERT: A 431 GLU cc_start: 0.7630 (tt0) cc_final: 0.7334 (mt-10) REVERT: A 450 GLU cc_start: 0.6478 (pt0) cc_final: 0.6269 (pp20) REVERT: A 543 TYR cc_start: 0.7310 (p90) cc_final: 0.7016 (p90) REVERT: A 562 THR cc_start: 0.7966 (p) cc_final: 0.7652 (p) REVERT: B 266 ASN cc_start: 0.7416 (t0) cc_final: 0.7172 (t0) REVERT: B 431 GLU cc_start: 0.7628 (tt0) cc_final: 0.7339 (mt-10) REVERT: B 450 GLU cc_start: 0.6475 (pt0) cc_final: 0.6274 (pp20) REVERT: B 496 GLN cc_start: 0.7384 (mm-40) cc_final: 0.7106 (mt0) REVERT: B 540 ASP cc_start: 0.6785 (OUTLIER) cc_final: 0.6499 (m-30) REVERT: B 562 THR cc_start: 0.7969 (p) cc_final: 0.7654 (p) REVERT: C 266 ASN cc_start: 0.7413 (t0) cc_final: 0.7168 (t0) REVERT: C 431 GLU cc_start: 0.7632 (tt0) cc_final: 0.7343 (mt-10) REVERT: C 450 GLU cc_start: 0.6477 (pt0) cc_final: 0.6265 (pp20) REVERT: C 540 ASP cc_start: 0.6818 (OUTLIER) cc_final: 0.6549 (m-30) REVERT: C 562 THR cc_start: 0.7972 (p) cc_final: 0.7658 (p) REVERT: D 266 ASN cc_start: 0.7367 (t0) cc_final: 0.7132 (t0) REVERT: D 431 GLU cc_start: 0.7628 (tt0) cc_final: 0.7334 (mt-10) REVERT: D 450 GLU cc_start: 0.6476 (pt0) cc_final: 0.6264 (pp20) REVERT: D 562 THR cc_start: 0.7966 (p) cc_final: 0.7647 (p) outliers start: 15 outliers final: 2 residues processed: 170 average time/residue: 1.2623 time to fit residues: 237.3561 Evaluate side-chains 156 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 152 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain C residue 540 ASP Chi-restraints excluded: chain D residue 540 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 0.9990 chunk 166 optimal weight: 8.9990 chunk 151 optimal weight: 0.7980 chunk 161 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 126 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 146 optimal weight: 0.8980 chunk 152 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 395 ASN A 419 GLN ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 ASN B 419 GLN ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 395 ASN C 419 GLN ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 395 ASN D 419 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15196 Z= 0.165 Angle : 0.498 9.272 20608 Z= 0.248 Chirality : 0.039 0.133 2312 Planarity : 0.003 0.026 2540 Dihedral : 4.172 21.788 2032 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.62 % Allowed : 17.28 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.20), residues: 1792 helix: 1.10 (0.15), residues: 1132 sheet: -0.91 (0.74), residues: 48 loop : -0.07 (0.28), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 168 HIS 0.002 0.001 HIS D 312 PHE 0.012 0.001 PHE C 535 TYR 0.013 0.001 TYR C 349 ARG 0.004 0.000 ARG A 413 *********************** 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 176 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 166 time to evaluate : 1.722 Fit side-chains REVERT: A 266 ASN cc_start: 0.7400 (t0) cc_final: 0.7166 (t0) REVERT: A 431 GLU cc_start: 0.7604 (tt0) cc_final: 0.7304 (mt-10) REVERT: A 450 GLU cc_start: 0.6474 (pt0) cc_final: 0.6271 (pp20) REVERT: A 496 GLN cc_start: 0.7388 (mm-40) cc_final: 0.7121 (mt0) REVERT: A 562 THR cc_start: 0.7956 (p) cc_final: 0.7625 (p) REVERT: A 582 MET cc_start: 0.5122 (mmm) cc_final: 0.4417 (mtt) REVERT: B 266 ASN cc_start: 0.7402 (t0) cc_final: 0.7169 (t0) REVERT: B 431 GLU cc_start: 0.7603 (tt0) cc_final: 0.7310 (mt-10) REVERT: B 450 GLU cc_start: 0.6479 (pt0) cc_final: 0.6277 (pp20) REVERT: B 496 GLN cc_start: 0.7397 (mm-40) cc_final: 0.7129 (mt0) REVERT: B 562 THR cc_start: 0.7956 (p) cc_final: 0.7628 (p) REVERT: B 582 MET cc_start: 0.5097 (mmm) cc_final: 0.4429 (mtt) REVERT: C 266 ASN cc_start: 0.7396 (t0) cc_final: 0.7161 (t0) REVERT: C 431 GLU cc_start: 0.7614 (tt0) cc_final: 0.7322 (mt-10) REVERT: C 450 GLU cc_start: 0.6473 (pt0) cc_final: 0.6264 (pp20) REVERT: C 496 GLN cc_start: 0.7390 (mm-40) cc_final: 0.7126 (mt0) REVERT: C 562 THR cc_start: 0.7960 (p) cc_final: 0.7635 (p) REVERT: C 582 MET cc_start: 0.5149 (mmm) cc_final: 0.4484 (mtt) REVERT: D 266 ASN cc_start: 0.7410 (t0) cc_final: 0.7183 (t0) REVERT: D 431 GLU cc_start: 0.7603 (tt0) cc_final: 0.7307 (mt-10) REVERT: D 450 GLU cc_start: 0.6466 (pt0) cc_final: 0.6254 (pp20) REVERT: D 496 GLN cc_start: 0.7376 (mm-40) cc_final: 0.7131 (mt0) REVERT: D 562 THR cc_start: 0.7957 (p) cc_final: 0.7625 (p) REVERT: D 582 MET cc_start: 0.5147 (mmm) cc_final: 0.4488 (mtt) outliers start: 10 outliers final: 4 residues processed: 172 average time/residue: 1.4219 time to fit residues: 267.6747 Evaluate side-chains 163 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 159 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain C residue 540 ASP Chi-restraints excluded: chain D residue 540 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 8.9990 chunk 104 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 118 optimal weight: 2.9990 chunk 179 optimal weight: 9.9990 chunk 165 optimal weight: 0.4980 chunk 142 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 395 ASN A 419 GLN ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 ASN B 419 GLN ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 395 ASN C 419 GLN C 422 HIS ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 395 ASN D 419 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15196 Z= 0.225 Angle : 0.534 8.834 20608 Z= 0.267 Chirality : 0.040 0.133 2312 Planarity : 0.004 0.026 2540 Dihedral : 4.322 22.636 2032 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.31 % Allowed : 17.10 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.20), residues: 1792 helix: 0.99 (0.15), residues: 1128 sheet: -1.11 (0.73), residues: 48 loop : -0.04 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 168 HIS 0.002 0.001 HIS C 312 PHE 0.015 0.002 PHE C 535 TYR 0.016 0.001 TYR D 349 ARG 0.005 0.000 ARG A 413 ********************** 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 167 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 162 time to evaluate : 1.677 Fit side-chains REVERT: A 266 ASN cc_start: 0.7386 (t0) cc_final: 0.7180 (t0) REVERT: A 395 ASN cc_start: 0.6181 (m-40) cc_final: 0.5775 (t0) REVERT: A 450 GLU cc_start: 0.6502 (pt0) cc_final: 0.6222 (pp20) REVERT: A 475 LYS cc_start: 0.7926 (mmtt) cc_final: 0.7426 (ptpt) REVERT: A 496 GLN cc_start: 0.7377 (mm-40) cc_final: 0.7128 (mt0) REVERT: A 562 THR cc_start: 0.7959 (p) cc_final: 0.7681 (p) REVERT: B 266 ASN cc_start: 0.7391 (t0) cc_final: 0.7184 (t0) REVERT: B 395 ASN cc_start: 0.6155 (m-40) cc_final: 0.5760 (t0) REVERT: B 431 GLU cc_start: 0.7656 (tt0) cc_final: 0.7329 (mt-10) REVERT: B 450 GLU cc_start: 0.6499 (pt0) cc_final: 0.6221 (pp20) REVERT: B 475 LYS cc_start: 0.7908 (mmtt) cc_final: 0.7452 (ptpt) REVERT: B 496 GLN cc_start: 0.7367 (mm-40) cc_final: 0.7135 (mt0) REVERT: B 562 THR cc_start: 0.7962 (p) cc_final: 0.7686 (p) REVERT: B 582 MET cc_start: 0.5146 (mmm) cc_final: 0.4500 (mtt) REVERT: C 266 ASN cc_start: 0.7384 (t0) cc_final: 0.7178 (t0) REVERT: C 395 ASN cc_start: 0.6155 (m-40) cc_final: 0.5762 (t0) REVERT: C 450 GLU cc_start: 0.6501 (pt0) cc_final: 0.6218 (pp20) REVERT: C 475 LYS cc_start: 0.7941 (mmtt) cc_final: 0.7457 (ptpt) REVERT: C 496 GLN cc_start: 0.7423 (mm-40) cc_final: 0.7174 (mt0) REVERT: C 562 THR cc_start: 0.7958 (p) cc_final: 0.7667 (p) REVERT: C 582 MET cc_start: 0.5198 (mmm) cc_final: 0.4534 (mtt) REVERT: D 395 ASN cc_start: 0.6208 (m-40) cc_final: 0.5796 (t0) REVERT: D 431 GLU cc_start: 0.7658 (tt0) cc_final: 0.7324 (mt-10) REVERT: D 450 GLU cc_start: 0.6510 (pt0) cc_final: 0.6232 (pp20) REVERT: D 475 LYS cc_start: 0.7923 (mmtt) cc_final: 0.7419 (ptpt) REVERT: D 496 GLN cc_start: 0.7427 (mm-40) cc_final: 0.7176 (mt0) REVERT: D 562 THR cc_start: 0.7961 (p) cc_final: 0.7669 (p) REVERT: D 582 MET cc_start: 0.5141 (mmm) cc_final: 0.4486 (mtt) outliers start: 5 outliers final: 4 residues processed: 163 average time/residue: 1.4444 time to fit residues: 257.0579 Evaluate side-chains 164 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 160 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain C residue 540 ASP Chi-restraints excluded: chain D residue 540 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 131 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 143 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 146 optimal weight: 0.8980 chunk 18 optimal weight: 0.2980 chunk 26 optimal weight: 0.8980 chunk 125 optimal weight: 10.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 GLN ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 GLN ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 419 GLN ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.154869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.121783 restraints weight = 17886.142| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.71 r_work: 0.3122 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15196 Z= 0.179 Angle : 0.512 8.652 20608 Z= 0.255 Chirality : 0.039 0.134 2312 Planarity : 0.003 0.026 2540 Dihedral : 4.252 22.074 2032 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.37 % Allowed : 16.91 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.21), residues: 1792 helix: 1.09 (0.16), residues: 1108 sheet: -1.16 (0.72), residues: 48 loop : 0.15 (0.28), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 168 HIS 0.002 0.001 HIS C 312 PHE 0.015 0.001 PHE B 535 TYR 0.013 0.001 TYR D 199 ARG 0.004 0.000 ARG A 413 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4870.54 seconds wall clock time: 88 minutes 15.59 seconds (5295.59 seconds total)