Starting phenix.real_space_refine on Tue Apr 9 00:08:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lfx_23308/04_2024/7lfx_23308_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lfx_23308/04_2024/7lfx_23308.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lfx_23308/04_2024/7lfx_23308_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lfx_23308/04_2024/7lfx_23308_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lfx_23308/04_2024/7lfx_23308_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lfx_23308/04_2024/7lfx_23308.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lfx_23308/04_2024/7lfx_23308.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lfx_23308/04_2024/7lfx_23308_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lfx_23308/04_2024/7lfx_23308_neut_updated.pdb" } resolution = 3.1 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= 0.000 sd= 0.004 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 7.69, per 1000 atoms: 0.52 Number of scatterers: 14846 At special positions: 0 Unit cell: (94.185, 94.185, 115.115, 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: 6.25 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: 2.87 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: 3.828A 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: 4.726A 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: 5.846A 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: 4.726A pdb=" N SER B 279 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 4.198A 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: 5.848A 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: 3.586A 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: 4.344A pdb=" N LEU C 263 " --> pdb=" O TYR C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 291 removed outlier: 4.056A pdb=" N ASN C 273 " --> pdb=" O ILE C 270 " (cutoff:3.500A) removed outlier: 3.651A 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: 4.342A 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: 5.741A pdb=" N THR D 473 " --> pdb=" O VAL D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 492 removed outlier: 3.726A 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: 6.563A 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: 4.434A 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: 6.562A pdb=" N PHE B 574 " --> pdb=" O ILE B 519 " (cutoff:3.500A) removed outlier: 5.862A 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: 6.583A 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: 4.434A pdb=" N ASN C 564 " --> pdb=" O VAL C 527 " (cutoff:3.500A) removed outlier: 3.984A 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: 6.582A 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: 4.56 Time building geometry restraints manager: 6.79 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: 4304 1.34 - 1.45: 2412 1.45 - 1.57: 8344 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 2.46e+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 A 701 " pdb=" C3' PCG A 701 " ideal model delta sigma weight residual 1.200 1.508 -0.308 2.00e-02 2.50e+03 2.37e+02 ... (remaining 15191 not shown) Histogram of bond angle deviations from ideal: 100.38 - 107.13: 362 107.13 - 113.89: 8590 113.89 - 120.64: 6267 120.64 - 127.39: 5261 127.39 - 134.15: 128 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 112.89 119.23 -6.34 1.24e+00 6.50e-01 2.61e+01 angle pdb=" N ARG D 291 " pdb=" CA ARG D 291 " pdb=" C ARG D 291 " ideal model delta sigma weight residual 112.89 119.20 -6.31 1.24e+00 6.50e-01 2.59e+01 angle pdb=" N ARG A 291 " pdb=" CA ARG A 291 " pdb=" C ARG A 291 " ideal model delta sigma weight residual 112.89 119.18 -6.29 1.24e+00 6.50e-01 2.57e+01 angle pdb=" N ARG B 291 " pdb=" CA ARG B 291 " pdb=" C ARG B 291 " ideal model delta sigma weight residual 112.89 119.17 -6.28 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 111.92 101.72 10.20 3.00e+00 1.11e-01 1.16e+01 ... (remaining 20603 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.64: 8044 16.64 - 33.28: 820 33.28 - 49.92: 120 49.92 - 66.57: 28 66.57 - 83.21: 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 180.00 158.83 21.17 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 180.00 158.87 21.13 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA GLU D 596 " pdb=" C GLU D 596 " pdb=" N GLU D 597 " pdb=" CA GLU D 597 " ideal model delta harmonic sigma weight residual 180.00 158.87 21.13 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 9013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 2196 0.088 - 0.176: 96 0.176 - 0.264: 8 0.264 - 0.352: 4 0.352 - 0.440: 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 4.84e+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 4.77e+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 4.76e+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 1.55e-02 2.39e+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 2.37e+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 A 526 " -0.008 2.00e-02 2.50e+03 1.52e-02 2.31e+00 pdb=" C VAL A 526 " 0.026 2.00e-02 2.50e+03 pdb=" O VAL A 526 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL A 527 " -0.009 2.00e-02 2.50e+03 ... (remaining 2537 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2687 2.76 - 3.30: 15717 3.30 - 3.83: 26991 3.83 - 4.37: 32682 4.37 - 4.90: 53459 Nonbonded interactions: 131536 Sorted by model distance: nonbonded pdb=" O PHE C 216 " pdb=" OG1 THR C 219 " model vdw 2.226 2.440 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 2.227 2.440 nonbonded pdb=" O PHE D 216 " pdb=" OG1 THR D 219 " model vdw 2.227 2.440 nonbonded pdb=" O THR D 357 " pdb=" OG1 THR D 361 " model vdw 2.319 2.440 ... (remaining 131531 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: 1.420 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: 5.910 Check model and map are aligned: 0.230 Set scattering table: 0.130 Process input model: 42.220 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 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 10.200 20608 Z= 0.359 Chirality : 0.050 0.440 2312 Planarity : 0.003 0.028 2540 Dihedral : 13.108 83.206 5608 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.25 % Allowed : 2.65 % Favored : 97.10 % 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: -1.18 (0.19), residues: 1792 helix: -0.53 (0.14), residues: 1080 sheet: -1.27 (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 0.015 0.001 TYR A 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 370 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 366 time to evaluate : 1.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 LEU cc_start: 0.8512 (mt) cc_final: 0.8307 (mt) REVERT: A 594 MET cc_start: 0.4708 (ppp) cc_final: 0.3440 (ttt) REVERT: B 387 LEU cc_start: 0.8518 (mt) cc_final: 0.8310 (mt) REVERT: B 594 MET cc_start: 0.4704 (ppp) cc_final: 0.3432 (ttt) REVERT: C 220 ARG cc_start: 0.7772 (mmt90) cc_final: 0.7463 (mmt90) REVERT: C 387 LEU cc_start: 0.8529 (mt) cc_final: 0.8322 (mt) REVERT: C 594 MET cc_start: 0.4702 (ppp) cc_final: 0.3429 (ttt) REVERT: D 387 LEU cc_start: 0.8510 (mt) cc_final: 0.8305 (mt) REVERT: D 407 ARG cc_start: 0.7295 (ttt90) cc_final: 0.7031 (tpt170) REVERT: D 594 MET cc_start: 0.4692 (ppp) cc_final: 0.3433 (ttt) outliers start: 4 outliers final: 0 residues processed: 370 average time/residue: 0.3129 time to fit residues: 162.2117 Evaluate side-chains 214 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 0.9980 chunk 136 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 92 optimal weight: 0.2980 chunk 72 optimal weight: 7.9990 chunk 141 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 85 optimal weight: 30.0000 chunk 105 optimal weight: 1.9990 chunk 163 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 422 HIS A 468 ASN A 496 GLN A 498 GLN A 534 GLN B 238 ASN B 338 ASN B 395 ASN B 468 ASN B 496 GLN B 498 GLN B 534 GLN C 238 ASN C 338 ASN C 395 ASN C 468 ASN C 496 GLN C 498 GLN C 534 GLN D 238 ASN D 395 ASN D 411 GLN D 422 HIS D 444 ASN D 468 ASN D 496 GLN D 498 GLN D 534 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15196 Z= 0.187 Angle : 0.496 6.733 20608 Z= 0.260 Chirality : 0.040 0.176 2312 Planarity : 0.004 0.026 2540 Dihedral : 4.597 22.149 2032 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.53 % Allowed : 10.31 % Favored : 87.16 % 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: 0.21 (0.21), residues: 1792 helix: 0.59 (0.16), residues: 1092 sheet: -0.86 (0.78), residues: 56 loop : -0.37 (0.28), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 168 HIS 0.004 0.001 HIS C 422 PHE 0.011 0.001 PHE C 574 TYR 0.010 0.001 TYR D 349 ARG 0.003 0.000 ARG D 220 *********************** 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 278 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 237 time to evaluate : 1.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7453 (m-30) cc_final: 0.6720 (m-30) REVERT: A 547 ILE cc_start: 0.7622 (OUTLIER) cc_final: 0.7252 (mp) REVERT: A 594 MET cc_start: 0.4605 (ppp) cc_final: 0.3142 (ttt) REVERT: B 204 ASP cc_start: 0.7441 (m-30) cc_final: 0.6716 (m-30) REVERT: B 286 GLN cc_start: 0.7503 (tm-30) cc_final: 0.7193 (mt0) REVERT: B 498 GLN cc_start: 0.7336 (OUTLIER) cc_final: 0.7130 (mt0) REVERT: B 547 ILE cc_start: 0.7588 (OUTLIER) cc_final: 0.7239 (mp) REVERT: B 594 MET cc_start: 0.4672 (ppp) cc_final: 0.3099 (ttt) REVERT: C 204 ASP cc_start: 0.7459 (m-30) cc_final: 0.6711 (m-30) REVERT: C 286 GLN cc_start: 0.7489 (tm-30) cc_final: 0.7178 (mt0) REVERT: C 464 GLU cc_start: 0.6643 (tp30) cc_final: 0.6404 (tt0) REVERT: C 547 ILE cc_start: 0.7594 (OUTLIER) cc_final: 0.7246 (mp) REVERT: C 594 MET cc_start: 0.4662 (ppp) cc_final: 0.3100 (ttt) REVERT: D 204 ASP cc_start: 0.7461 (m-30) cc_final: 0.6714 (m-30) REVERT: D 286 GLN cc_start: 0.7497 (tm-30) cc_final: 0.7187 (mt0) REVERT: D 464 GLU cc_start: 0.6646 (tp30) cc_final: 0.6389 (tt0) REVERT: D 547 ILE cc_start: 0.7609 (OUTLIER) cc_final: 0.7260 (mp) REVERT: D 594 MET cc_start: 0.4600 (ppp) cc_final: 0.3144 (ttt) outliers start: 41 outliers final: 17 residues processed: 257 average time/residue: 0.2740 time to fit residues: 106.2255 Evaluate side-chains 215 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 193 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 575 CYS Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 540 ASP Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 336 ASP Chi-restraints excluded: chain D residue 460 LYS Chi-restraints excluded: chain D residue 540 ASP Chi-restraints excluded: chain D residue 547 ILE Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 111 optimal weight: 0.0670 chunk 45 optimal weight: 7.9990 chunk 163 optimal weight: 0.6980 chunk 176 optimal weight: 10.0000 chunk 145 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 55 optimal weight: 0.0870 chunk 131 optimal weight: 0.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 ASN ** A 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 HIS ** B 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 HIS ** C 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15196 Z= 0.149 Angle : 0.454 4.786 20608 Z= 0.240 Chirality : 0.039 0.154 2312 Planarity : 0.003 0.027 2540 Dihedral : 4.413 22.505 2032 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.04 % Allowed : 13.27 % Favored : 84.69 % 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: 0.64 (0.21), residues: 1792 helix: 0.98 (0.16), residues: 1096 sheet: -0.60 (0.78), residues: 56 loop : -0.31 (0.28), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 168 HIS 0.002 0.001 HIS D 422 PHE 0.009 0.001 PHE D 574 TYR 0.008 0.001 TYR A 260 ARG 0.003 0.000 ARG C 220 *********************** 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 250 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 217 time to evaluate : 1.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7459 (m-30) cc_final: 0.6769 (m-30) REVERT: A 547 ILE cc_start: 0.7560 (OUTLIER) cc_final: 0.7207 (mp) REVERT: A 594 MET cc_start: 0.4645 (ppp) cc_final: 0.3679 (tpt) REVERT: B 204 ASP cc_start: 0.7456 (m-30) cc_final: 0.6773 (m-30) REVERT: B 286 GLN cc_start: 0.7393 (tm-30) cc_final: 0.7190 (mt0) REVERT: B 498 GLN cc_start: 0.7401 (mt0) cc_final: 0.7140 (mt0) REVERT: B 547 ILE cc_start: 0.7570 (OUTLIER) cc_final: 0.7210 (mp) REVERT: B 594 MET cc_start: 0.4667 (ppp) cc_final: 0.3726 (tpt) REVERT: C 204 ASP cc_start: 0.7465 (m-30) cc_final: 0.6770 (m-30) REVERT: C 286 GLN cc_start: 0.7388 (tm-30) cc_final: 0.7186 (mt0) REVERT: C 547 ILE cc_start: 0.7566 (OUTLIER) cc_final: 0.7205 (mp) REVERT: C 594 MET cc_start: 0.4651 (ppp) cc_final: 0.3716 (tpt) REVERT: D 204 ASP cc_start: 0.7455 (m-30) cc_final: 0.6769 (m-30) REVERT: D 547 ILE cc_start: 0.7579 (OUTLIER) cc_final: 0.7228 (mp) REVERT: D 594 MET cc_start: 0.4629 (ppp) cc_final: 0.3676 (tpt) outliers start: 33 outliers final: 15 residues processed: 230 average time/residue: 0.2275 time to fit residues: 82.1139 Evaluate side-chains 222 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 203 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 575 CYS Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 540 ASP Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 460 LYS Chi-restraints excluded: chain D residue 540 ASP Chi-restraints excluded: chain D residue 547 ILE Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 1.9990 chunk 123 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 78 optimal weight: 0.0980 chunk 109 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 173 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 155 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- 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 338 ASN A 468 ASN A 498 GLN ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 286 GLN D 338 ASN D 498 GLN ** D 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15196 Z= 0.265 Angle : 0.510 5.688 20608 Z= 0.272 Chirality : 0.041 0.154 2312 Planarity : 0.004 0.029 2540 Dihedral : 4.546 23.658 2032 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.09 % Allowed : 13.95 % Favored : 82.96 % 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: 0.52 (0.20), residues: 1792 helix: 0.90 (0.15), residues: 1100 sheet: -1.31 (0.68), residues: 56 loop : -0.32 (0.28), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 168 HIS 0.003 0.001 HIS A 312 PHE 0.015 0.002 PHE A 298 TYR 0.017 0.002 TYR B 349 ARG 0.003 0.001 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 255 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 205 time to evaluate : 1.785 Fit side-chains REVERT: A 204 ASP cc_start: 0.7414 (m-30) cc_final: 0.6966 (m-30) REVERT: A 543 TYR cc_start: 0.6621 (p90) cc_final: 0.6340 (p90) REVERT: A 547 ILE cc_start: 0.7847 (OUTLIER) cc_final: 0.7466 (mp) REVERT: A 594 MET cc_start: 0.4709 (ppp) cc_final: 0.3769 (tpt) REVERT: B 204 ASP cc_start: 0.7411 (m-30) cc_final: 0.6963 (m-30) REVERT: B 543 TYR cc_start: 0.6615 (p90) cc_final: 0.6332 (p90) REVERT: B 547 ILE cc_start: 0.7867 (OUTLIER) cc_final: 0.7482 (mp) REVERT: B 594 MET cc_start: 0.4629 (ppp) cc_final: 0.3706 (tpt) REVERT: C 204 ASP cc_start: 0.7427 (m-30) cc_final: 0.6753 (m-30) REVERT: C 498 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.7540 (mt0) REVERT: C 543 TYR cc_start: 0.6609 (p90) cc_final: 0.6323 (p90) REVERT: C 547 ILE cc_start: 0.7863 (OUTLIER) cc_final: 0.7479 (mp) REVERT: C 594 MET cc_start: 0.4620 (ppp) cc_final: 0.3698 (tpt) REVERT: D 204 ASP cc_start: 0.7408 (m-30) cc_final: 0.6961 (m-30) REVERT: D 543 TYR cc_start: 0.6625 (p90) cc_final: 0.6343 (p90) REVERT: D 547 ILE cc_start: 0.7863 (OUTLIER) cc_final: 0.7478 (mp) REVERT: D 594 MET cc_start: 0.4680 (ppp) cc_final: 0.3758 (tpt) outliers start: 50 outliers final: 28 residues processed: 234 average time/residue: 0.2203 time to fit residues: 82.2224 Evaluate side-chains 220 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 187 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 575 CYS Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 498 GLN Chi-restraints excluded: chain C residue 540 ASP Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 260 TYR Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain D residue 540 ASP Chi-restraints excluded: chain D residue 547 ILE 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 144 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 129 optimal weight: 9.9990 chunk 71 optimal weight: 0.5980 chunk 148 optimal weight: 0.7980 chunk 120 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 88 optimal weight: 4.9990 chunk 156 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 GLN B 422 HIS C 286 GLN C 422 HIS D 286 GLN D 444 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15196 Z= 0.184 Angle : 0.477 5.006 20608 Z= 0.250 Chirality : 0.039 0.152 2312 Planarity : 0.003 0.032 2540 Dihedral : 4.444 23.649 2032 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.22 % Allowed : 14.94 % Favored : 82.84 % 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: 0.72 (0.21), residues: 1792 helix: 1.02 (0.15), residues: 1100 sheet: -1.43 (0.67), residues: 56 loop : -0.13 (0.28), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 168 HIS 0.002 0.001 HIS A 312 PHE 0.009 0.001 PHE A 298 TYR 0.014 0.001 TYR B 456 ARG 0.002 0.000 ARG C 220 *********************** 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 234 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 198 time to evaluate : 1.802 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7429 (m-30) cc_final: 0.6768 (m-30) REVERT: A 498 GLN cc_start: 0.7684 (mt0) cc_final: 0.7394 (mt0) REVERT: A 543 TYR cc_start: 0.6698 (p90) cc_final: 0.6382 (p90) REVERT: A 547 ILE cc_start: 0.7754 (OUTLIER) cc_final: 0.7360 (mp) REVERT: A 594 MET cc_start: 0.4527 (ppp) cc_final: 0.3709 (tpt) REVERT: B 204 ASP cc_start: 0.7432 (m-30) cc_final: 0.6842 (m-30) REVERT: B 543 TYR cc_start: 0.6681 (p90) cc_final: 0.6373 (p90) REVERT: B 547 ILE cc_start: 0.7757 (OUTLIER) cc_final: 0.7376 (mp) REVERT: B 594 MET cc_start: 0.4559 (ppp) cc_final: 0.3728 (tpt) REVERT: C 498 GLN cc_start: 0.7704 (mt0) cc_final: 0.7408 (mt0) REVERT: C 543 TYR cc_start: 0.6662 (p90) cc_final: 0.6352 (p90) REVERT: C 547 ILE cc_start: 0.7755 (OUTLIER) cc_final: 0.7370 (mp) REVERT: C 594 MET cc_start: 0.4548 (ppp) cc_final: 0.3720 (tpt) REVERT: D 498 GLN cc_start: 0.7707 (mt0) cc_final: 0.7424 (mt0) REVERT: D 543 TYR cc_start: 0.6701 (p90) cc_final: 0.6388 (p90) REVERT: D 547 ILE cc_start: 0.7751 (OUTLIER) cc_final: 0.7359 (mp) REVERT: D 556 LYS cc_start: 0.2368 (OUTLIER) cc_final: 0.2138 (mptt) REVERT: D 594 MET cc_start: 0.4472 (ppp) cc_final: 0.3657 (tpt) outliers start: 36 outliers final: 17 residues processed: 221 average time/residue: 0.2465 time to fit residues: 84.0356 Evaluate side-chains 204 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 182 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 575 CYS Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 260 TYR Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 547 ILE Chi-restraints excluded: chain D residue 556 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 58 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 102 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 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: 0.9980 chunk 91 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 GLN B 422 HIS C 286 GLN D 286 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15196 Z= 0.280 Angle : 0.522 6.812 20608 Z= 0.275 Chirality : 0.041 0.156 2312 Planarity : 0.004 0.032 2540 Dihedral : 4.569 24.400 2032 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.72 % Allowed : 14.63 % Favored : 82.65 % 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: 0.47 (0.20), residues: 1792 helix: 0.80 (0.15), residues: 1120 sheet: -1.41 (0.67), residues: 56 loop : -0.24 (0.28), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 168 HIS 0.003 0.001 HIS B 312 PHE 0.018 0.002 PHE D 298 TYR 0.014 0.002 TYR C 349 ARG 0.003 0.000 ARG B 462 *********************** 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 243 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 199 time to evaluate : 1.772 Fit side-chains REVERT: A 204 ASP cc_start: 0.7449 (m-30) cc_final: 0.7033 (m-30) REVERT: A 262 LYS cc_start: 0.7709 (mmtt) cc_final: 0.7153 (tttt) REVERT: A 498 GLN cc_start: 0.7805 (mt0) cc_final: 0.7566 (mt0) REVERT: A 509 LYS cc_start: 0.6396 (mttt) cc_final: 0.6062 (mtpp) REVERT: A 515 GLU cc_start: 0.7016 (mt-10) cc_final: 0.6786 (mt-10) REVERT: A 543 TYR cc_start: 0.6987 (p90) cc_final: 0.6546 (p90) REVERT: A 594 MET cc_start: 0.4640 (ppp) cc_final: 0.3995 (tpt) REVERT: B 204 ASP cc_start: 0.7446 (m-30) cc_final: 0.7033 (m-30) REVERT: B 262 LYS cc_start: 0.7686 (mmtt) cc_final: 0.7160 (tttt) REVERT: B 407 ARG cc_start: 0.7930 (tpt90) cc_final: 0.7690 (tpt-90) REVERT: B 515 GLU cc_start: 0.7027 (mt-10) cc_final: 0.6787 (mt-10) REVERT: B 543 TYR cc_start: 0.6982 (p90) cc_final: 0.6555 (p90) REVERT: B 594 MET cc_start: 0.4704 (ppp) cc_final: 0.4101 (tpt) REVERT: C 204 ASP cc_start: 0.7454 (m-30) cc_final: 0.6748 (m-30) REVERT: C 262 LYS cc_start: 0.7707 (mmtt) cc_final: 0.7155 (tttt) REVERT: C 498 GLN cc_start: 0.7828 (mt0) cc_final: 0.7577 (mt0) REVERT: C 515 GLU cc_start: 0.7031 (mt-10) cc_final: 0.6789 (mt-10) REVERT: C 543 TYR cc_start: 0.6992 (p90) cc_final: 0.6556 (p90) REVERT: C 547 ILE cc_start: 0.7876 (OUTLIER) cc_final: 0.7594 (mt) REVERT: C 594 MET cc_start: 0.4692 (ppp) cc_final: 0.4085 (tpt) REVERT: D 204 ASP cc_start: 0.7450 (m-30) cc_final: 0.7033 (m-30) REVERT: D 262 LYS cc_start: 0.7701 (mmtt) cc_final: 0.7161 (tttt) REVERT: D 430 MET cc_start: 0.7622 (tmm) cc_final: 0.7232 (tmm) REVERT: D 498 GLN cc_start: 0.7828 (mt0) cc_final: 0.7581 (mt0) REVERT: D 509 LYS cc_start: 0.6394 (mttt) cc_final: 0.6089 (mtpp) REVERT: D 515 GLU cc_start: 0.7032 (mt-10) cc_final: 0.6791 (mt-10) REVERT: D 543 TYR cc_start: 0.7002 (p90) cc_final: 0.6557 (p90) REVERT: D 556 LYS cc_start: 0.2143 (OUTLIER) cc_final: 0.1669 (tptt) REVERT: D 594 MET cc_start: 0.4591 (ppp) cc_final: 0.3969 (tpt) outliers start: 44 outliers final: 26 residues processed: 232 average time/residue: 0.2387 time to fit residues: 85.5364 Evaluate side-chains 217 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 189 time to evaluate : 1.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 575 CYS Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 389 PHE Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 260 TYR Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 389 PHE Chi-restraints excluded: chain D residue 556 LYS Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 127 optimal weight: 0.5980 chunk 98 optimal weight: 0.7980 chunk 146 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 173 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 105 optimal weight: 0.5980 chunk 80 optimal weight: 9.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 HIS B 286 GLN C 286 GLN D 286 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.4485 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= 0.175 Angle : 0.462 5.909 20608 Z= 0.244 Chirality : 0.039 0.157 2312 Planarity : 0.003 0.032 2540 Dihedral : 4.430 25.346 2032 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.73 % Allowed : 16.11 % Favored : 82.16 % 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: 0.69 (0.20), residues: 1792 helix: 1.01 (0.15), residues: 1120 sheet: -0.89 (0.71), residues: 56 loop : -0.29 (0.28), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 168 HIS 0.002 0.001 HIS B 422 PHE 0.009 0.001 PHE A 298 TYR 0.010 0.001 TYR A 260 ARG 0.004 0.000 ARG A 433 *********************** 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 237 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 209 time to evaluate : 1.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 LYS cc_start: 0.7743 (mmtt) cc_final: 0.7194 (tttt) REVERT: A 498 GLN cc_start: 0.7920 (mt0) cc_final: 0.7472 (mt0) REVERT: A 509 LYS cc_start: 0.6289 (mttt) cc_final: 0.5959 (mtpp) REVERT: A 515 GLU cc_start: 0.6912 (mt-10) cc_final: 0.6611 (mp0) REVERT: A 543 TYR cc_start: 0.6925 (p90) cc_final: 0.6496 (p90) REVERT: A 594 MET cc_start: 0.4581 (ppp) cc_final: 0.3936 (tpt) REVERT: B 262 LYS cc_start: 0.7744 (mmtt) cc_final: 0.7175 (tttt) REVERT: B 509 LYS cc_start: 0.6271 (mttt) cc_final: 0.5937 (mtpp) REVERT: B 515 GLU cc_start: 0.6921 (mt-10) cc_final: 0.6615 (mp0) REVERT: B 543 TYR cc_start: 0.6936 (p90) cc_final: 0.6506 (p90) REVERT: B 594 MET cc_start: 0.4545 (ppp) cc_final: 0.3960 (tpt) REVERT: C 262 LYS cc_start: 0.7723 (mmtt) cc_final: 0.7148 (tttt) REVERT: C 498 GLN cc_start: 0.7915 (mt0) cc_final: 0.7461 (mt0) REVERT: C 509 LYS cc_start: 0.6267 (mttt) cc_final: 0.5938 (mtpp) REVERT: C 515 GLU cc_start: 0.6932 (mt-10) cc_final: 0.6619 (mp0) REVERT: C 543 TYR cc_start: 0.6889 (p90) cc_final: 0.6484 (p90) REVERT: C 594 MET cc_start: 0.4601 (ppp) cc_final: 0.4016 (tpt) REVERT: D 262 LYS cc_start: 0.7729 (mmtt) cc_final: 0.7156 (tttt) REVERT: D 399 MET cc_start: 0.6329 (OUTLIER) cc_final: 0.6001 (ptp) REVERT: D 498 GLN cc_start: 0.7924 (mt0) cc_final: 0.7469 (mt0) REVERT: D 509 LYS cc_start: 0.6253 (mttt) cc_final: 0.5974 (mtpp) REVERT: D 515 GLU cc_start: 0.6972 (mt-10) cc_final: 0.6659 (mp0) REVERT: D 543 TYR cc_start: 0.6939 (p90) cc_final: 0.6509 (p90) REVERT: D 556 LYS cc_start: 0.2159 (OUTLIER) cc_final: 0.1654 (mtmm) REVERT: D 594 MET cc_start: 0.4623 (ppp) cc_final: 0.3984 (tpt) outliers start: 28 outliers final: 21 residues processed: 228 average time/residue: 0.2455 time to fit residues: 86.1547 Evaluate side-chains 224 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 201 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 575 CYS Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 389 PHE Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 260 TYR Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 389 PHE Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 556 LYS Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 0.3980 chunk 69 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 136 optimal weight: 0.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 HIS B 286 GLN B 422 HIS C 286 GLN D 286 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.4649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15196 Z= 0.278 Angle : 0.511 8.079 20608 Z= 0.270 Chirality : 0.041 0.163 2312 Planarity : 0.004 0.032 2540 Dihedral : 4.529 26.206 2032 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.60 % Allowed : 16.73 % Favored : 81.67 % 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: 0.54 (0.20), residues: 1792 helix: 0.87 (0.15), residues: 1120 sheet: -1.20 (0.69), residues: 56 loop : -0.26 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 168 HIS 0.004 0.001 HIS D 312 PHE 0.014 0.002 PHE A 298 TYR 0.014 0.002 TYR C 349 ARG 0.004 0.000 ARG D 424 *********************** 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 239 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 213 time to evaluate : 1.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7456 (m-30) cc_final: 0.7052 (m-30) REVERT: A 262 LYS cc_start: 0.7759 (mmtt) cc_final: 0.7204 (tttt) REVERT: A 286 GLN cc_start: 0.7817 (tm-30) cc_final: 0.7610 (tp40) REVERT: A 407 ARG cc_start: 0.7868 (tpt90) cc_final: 0.7599 (tpt-90) REVERT: A 498 GLN cc_start: 0.7958 (mt0) cc_final: 0.7564 (mt0) REVERT: A 509 LYS cc_start: 0.6574 (mttt) cc_final: 0.6243 (mtpp) REVERT: A 515 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6852 (mp0) REVERT: A 543 TYR cc_start: 0.7041 (p90) cc_final: 0.6556 (p90) REVERT: A 594 MET cc_start: 0.4883 (ppp) cc_final: 0.4357 (tpt) REVERT: B 204 ASP cc_start: 0.7452 (m-30) cc_final: 0.7050 (m-30) REVERT: B 262 LYS cc_start: 0.7759 (mmtt) cc_final: 0.7192 (tttt) REVERT: B 407 ARG cc_start: 0.7913 (tpt90) cc_final: 0.7662 (tpt-90) REVERT: B 509 LYS cc_start: 0.6563 (mttt) cc_final: 0.6231 (mtpp) REVERT: B 515 GLU cc_start: 0.7121 (mt-10) cc_final: 0.6835 (mp0) REVERT: B 543 TYR cc_start: 0.7087 (p90) cc_final: 0.6608 (p90) REVERT: B 594 MET cc_start: 0.4881 (ppp) cc_final: 0.4358 (tpt) REVERT: C 204 ASP cc_start: 0.7462 (m-30) cc_final: 0.7052 (m-30) REVERT: C 262 LYS cc_start: 0.7753 (mmtt) cc_final: 0.7172 (tttt) REVERT: C 407 ARG cc_start: 0.7881 (tpt90) cc_final: 0.7616 (tpt-90) REVERT: C 498 GLN cc_start: 0.7985 (mt0) cc_final: 0.7608 (mt0) REVERT: C 509 LYS cc_start: 0.6552 (mttt) cc_final: 0.6223 (mtpp) REVERT: C 515 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6856 (mp0) REVERT: C 543 TYR cc_start: 0.7022 (p90) cc_final: 0.6543 (p90) REVERT: C 594 MET cc_start: 0.4911 (ppp) cc_final: 0.4395 (tpt) REVERT: D 204 ASP cc_start: 0.7455 (m-30) cc_final: 0.7048 (m-30) REVERT: D 262 LYS cc_start: 0.7752 (mmtt) cc_final: 0.7176 (tttt) REVERT: D 430 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.7461 (tmm) REVERT: D 498 GLN cc_start: 0.7950 (mt0) cc_final: 0.7553 (mt0) REVERT: D 509 LYS cc_start: 0.6572 (mttt) cc_final: 0.6243 (mtpp) REVERT: D 515 GLU cc_start: 0.7150 (mt-10) cc_final: 0.6865 (mp0) REVERT: D 543 TYR cc_start: 0.7049 (p90) cc_final: 0.6556 (p90) REVERT: D 556 LYS cc_start: 0.2006 (OUTLIER) cc_final: 0.1411 (mtmm) REVERT: D 594 MET cc_start: 0.4886 (ppp) cc_final: 0.4365 (tpt) outliers start: 26 outliers final: 21 residues processed: 229 average time/residue: 0.2936 time to fit residues: 101.6576 Evaluate side-chains 225 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 202 time to evaluate : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 575 CYS Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 389 PHE Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 260 TYR Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 389 PHE Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 430 MET Chi-restraints excluded: chain D residue 556 LYS Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 0.9980 chunk 166 optimal weight: 3.9990 chunk 151 optimal weight: 0.9990 chunk 161 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 146 optimal weight: 0.2980 chunk 152 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 GLN B 422 HIS C 286 GLN C 422 HIS D 286 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.4744 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= 0.179 Angle : 0.458 5.413 20608 Z= 0.243 Chirality : 0.039 0.159 2312 Planarity : 0.004 0.059 2540 Dihedral : 4.420 24.966 2032 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.67 % Allowed : 17.10 % Favored : 81.23 % 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: 0.80 (0.20), residues: 1792 helix: 1.10 (0.15), residues: 1096 sheet: -0.76 (0.70), residues: 56 loop : -0.20 (0.27), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 168 HIS 0.002 0.001 HIS B 422 PHE 0.009 0.001 PHE A 298 TYR 0.009 0.001 TYR C 351 ARG 0.002 0.000 ARG C 220 *********************** 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 237 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 210 time to evaluate : 1.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 LYS cc_start: 0.7729 (mmtt) cc_final: 0.7242 (tttt) REVERT: A 407 ARG cc_start: 0.7895 (tpt90) cc_final: 0.7633 (tpt-90) REVERT: A 498 GLN cc_start: 0.7915 (mt0) cc_final: 0.7493 (mt0) REVERT: A 509 LYS cc_start: 0.6406 (mttt) cc_final: 0.6068 (mtpp) REVERT: A 515 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6805 (mp0) REVERT: A 543 TYR cc_start: 0.7000 (p90) cc_final: 0.6530 (p90) REVERT: A 594 MET cc_start: 0.4861 (ppp) cc_final: 0.4361 (tpt) REVERT: B 204 ASP cc_start: 0.7417 (m-30) cc_final: 0.6830 (m-30) REVERT: B 262 LYS cc_start: 0.7763 (mmtt) cc_final: 0.7229 (tttt) REVERT: B 407 ARG cc_start: 0.7880 (tpt90) cc_final: 0.7614 (tpt-90) REVERT: B 498 GLN cc_start: 0.7935 (mt0) cc_final: 0.7469 (mt0) REVERT: B 509 LYS cc_start: 0.6378 (mttt) cc_final: 0.6052 (mtpp) REVERT: B 515 GLU cc_start: 0.7044 (mt-10) cc_final: 0.6786 (mp0) REVERT: B 543 TYR cc_start: 0.6986 (p90) cc_final: 0.6509 (p90) REVERT: B 594 MET cc_start: 0.4864 (ppp) cc_final: 0.4366 (tpt) REVERT: C 204 ASP cc_start: 0.7423 (m-30) cc_final: 0.6833 (m-30) REVERT: C 262 LYS cc_start: 0.7765 (mmtt) cc_final: 0.7169 (tttt) REVERT: C 407 ARG cc_start: 0.7920 (tpt90) cc_final: 0.7657 (tpt-90) REVERT: C 429 ASP cc_start: 0.7842 (t70) cc_final: 0.7566 (t70) REVERT: C 498 GLN cc_start: 0.7916 (mt0) cc_final: 0.7489 (mt0) REVERT: C 509 LYS cc_start: 0.6392 (mttt) cc_final: 0.6052 (mtpp) REVERT: C 515 GLU cc_start: 0.7070 (mt-10) cc_final: 0.6802 (mp0) REVERT: C 543 TYR cc_start: 0.6944 (p90) cc_final: 0.6479 (p90) REVERT: C 594 MET cc_start: 0.4865 (ppp) cc_final: 0.4364 (tpt) REVERT: D 204 ASP cc_start: 0.7422 (m-30) cc_final: 0.6833 (m-30) REVERT: D 262 LYS cc_start: 0.7760 (mmtt) cc_final: 0.7187 (tttt) REVERT: D 399 MET cc_start: 0.6355 (OUTLIER) cc_final: 0.6064 (ptp) REVERT: D 498 GLN cc_start: 0.7891 (mt0) cc_final: 0.7458 (mt0) REVERT: D 509 LYS cc_start: 0.6425 (mttt) cc_final: 0.6090 (mtpp) REVERT: D 515 GLU cc_start: 0.7045 (mt-10) cc_final: 0.6796 (mp0) REVERT: D 543 TYR cc_start: 0.7007 (p90) cc_final: 0.6526 (p90) REVERT: D 556 LYS cc_start: 0.2174 (OUTLIER) cc_final: 0.1631 (mtmm) REVERT: D 594 MET cc_start: 0.4858 (ppp) cc_final: 0.4350 (tpt) outliers start: 27 outliers final: 22 residues processed: 227 average time/residue: 0.2571 time to fit residues: 87.9006 Evaluate side-chains 226 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 202 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 575 CYS Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 389 PHE Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 260 TYR Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 389 PHE Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 556 LYS 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 170 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 118 optimal weight: 0.7980 chunk 179 optimal weight: 7.9990 chunk 165 optimal weight: 0.7980 chunk 142 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 113 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 GLN B 422 HIS C 286 GLN C 422 HIS D 286 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.4796 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= 0.198 Angle : 0.475 8.615 20608 Z= 0.252 Chirality : 0.039 0.161 2312 Planarity : 0.004 0.055 2540 Dihedral : 4.378 24.983 2032 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.73 % Allowed : 17.41 % Favored : 80.86 % 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: 0.80 (0.20), residues: 1792 helix: 1.09 (0.15), residues: 1100 sheet: -0.77 (0.69), residues: 56 loop : -0.20 (0.27), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 168 HIS 0.003 0.001 HIS D 312 PHE 0.013 0.001 PHE C 389 TYR 0.010 0.001 TYR A 349 ARG 0.002 0.000 ARG B 424 ********************** 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 237 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 209 time to evaluate : 1.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7423 (m-30) cc_final: 0.6836 (m-30) REVERT: A 262 LYS cc_start: 0.7719 (mmtt) cc_final: 0.7246 (tttt) REVERT: A 407 ARG cc_start: 0.7887 (tpt90) cc_final: 0.7617 (tpt-90) REVERT: A 498 GLN cc_start: 0.7868 (mt0) cc_final: 0.7432 (mt0) REVERT: A 509 LYS cc_start: 0.6454 (mttt) cc_final: 0.6119 (mtpp) REVERT: A 515 GLU cc_start: 0.6996 (mt-10) cc_final: 0.6769 (mp0) REVERT: A 543 TYR cc_start: 0.6948 (p90) cc_final: 0.6472 (p90) REVERT: A 594 MET cc_start: 0.4877 (ppp) cc_final: 0.4382 (tpt) REVERT: B 204 ASP cc_start: 0.7410 (m-30) cc_final: 0.6826 (m-30) REVERT: B 262 LYS cc_start: 0.7753 (mmtt) cc_final: 0.7211 (tttt) REVERT: B 407 ARG cc_start: 0.7887 (tpt90) cc_final: 0.7615 (tpt-90) REVERT: B 498 GLN cc_start: 0.7893 (mt0) cc_final: 0.7459 (mt0) REVERT: B 509 LYS cc_start: 0.6430 (mttt) cc_final: 0.6101 (mtpp) REVERT: B 515 GLU cc_start: 0.7003 (mt-10) cc_final: 0.6771 (mp0) REVERT: B 543 TYR cc_start: 0.6943 (p90) cc_final: 0.6471 (p90) REVERT: B 594 MET cc_start: 0.4906 (ppp) cc_final: 0.4410 (tpt) REVERT: C 204 ASP cc_start: 0.7423 (m-30) cc_final: 0.6831 (m-30) REVERT: C 262 LYS cc_start: 0.7760 (mmtt) cc_final: 0.7162 (tttt) REVERT: C 407 ARG cc_start: 0.7895 (tpt90) cc_final: 0.7616 (tpt-90) REVERT: C 498 GLN cc_start: 0.7879 (mt0) cc_final: 0.7488 (mt0) REVERT: C 509 LYS cc_start: 0.6437 (mttt) cc_final: 0.6102 (mtpp) REVERT: C 515 GLU cc_start: 0.7079 (mt-10) cc_final: 0.6822 (mp0) REVERT: C 543 TYR cc_start: 0.6925 (p90) cc_final: 0.6459 (p90) REVERT: C 594 MET cc_start: 0.4884 (ppp) cc_final: 0.4388 (tpt) REVERT: D 204 ASP cc_start: 0.7418 (m-30) cc_final: 0.6826 (m-30) REVERT: D 262 LYS cc_start: 0.7755 (mmtt) cc_final: 0.7173 (tttt) REVERT: D 399 MET cc_start: 0.6344 (OUTLIER) cc_final: 0.5989 (ptp) REVERT: D 498 GLN cc_start: 0.7861 (mt0) cc_final: 0.7451 (mt0) REVERT: D 509 LYS cc_start: 0.6471 (mttt) cc_final: 0.6145 (mtpp) REVERT: D 515 GLU cc_start: 0.7049 (mt-10) cc_final: 0.6806 (mp0) REVERT: D 543 TYR cc_start: 0.6966 (p90) cc_final: 0.6492 (p90) REVERT: D 594 MET cc_start: 0.4879 (ppp) cc_final: 0.4383 (tpt) outliers start: 28 outliers final: 23 residues processed: 228 average time/residue: 0.2643 time to fit residues: 91.5466 Evaluate side-chains 230 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 206 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 575 CYS Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 389 PHE Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 260 TYR Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 389 PHE Chi-restraints excluded: chain D residue 399 MET 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 152 optimal weight: 0.6980 chunk 43 optimal weight: 8.9990 chunk 131 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 143 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 146 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 125 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 GLN B 422 HIS C 286 GLN C 422 HIS D 286 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.147823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.112761 restraints weight = 18470.348| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.59 r_work: 0.3145 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15196 Z= 0.193 Angle : 0.467 7.816 20608 Z= 0.248 Chirality : 0.039 0.160 2312 Planarity : 0.004 0.051 2540 Dihedral : 4.349 24.792 2032 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.85 % Allowed : 17.28 % Favored : 80.86 % 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: 0.82 (0.20), residues: 1792 helix: 1.11 (0.15), residues: 1100 sheet: -0.71 (0.69), residues: 56 loop : -0.19 (0.27), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 168 HIS 0.002 0.001 HIS B 312 PHE 0.011 0.001 PHE D 389 TYR 0.010 0.001 TYR B 349 ARG 0.002 0.000 ARG A 433 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3257.54 seconds wall clock time: 64 minutes 13.91 seconds (3853.91 seconds total)