Starting phenix.real_space_refine on Fri Feb 16 08:32:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lfy_23309/02_2024/7lfy_23309_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lfy_23309/02_2024/7lfy_23309.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lfy_23309/02_2024/7lfy_23309_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lfy_23309/02_2024/7lfy_23309_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lfy_23309/02_2024/7lfy_23309_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lfy_23309/02_2024/7lfy_23309.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lfy_23309/02_2024/7lfy_23309.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lfy_23309/02_2024/7lfy_23309_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lfy_23309/02_2024/7lfy_23309_neut_updated.pdb" } resolution = 3.6 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 P 4 5.49 5 S 76 5.16 5 Na 3 4.78 5 C 9684 2.51 5 N 2396 2.21 5 O 2688 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 186": "NH1" <-> "NH2" Residue "A ARG 218": "NH1" <-> "NH2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A ARG 280": "NH1" <-> "NH2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A ARG 287": "NH1" <-> "NH2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A GLU 341": "OE1" <-> "OE2" Residue "A ARG 344": "NH1" <-> "NH2" Residue "A ARG 407": "NH1" <-> "NH2" Residue "A GLU 409": "OE1" <-> "OE2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "A ARG 462": "NH1" <-> "NH2" Residue "A ARG 514": "NH1" <-> "NH2" Residue "A ARG 560": "NH1" <-> "NH2" Residue "A ARG 561": "NH1" <-> "NH2" Residue "B ARG 186": "NH1" <-> "NH2" Residue "B ARG 218": "NH1" <-> "NH2" Residue "B ARG 220": "NH1" <-> "NH2" Residue "B ARG 280": "NH1" <-> "NH2" Residue "B GLU 283": "OE1" <-> "OE2" Residue "B ARG 287": "NH1" <-> "NH2" Residue "B GLU 289": "OE1" <-> "OE2" Residue "B GLU 341": "OE1" <-> "OE2" Residue "B ARG 344": "NH1" <-> "NH2" Residue "B ARG 407": "NH1" <-> "NH2" Residue "B GLU 409": "OE1" <-> "OE2" Residue "B GLU 431": "OE1" <-> "OE2" Residue "B ARG 462": "NH1" <-> "NH2" Residue "B ARG 514": "NH1" <-> "NH2" Residue "B ARG 560": "NH1" <-> "NH2" Residue "B ARG 561": "NH1" <-> "NH2" Residue "C ARG 186": "NH1" <-> "NH2" Residue "C ARG 218": "NH1" <-> "NH2" Residue "C ARG 220": "NH1" <-> "NH2" Residue "C ARG 280": "NH1" <-> "NH2" Residue "C GLU 283": "OE1" <-> "OE2" Residue "C ARG 287": "NH1" <-> "NH2" Residue "C GLU 289": "OE1" <-> "OE2" Residue "C ARG 344": "NH1" <-> "NH2" Residue "C ARG 407": "NH1" <-> "NH2" Residue "C GLU 409": "OE1" <-> "OE2" Residue "C GLU 431": "OE1" <-> "OE2" Residue "C ARG 462": "NH1" <-> "NH2" Residue "C ARG 514": "NH1" <-> "NH2" Residue "C ARG 560": "NH1" <-> "NH2" Residue "C ARG 561": "NH1" <-> "NH2" Residue "D ARG 186": "NH1" <-> "NH2" Residue "D ARG 218": "NH1" <-> "NH2" Residue "D ARG 220": "NH1" <-> "NH2" Residue "D ARG 280": "NH1" <-> "NH2" Residue "D GLU 283": "OE1" <-> "OE2" Residue "D ARG 287": "NH1" <-> "NH2" Residue "D GLU 289": "OE1" <-> "OE2" Residue "D GLU 341": "OE1" <-> "OE2" Residue "D ARG 344": "NH1" <-> "NH2" Residue "D ARG 407": "NH1" <-> "NH2" Residue "D GLU 409": "OE1" <-> "OE2" Residue "D GLU 431": "OE1" <-> "OE2" Residue "D ARG 462": "NH1" <-> "NH2" Residue "D ARG 514": "NH1" <-> "NH2" Residue "D ARG 560": "NH1" <-> "NH2" Residue "D ARG 561": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14851 Number of models: 1 Model: "" Number of chains: 12 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: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Unusual residues: {' NA': 3, 'PCG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 7.66, per 1000 atoms: 0.52 Number of scatterers: 14851 At special positions: 0 Unit cell: (96.993, 96.993, 114.402, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 76 16.00 P 4 15.00 Na 3 11.00 O 2688 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: 5.87 Conformation dependent library (CDL) restraints added in 2.7 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: 3.54 Creating SS restraints... Processing helix chain 'A' and resid 163 through 188 Proline residue: A 175 - end of helix removed outlier: 5.260A pdb=" N ILE A 184 " --> pdb=" O TRP A 180 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 195 Processing helix chain 'A' and resid 197 through 219 removed outlier: 3.588A pdb=" N ILE A 202 " --> pdb=" O GLU A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 241 Processing helix chain 'A' and resid 244 through 252 Processing helix chain 'A' and resid 256 through 263 removed outlier: 4.343A pdb=" N LEU A 263 " --> pdb=" O TYR A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 291 removed outlier: 4.055A pdb=" N ASN A 273 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG A 277 " --> pdb=" O ARG A 274 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N SER A 279 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 4.201A 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: 3.518A pdb=" N GLY A 397 " --> pdb=" O VAL A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 423 Processing helix chain 'A' and resid 428 through 443 Processing helix chain 'A' and resid 450 through 456 removed outlier: 4.905A pdb=" N TYR A 456 " --> pdb=" O GLU A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 474 removed outlier: 5.039A pdb=" N GLU A 464 " --> pdb=" O LYS A 460 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ASP A 472 " --> pdb=" O ASN A 468 " (cutoff:3.500A) removed outlier: 5.740A 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: 3.587A 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: 4.055A pdb=" N ASN B 273 " --> pdb=" O ILE B 270 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG B 277 " --> pdb=" O ARG B 274 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N SER B 279 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLU B 289 " --> pdb=" O GLN B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 325 Processing helix chain 'B' and resid 345 through 360 Processing helix chain 'B' and resid 372 through 403 removed outlier: 3.519A pdb=" N GLY B 397 " --> pdb=" O VAL B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 423 Processing helix chain 'B' and resid 428 through 443 Processing helix chain 'B' and resid 450 through 456 removed outlier: 4.905A pdb=" N TYR B 456 " --> pdb=" O GLU B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 474 removed outlier: 5.040A pdb=" N GLU B 464 " --> pdb=" O LYS B 460 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ASP B 472 " --> pdb=" O ASN B 468 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N THR B 473 " --> pdb=" O VAL B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 492 removed outlier: 3.727A 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: 5.252A 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: 3.587A 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: 4.055A pdb=" N ASN C 273 " --> pdb=" O ILE C 270 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG C 277 " --> pdb=" O ARG C 274 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N SER C 279 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU C 289 " --> pdb=" O GLN C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 325 Processing helix chain 'C' and resid 345 through 360 Processing helix chain 'C' and resid 372 through 403 removed outlier: 3.519A pdb=" N GLY C 397 " --> pdb=" O VAL C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 423 Processing helix chain 'C' and resid 428 through 443 Processing helix chain 'C' and resid 450 through 456 removed outlier: 4.905A pdb=" N TYR C 456 " --> pdb=" O GLU C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 474 removed outlier: 5.041A pdb=" N GLU C 464 " --> pdb=" O LYS C 460 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ASP C 472 " --> pdb=" O ASN C 468 " (cutoff:3.500A) removed outlier: 5.740A 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: 3.589A pdb=" N ILE D 202 " --> pdb=" O GLU D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 241 Processing helix chain 'D' and resid 244 through 252 Processing helix chain 'D' and resid 256 through 263 removed outlier: 4.343A pdb=" N LEU D 263 " --> pdb=" O TYR D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 291 removed outlier: 4.057A pdb=" N ASN D 273 " --> pdb=" O ILE D 270 " (cutoff:3.500A) removed outlier: 3.651A 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: 3.520A pdb=" N GLY D 397 " --> pdb=" O VAL D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 423 Processing helix chain 'D' and resid 428 through 443 Processing helix chain 'D' and resid 450 through 456 removed outlier: 4.905A pdb=" N TYR D 456 " --> pdb=" O GLU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 474 removed outlier: 5.040A pdb=" N GLU D 464 " --> pdb=" O LYS D 460 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ASP D 472 " --> pdb=" O ASN D 468 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N THR D 473 " --> pdb=" O VAL D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 492 removed outlier: 3.726A 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: 6.562A pdb=" N PHE A 574 " --> pdb=" O ILE A 519 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ILE A 519 " --> pdb=" O PHE A 574 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU A 576 " --> pdb=" O TYR A 517 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N TYR A 517 " --> pdb=" O LEU A 576 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 564 through 568 removed outlier: 4.434A pdb=" N ASN A 564 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 3.982A 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: 5.863A pdb=" N ILE B 519 " --> pdb=" O PHE B 574 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU B 576 " --> pdb=" O TYR B 517 " (cutoff:3.500A) removed outlier: 5.009A 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: 5.863A pdb=" N ILE C 519 " --> pdb=" O PHE C 574 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU C 576 " --> pdb=" O TYR C 517 " (cutoff:3.500A) removed outlier: 5.010A 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: 3.983A pdb=" N LYS C 523 " --> pdb=" O ILE C 568 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 496 through 500 removed outlier: 6.561A pdb=" N PHE D 574 " --> pdb=" O ILE D 519 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ILE D 519 " --> pdb=" O PHE D 574 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU D 576 " --> pdb=" O TYR D 517 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N TYR D 517 " --> pdb=" O LEU D 576 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 564 through 568 removed outlier: 4.434A pdb=" N ASN D 564 " --> pdb=" O VAL D 527 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS D 523 " --> pdb=" O ILE D 568 " (cutoff:3.500A) 808 hydrogen bonds defined for protein. 2148 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.54 Time building geometry restraints manager: 6.34 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: 4290 1.34 - 1.45: 2431 1.45 - 1.57: 8339 1.57 - 1.69: 8 1.69 - 1.81: 128 Bond restraints: 15196 Sorted by residual: bond pdb=" C3' PCG A 701 " pdb=" C4' PCG A 701 " ideal model delta sigma weight residual 1.808 1.494 0.314 2.00e-02 2.50e+03 2.46e+02 bond pdb=" C3' PCG B 701 " pdb=" C4' PCG B 701 " ideal model delta sigma weight residual 1.808 1.495 0.313 2.00e-02 2.50e+03 2.45e+02 bond pdb=" C3' PCG C 701 " pdb=" C4' PCG C 701 " ideal model delta sigma weight residual 1.808 1.495 0.313 2.00e-02 2.50e+03 2.45e+02 bond pdb=" C3' PCG D 701 " pdb=" C4' PCG D 701 " ideal model delta sigma weight residual 1.808 1.495 0.313 2.00e-02 2.50e+03 2.44e+02 bond pdb=" C2' PCG C 701 " pdb=" C3' PCG C 701 " ideal model delta sigma weight residual 1.200 1.509 -0.309 2.00e-02 2.50e+03 2.38e+02 ... (remaining 15191 not shown) Histogram of bond angle deviations from ideal: 100.39 - 107.13: 360 107.13 - 113.87: 8583 113.87 - 120.62: 6184 120.62 - 127.36: 5351 127.36 - 134.10: 130 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 2.62e+01 angle pdb=" N ARG D 291 " pdb=" CA ARG D 291 " pdb=" C ARG D 291 " ideal model delta sigma weight residual 112.89 119.21 -6.32 1.24e+00 6.50e-01 2.60e+01 angle pdb=" N ARG B 291 " pdb=" CA ARG B 291 " pdb=" C ARG B 291 " ideal model delta sigma weight residual 112.89 119.18 -6.29 1.24e+00 6.50e-01 2.57e+01 angle pdb=" N ARG A 291 " pdb=" CA ARG A 291 " pdb=" C ARG A 291 " ideal model delta sigma weight residual 112.89 119.15 -6.26 1.24e+00 6.50e-01 2.55e+01 angle pdb=" O3' PCG B 701 " pdb=" PA PCG B 701 " pdb=" O5' PCG B 701 " ideal model delta sigma weight residual 111.92 101.69 10.23 3.00e+00 1.11e-01 1.16e+01 ... (remaining 20603 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.64: 8043 16.64 - 33.29: 819 33.29 - 49.93: 122 49.93 - 66.58: 28 66.58 - 83.22: 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 180.00 158.78 21.22 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA GLU C 596 " pdb=" C GLU C 596 " pdb=" N GLU C 597 " pdb=" CA GLU C 597 " ideal model delta harmonic sigma weight residual 180.00 158.86 21.14 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 ... (remaining 9013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 2192 0.088 - 0.176: 100 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 B 701 " pdb=" C2' PCG B 701 " pdb=" C4' PCG B 701 " pdb=" O3' PCG B 701 " both_signs ideal model delta sigma weight residual False -2.10 -2.54 0.44 2.00e-01 2.50e+01 4.75e+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 4.74e+00 ... (remaining 2309 not shown) Planarity restraints: 2540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 526 " -0.008 2.00e-02 2.50e+03 1.55e-02 2.39e+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 D 526 " -0.008 2.00e-02 2.50e+03 1.54e-02 2.38e+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 B 526 " -0.007 2.00e-02 2.50e+03 1.51e-02 2.27e+00 pdb=" C VAL B 526 " 0.026 2.00e-02 2.50e+03 pdb=" O VAL B 526 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL B 527 " -0.009 2.00e-02 2.50e+03 ... (remaining 2537 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2697 2.76 - 3.30: 15722 3.30 - 3.83: 27016 3.83 - 4.37: 32709 4.37 - 4.90: 53472 Nonbonded interactions: 131616 Sorted by model distance: nonbonded pdb=" O PHE A 216 " pdb=" OG1 THR A 219 " model vdw 2.226 2.440 nonbonded pdb=" O PHE D 216 " pdb=" OG1 THR D 219 " model vdw 2.226 2.440 nonbonded pdb=" O PHE B 216 " pdb=" OG1 THR B 219 " model vdw 2.227 2.440 nonbonded pdb=" O PHE C 216 " pdb=" OG1 THR C 219 " model vdw 2.227 2.440 nonbonded pdb=" OE2 GLU C 365 " pdb="NA NA A 704 " model vdw 2.290 2.470 ... (remaining 131611 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 group one per residue 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: 1.130 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: 5.860 Check model and map are aligned: 0.230 Set scattering table: 0.120 Process input model: 41.760 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 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 10.229 20608 Z= 0.359 Chirality : 0.050 0.440 2312 Planarity : 0.003 0.028 2540 Dihedral : 13.108 83.221 5608 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % 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: -1.26 (0.82), residues: 56 loop : -0.92 (0.27), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 168 HIS 0.003 0.001 HIS A 312 PHE 0.014 0.002 PHE B 389 TYR 0.015 0.001 TYR C 349 ARG 0.003 0.000 ARG D 561 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 382 time to evaluate : 1.799 Fit side-chains revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7504 (m-30) cc_final: 0.6936 (m-30) REVERT: A 269 GLU cc_start: 0.8228 (pm20) cc_final: 0.7767 (pt0) REVERT: A 302 ASN cc_start: 0.8411 (t0) cc_final: 0.7873 (t0) REVERT: A 305 MET cc_start: 0.7662 (ttp) cc_final: 0.7418 (ttm) REVERT: A 399 MET cc_start: 0.6409 (mtt) cc_final: 0.6177 (mtt) REVERT: A 604 MET cc_start: 0.4282 (mmt) cc_final: 0.3997 (mpp) REVERT: B 204 ASP cc_start: 0.7497 (m-30) cc_final: 0.6922 (m-30) REVERT: B 269 GLU cc_start: 0.8257 (pm20) cc_final: 0.7761 (pt0) REVERT: B 305 MET cc_start: 0.7631 (ttp) cc_final: 0.7391 (ttm) REVERT: B 399 MET cc_start: 0.6383 (mtt) cc_final: 0.6179 (mtt) REVERT: B 604 MET cc_start: 0.4176 (mmt) cc_final: 0.3880 (mpp) REVERT: C 204 ASP cc_start: 0.7498 (m-30) cc_final: 0.6925 (m-30) REVERT: C 269 GLU cc_start: 0.8237 (pm20) cc_final: 0.7747 (pt0) REVERT: C 305 MET cc_start: 0.7641 (ttp) cc_final: 0.7371 (ttm) REVERT: C 399 MET cc_start: 0.6383 (mtt) cc_final: 0.6067 (mtt) REVERT: C 604 MET cc_start: 0.4174 (mmt) cc_final: 0.3894 (mpp) REVERT: D 204 ASP cc_start: 0.7502 (m-30) cc_final: 0.6933 (m-30) REVERT: D 269 GLU cc_start: 0.8245 (pm20) cc_final: 0.7773 (pt0) REVERT: D 302 ASN cc_start: 0.8386 (t0) cc_final: 0.7839 (t0) REVERT: D 305 MET cc_start: 0.7672 (ttp) cc_final: 0.7400 (ttm) REVERT: D 399 MET cc_start: 0.6408 (mtt) cc_final: 0.6095 (mtt) REVERT: D 604 MET cc_start: 0.4206 (mmt) cc_final: 0.3949 (mpp) outliers start: 4 outliers final: 0 residues processed: 386 average time/residue: 0.3151 time to fit residues: 168.9917 Evaluate side-chains 204 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.834 ------------------------------------------------------------------------------- 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: 0.9990 chunk 136 optimal weight: 0.9990 chunk 75 optimal weight: 0.4980 chunk 46 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 141 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 85 optimal weight: 20.0000 chunk 105 optimal weight: 1.9990 chunk 163 optimal weight: 0.7980 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 402 ASN A 411 GLN A 468 ASN A 496 GLN B 238 ASN B 302 ASN B 402 ASN B 411 GLN B 468 ASN B 496 GLN C 238 ASN C 302 ASN C 402 ASN C 411 GLN C 468 ASN C 496 GLN D 238 ASN D 302 ASN D 402 ASN D 411 GLN D 468 ASN D 496 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15196 Z= 0.175 Angle : 0.521 8.359 20608 Z= 0.267 Chirality : 0.040 0.142 2312 Planarity : 0.003 0.027 2540 Dihedral : 4.529 22.852 2032 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.42 % Allowed : 10.56 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.21), residues: 1792 helix: 0.60 (0.16), residues: 1084 sheet: -1.10 (0.78), residues: 56 loop : -0.42 (0.28), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 168 HIS 0.002 0.001 HIS A 422 PHE 0.012 0.001 PHE D 574 TYR 0.011 0.001 TYR C 349 ARG 0.002 0.000 ARG C 218 *********************** 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 257 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 234 time to evaluate : 1.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 GLU cc_start: 0.8233 (pm20) cc_final: 0.7763 (pt0) REVERT: A 302 ASN cc_start: 0.8317 (OUTLIER) cc_final: 0.8009 (t0) REVERT: A 604 MET cc_start: 0.4272 (mmt) cc_final: 0.3676 (mpp) REVERT: B 269 GLU cc_start: 0.8220 (pm20) cc_final: 0.7731 (pt0) REVERT: B 302 ASN cc_start: 0.8343 (OUTLIER) cc_final: 0.8014 (t0) REVERT: B 604 MET cc_start: 0.4223 (mmt) cc_final: 0.3672 (mpp) REVERT: C 269 GLU cc_start: 0.8191 (pm20) cc_final: 0.7747 (pt0) REVERT: C 302 ASN cc_start: 0.8336 (OUTLIER) cc_final: 0.7993 (t0) REVERT: C 604 MET cc_start: 0.4299 (mmt) cc_final: 0.3712 (mpp) REVERT: D 269 GLU cc_start: 0.8190 (pm20) cc_final: 0.7765 (pt0) REVERT: D 302 ASN cc_start: 0.8331 (OUTLIER) cc_final: 0.8002 (t0) REVERT: D 604 MET cc_start: 0.4313 (mmt) cc_final: 0.3728 (mpp) outliers start: 23 outliers final: 11 residues processed: 241 average time/residue: 0.2656 time to fit residues: 97.2498 Evaluate side-chains 199 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 184 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain D residue 302 ASN Chi-restraints excluded: chain D residue 465 ILE Chi-restraints excluded: chain D residue 526 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 136 optimal weight: 0.7980 chunk 111 optimal weight: 0.0000 chunk 45 optimal weight: 10.0000 chunk 163 optimal weight: 7.9990 chunk 176 optimal weight: 0.9990 chunk 145 optimal weight: 10.0000 chunk 162 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 131 optimal weight: 0.5980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 GLN A 302 ASN B 238 ASN B 245 GLN B 302 ASN C 238 ASN C 245 GLN C 302 ASN D 245 GLN D 302 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 15196 Z= 0.155 Angle : 0.471 7.280 20608 Z= 0.246 Chirality : 0.039 0.145 2312 Planarity : 0.003 0.028 2540 Dihedral : 4.324 21.768 2032 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.48 % Allowed : 11.67 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.38 (0.20), residues: 1792 helix: 0.84 (0.16), residues: 1092 sheet: -0.90 (0.75), residues: 56 loop : -0.52 (0.27), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 168 HIS 0.003 0.001 HIS D 422 PHE 0.008 0.001 PHE B 298 TYR 0.011 0.001 TYR D 196 ARG 0.002 0.000 ARG B 218 *********************** 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 232 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 208 time to evaluate : 1.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.8319 (tp) cc_final: 0.8003 (tp) REVERT: A 269 GLU cc_start: 0.8133 (pm20) cc_final: 0.7669 (pt0) REVERT: A 302 ASN cc_start: 0.8324 (OUTLIER) cc_final: 0.8100 (t0) REVERT: A 399 MET cc_start: 0.6564 (mtt) cc_final: 0.6268 (mtt) REVERT: A 604 MET cc_start: 0.4257 (mmt) cc_final: 0.3673 (mpp) REVERT: B 269 GLU cc_start: 0.8133 (pm20) cc_final: 0.7643 (pt0) REVERT: B 302 ASN cc_start: 0.8326 (OUTLIER) cc_final: 0.8099 (t0) REVERT: B 399 MET cc_start: 0.6533 (mtt) cc_final: 0.6301 (mtt) REVERT: B 578 LYS cc_start: 0.4685 (tttm) cc_final: 0.4459 (tttm) REVERT: B 604 MET cc_start: 0.4243 (mmt) cc_final: 0.3663 (mpp) REVERT: C 269 GLU cc_start: 0.8114 (pm20) cc_final: 0.7659 (pt0) REVERT: C 302 ASN cc_start: 0.8318 (OUTLIER) cc_final: 0.8073 (t0) REVERT: C 399 MET cc_start: 0.6507 (mtt) cc_final: 0.6230 (mtt) REVERT: C 604 MET cc_start: 0.4224 (mmt) cc_final: 0.3649 (mpp) REVERT: D 229 LEU cc_start: 0.8358 (tp) cc_final: 0.8056 (tp) REVERT: D 269 GLU cc_start: 0.8164 (pm20) cc_final: 0.7693 (pt0) REVERT: D 302 ASN cc_start: 0.8333 (OUTLIER) cc_final: 0.8101 (t0) REVERT: D 399 MET cc_start: 0.6576 (mtt) cc_final: 0.6243 (mtt) REVERT: D 582 MET cc_start: 0.7024 (mtp) cc_final: 0.6501 (ptm) REVERT: D 604 MET cc_start: 0.4254 (mmt) cc_final: 0.3714 (mpp) outliers start: 24 outliers final: 15 residues processed: 215 average time/residue: 0.2569 time to fit residues: 82.7335 Evaluate side-chains 202 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 183 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 542 SER Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain D residue 302 ASN Chi-restraints excluded: chain D residue 465 ILE Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 542 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 0.0970 chunk 123 optimal weight: 20.0000 chunk 84 optimal weight: 10.0000 chunk 18 optimal weight: 0.0060 chunk 78 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 173 optimal weight: 20.0000 chunk 85 optimal weight: 10.0000 chunk 155 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN B 302 ASN C 302 ASN D 302 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15196 Z= 0.185 Angle : 0.474 7.737 20608 Z= 0.245 Chirality : 0.039 0.140 2312 Planarity : 0.003 0.028 2540 Dihedral : 4.218 20.484 2032 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.48 % Allowed : 12.59 % Favored : 85.93 % 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 (0.21), residues: 1792 helix: 0.91 (0.16), residues: 1092 sheet: -0.96 (0.74), residues: 56 loop : -0.35 (0.27), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 168 HIS 0.002 0.001 HIS D 422 PHE 0.011 0.001 PHE D 298 TYR 0.013 0.001 TYR B 349 ARG 0.003 0.000 ARG B 271 *********************** 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 232 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 208 time to evaluate : 1.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 GLU cc_start: 0.8125 (pm20) cc_final: 0.7665 (pt0) REVERT: A 302 ASN cc_start: 0.8459 (OUTLIER) cc_final: 0.8143 (t0) REVERT: A 399 MET cc_start: 0.6443 (mtt) cc_final: 0.6133 (mtt) REVERT: A 604 MET cc_start: 0.4240 (mmt) cc_final: 0.3704 (mpp) REVERT: B 269 GLU cc_start: 0.8155 (pm20) cc_final: 0.7660 (pt0) REVERT: B 302 ASN cc_start: 0.8471 (OUTLIER) cc_final: 0.8148 (t0) REVERT: B 399 MET cc_start: 0.6433 (mtt) cc_final: 0.6138 (mtt) REVERT: B 604 MET cc_start: 0.4234 (mmt) cc_final: 0.3695 (mpp) REVERT: C 269 GLU cc_start: 0.8142 (pm20) cc_final: 0.7693 (pt0) REVERT: C 302 ASN cc_start: 0.8479 (OUTLIER) cc_final: 0.8137 (t0) REVERT: C 399 MET cc_start: 0.6443 (mtt) cc_final: 0.6144 (mtt) REVERT: C 578 LYS cc_start: 0.4594 (tttm) cc_final: 0.4234 (tptm) REVERT: C 582 MET cc_start: 0.7010 (mtp) cc_final: 0.6520 (ptm) REVERT: C 604 MET cc_start: 0.4242 (mmt) cc_final: 0.3697 (mpp) REVERT: D 269 GLU cc_start: 0.8139 (pm20) cc_final: 0.7671 (pt0) REVERT: D 302 ASN cc_start: 0.8486 (OUTLIER) cc_final: 0.8142 (t0) REVERT: D 578 LYS cc_start: 0.4489 (tttm) cc_final: 0.4260 (pttm) REVERT: D 604 MET cc_start: 0.4221 (mmt) cc_final: 0.3682 (mpp) outliers start: 24 outliers final: 11 residues processed: 213 average time/residue: 0.2474 time to fit residues: 80.0323 Evaluate side-chains 199 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 184 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 542 SER Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain D residue 302 ASN Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 542 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 129 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 0.0980 chunk 156 optimal weight: 0.7980 chunk 43 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN B 302 ASN C 302 ASN D 302 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15196 Z= 0.152 Angle : 0.458 7.923 20608 Z= 0.236 Chirality : 0.038 0.140 2312 Planarity : 0.003 0.028 2540 Dihedral : 4.120 18.339 2032 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.28 % Allowed : 12.28 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.20), residues: 1792 helix: 1.02 (0.16), residues: 1092 sheet: -1.07 (0.73), residues: 56 loop : -0.33 (0.27), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 168 HIS 0.001 0.000 HIS D 422 PHE 0.008 0.001 PHE A 298 TYR 0.013 0.001 TYR D 196 ARG 0.002 0.000 ARG C 271 *********************** 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 240 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 203 time to evaluate : 1.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 GLU cc_start: 0.8112 (pm20) cc_final: 0.7663 (pt0) REVERT: A 302 ASN cc_start: 0.8392 (OUTLIER) cc_final: 0.8181 (t0) REVERT: A 399 MET cc_start: 0.6328 (mtt) cc_final: 0.6083 (mtt) REVERT: A 604 MET cc_start: 0.4277 (mmt) cc_final: 0.3708 (mpp) REVERT: B 226 GLN cc_start: 0.7950 (mm110) cc_final: 0.7550 (mm110) REVERT: B 269 GLU cc_start: 0.8139 (pm20) cc_final: 0.7656 (pt0) REVERT: B 302 ASN cc_start: 0.8404 (OUTLIER) cc_final: 0.8177 (t0) REVERT: B 578 LYS cc_start: 0.4562 (tttm) cc_final: 0.4293 (pttm) REVERT: B 604 MET cc_start: 0.4303 (mmt) cc_final: 0.3724 (mpp) REVERT: C 226 GLN cc_start: 0.7967 (mm110) cc_final: 0.7584 (mm110) REVERT: C 269 GLU cc_start: 0.8120 (pm20) cc_final: 0.7663 (pt0) REVERT: C 302 ASN cc_start: 0.8412 (OUTLIER) cc_final: 0.8170 (t0) REVERT: C 399 MET cc_start: 0.6334 (mtt) cc_final: 0.6112 (mtt) REVERT: C 578 LYS cc_start: 0.4565 (tttm) cc_final: 0.4178 (tptm) REVERT: C 582 MET cc_start: 0.6988 (mtp) cc_final: 0.6576 (ptm) REVERT: C 604 MET cc_start: 0.4271 (mmt) cc_final: 0.3668 (mpp) REVERT: D 269 GLU cc_start: 0.8110 (pm20) cc_final: 0.7681 (pt0) REVERT: D 302 ASN cc_start: 0.8414 (OUTLIER) cc_final: 0.8186 (t0) REVERT: D 399 MET cc_start: 0.6343 (mtt) cc_final: 0.6088 (mtt) REVERT: D 578 LYS cc_start: 0.4775 (tttm) cc_final: 0.4411 (tptm) REVERT: D 604 MET cc_start: 0.4268 (mmt) cc_final: 0.3661 (mpp) outliers start: 37 outliers final: 13 residues processed: 216 average time/residue: 0.2538 time to fit residues: 83.3615 Evaluate side-chains 199 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 182 time to evaluate : 2.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 542 SER Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain D residue 302 ASN Chi-restraints excluded: chain D residue 465 ILE Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 542 SER 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: 0.8980 chunk 34 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 174 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 14 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN B 302 ASN C 302 ASN D 302 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15196 Z= 0.167 Angle : 0.468 7.888 20608 Z= 0.241 Chirality : 0.039 0.141 2312 Planarity : 0.003 0.037 2540 Dihedral : 4.112 18.675 2032 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.41 % Allowed : 12.65 % Favored : 84.94 % 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: 0.74 (0.20), residues: 1792 helix: 1.14 (0.16), residues: 1092 sheet: -1.21 (0.72), residues: 56 loop : -0.35 (0.27), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 168 HIS 0.001 0.001 HIS D 422 PHE 0.008 0.001 PHE B 298 TYR 0.014 0.001 TYR D 196 ARG 0.005 0.000 ARG B 271 *********************** 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 240 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 201 time to evaluate : 1.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7610 (t0) REVERT: A 226 GLN cc_start: 0.7993 (mm110) cc_final: 0.7597 (mm110) REVERT: A 269 GLU cc_start: 0.8094 (pm20) cc_final: 0.7649 (pt0) REVERT: A 271 ARG cc_start: 0.7264 (mtp-110) cc_final: 0.6746 (mtp-110) REVERT: A 399 MET cc_start: 0.6317 (mtt) cc_final: 0.6064 (mtt) REVERT: A 596 GLU cc_start: 0.6487 (mm-30) cc_final: 0.6225 (mm-30) REVERT: A 604 MET cc_start: 0.4281 (mmt) cc_final: 0.3656 (mpp) REVERT: B 204 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7655 (t0) REVERT: B 226 GLN cc_start: 0.7935 (mm110) cc_final: 0.7651 (mm-40) REVERT: B 269 GLU cc_start: 0.8081 (pm20) cc_final: 0.7632 (pt0) REVERT: B 271 ARG cc_start: 0.7284 (mtp-110) cc_final: 0.6857 (mtp-110) REVERT: B 578 LYS cc_start: 0.4622 (tttm) cc_final: 0.4395 (pttm) REVERT: B 596 GLU cc_start: 0.6519 (mm-30) cc_final: 0.6192 (mm-30) REVERT: B 604 MET cc_start: 0.4267 (mmt) cc_final: 0.3646 (mpp) REVERT: C 204 ASP cc_start: 0.8179 (OUTLIER) cc_final: 0.7617 (t0) REVERT: C 226 GLN cc_start: 0.7979 (mm110) cc_final: 0.7713 (mm110) REVERT: C 269 GLU cc_start: 0.8097 (pm20) cc_final: 0.7658 (pt0) REVERT: C 271 ARG cc_start: 0.7250 (mtp-110) cc_final: 0.6771 (mtp-110) REVERT: C 399 MET cc_start: 0.6320 (mtt) cc_final: 0.6097 (mtt) REVERT: C 582 MET cc_start: 0.7081 (mtp) cc_final: 0.6725 (ptm) REVERT: C 596 GLU cc_start: 0.6528 (mm-30) cc_final: 0.6197 (mm-30) REVERT: C 604 MET cc_start: 0.4269 (mmt) cc_final: 0.3649 (mpp) REVERT: D 204 ASP cc_start: 0.8200 (OUTLIER) cc_final: 0.7623 (t0) REVERT: D 226 GLN cc_start: 0.7990 (mm110) cc_final: 0.7605 (mm110) REVERT: D 269 GLU cc_start: 0.8078 (pm20) cc_final: 0.7644 (pt0) REVERT: D 271 ARG cc_start: 0.7234 (mtp-110) cc_final: 0.6745 (mtp-110) REVERT: D 399 MET cc_start: 0.6326 (mtt) cc_final: 0.6087 (mtt) REVERT: D 596 GLU cc_start: 0.6523 (mm-30) cc_final: 0.6204 (mm-30) REVERT: D 604 MET cc_start: 0.4253 (mmt) cc_final: 0.3629 (mpp) outliers start: 39 outliers final: 23 residues processed: 219 average time/residue: 0.2639 time to fit residues: 86.0023 Evaluate side-chains 224 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 197 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 542 SER Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 568 ILE Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 260 TYR Chi-restraints excluded: chain D residue 373 SER Chi-restraints excluded: chain D residue 465 ILE Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 542 SER Chi-restraints excluded: chain D residue 568 ILE Chi-restraints excluded: chain D residue 593 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 0.0770 chunk 19 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 146 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 173 optimal weight: 0.9980 chunk 108 optimal weight: 6.9990 chunk 105 optimal weight: 0.6980 chunk 80 optimal weight: 10.0000 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN B 302 ASN C 302 ASN D 302 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15196 Z= 0.163 Angle : 0.467 7.920 20608 Z= 0.242 Chirality : 0.038 0.140 2312 Planarity : 0.003 0.032 2540 Dihedral : 4.069 18.371 2032 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.78 % Allowed : 12.65 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.20), residues: 1792 helix: 1.21 (0.16), residues: 1092 sheet: -0.73 (0.80), residues: 48 loop : -0.37 (0.26), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 168 HIS 0.002 0.001 HIS C 422 PHE 0.007 0.001 PHE A 298 TYR 0.014 0.001 TYR B 196 ARG 0.005 0.000 ARG D 271 *********************** 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 271 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 226 time to evaluate : 1.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.8134 (OUTLIER) cc_final: 0.7245 (t0) REVERT: A 226 GLN cc_start: 0.7984 (mm110) cc_final: 0.7622 (mm110) REVERT: A 238 ASN cc_start: 0.7881 (m-40) cc_final: 0.7677 (m110) REVERT: A 269 GLU cc_start: 0.8083 (pm20) cc_final: 0.7621 (pt0) REVERT: A 271 ARG cc_start: 0.7223 (mtp-110) cc_final: 0.6767 (mtp-110) REVERT: A 320 SER cc_start: 0.8222 (m) cc_final: 0.7869 (t) REVERT: A 604 MET cc_start: 0.4394 (mmt) cc_final: 0.3754 (mpp) REVERT: B 204 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7248 (t0) REVERT: B 226 GLN cc_start: 0.7951 (mm110) cc_final: 0.7574 (mm-40) REVERT: B 269 GLU cc_start: 0.8029 (pm20) cc_final: 0.7540 (pt0) REVERT: B 271 ARG cc_start: 0.7248 (mtp-110) cc_final: 0.6805 (mtp-110) REVERT: B 320 SER cc_start: 0.8206 (m) cc_final: 0.7870 (t) REVERT: B 540 ASP cc_start: 0.5730 (m-30) cc_final: 0.5378 (m-30) REVERT: B 596 GLU cc_start: 0.6392 (mm-30) cc_final: 0.6156 (mm-30) REVERT: B 604 MET cc_start: 0.4420 (mmt) cc_final: 0.3729 (mpp) REVERT: C 204 ASP cc_start: 0.8131 (OUTLIER) cc_final: 0.7235 (t0) REVERT: C 226 GLN cc_start: 0.7982 (mm110) cc_final: 0.7549 (mm110) REVERT: C 269 GLU cc_start: 0.8067 (pm20) cc_final: 0.7614 (pt0) REVERT: C 271 ARG cc_start: 0.7227 (mtp-110) cc_final: 0.6754 (mtp-110) REVERT: C 320 SER cc_start: 0.8189 (m) cc_final: 0.7864 (t) REVERT: C 540 ASP cc_start: 0.5660 (m-30) cc_final: 0.5324 (m-30) REVERT: C 596 GLU cc_start: 0.6339 (mm-30) cc_final: 0.6128 (mm-30) REVERT: C 604 MET cc_start: 0.4394 (mmt) cc_final: 0.3737 (mpp) REVERT: D 204 ASP cc_start: 0.8138 (OUTLIER) cc_final: 0.7295 (t0) REVERT: D 226 GLN cc_start: 0.8004 (mm110) cc_final: 0.7547 (mm110) REVERT: D 269 GLU cc_start: 0.8081 (pm20) cc_final: 0.7626 (pt0) REVERT: D 271 ARG cc_start: 0.7213 (mtp-110) cc_final: 0.6762 (mtp-110) REVERT: D 320 SER cc_start: 0.8209 (m) cc_final: 0.7863 (t) REVERT: D 540 ASP cc_start: 0.5634 (m-30) cc_final: 0.5362 (m-30) REVERT: D 604 MET cc_start: 0.4434 (mmt) cc_final: 0.3741 (mpp) outliers start: 45 outliers final: 29 residues processed: 252 average time/residue: 0.2593 time to fit residues: 97.5712 Evaluate side-chains 243 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 210 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 542 SER Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 568 ILE Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 260 TYR Chi-restraints excluded: chain D residue 373 SER Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 465 ILE Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 542 SER Chi-restraints excluded: chain D residue 568 ILE Chi-restraints excluded: chain D residue 593 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 110 optimal weight: 0.8980 chunk 118 optimal weight: 6.9990 chunk 85 optimal weight: 0.3980 chunk 16 optimal weight: 4.9990 chunk 136 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN B 302 ASN C 302 ASN D 238 ASN D 302 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15196 Z= 0.161 Angle : 0.475 9.630 20608 Z= 0.243 Chirality : 0.039 0.142 2312 Planarity : 0.003 0.031 2540 Dihedral : 4.030 18.070 2032 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.41 % Allowed : 14.20 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.83 (0.20), residues: 1792 helix: 1.21 (0.16), residues: 1092 sheet: -0.56 (0.81), residues: 48 loop : -0.37 (0.26), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 168 HIS 0.001 0.001 HIS D 422 PHE 0.009 0.001 PHE B 298 TYR 0.015 0.001 TYR C 196 ARG 0.003 0.000 ARG D 271 *********************** 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 250 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 211 time to evaluate : 1.751 Fit side-chains REVERT: A 204 ASP cc_start: 0.8087 (OUTLIER) cc_final: 0.7158 (t0) REVERT: A 226 GLN cc_start: 0.7802 (mm110) cc_final: 0.7458 (mm-40) REVERT: A 238 ASN cc_start: 0.7873 (m-40) cc_final: 0.7657 (m110) REVERT: A 269 GLU cc_start: 0.8092 (pm20) cc_final: 0.7640 (pt0) REVERT: A 271 ARG cc_start: 0.7266 (mtp-110) cc_final: 0.6872 (mtp-110) REVERT: A 320 SER cc_start: 0.8232 (m) cc_final: 0.7876 (t) REVERT: A 490 GLU cc_start: 0.5795 (mp0) cc_final: 0.5517 (mp0) REVERT: A 590 ASP cc_start: 0.7232 (p0) cc_final: 0.5990 (t0) REVERT: A 604 MET cc_start: 0.4492 (mmt) cc_final: 0.3800 (mpp) REVERT: B 204 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.7048 (t0) REVERT: B 226 GLN cc_start: 0.7968 (mm110) cc_final: 0.7553 (mm-40) REVERT: B 269 GLU cc_start: 0.8012 (pm20) cc_final: 0.7529 (pt0) REVERT: B 271 ARG cc_start: 0.7312 (mtp-110) cc_final: 0.6927 (mtp-110) REVERT: B 320 SER cc_start: 0.8219 (m) cc_final: 0.7884 (t) REVERT: B 498 GLN cc_start: 0.7590 (mt0) cc_final: 0.7275 (mt0) REVERT: B 590 ASP cc_start: 0.7248 (p0) cc_final: 0.5976 (t0) REVERT: B 604 MET cc_start: 0.4461 (mmt) cc_final: 0.3772 (mpp) REVERT: C 204 ASP cc_start: 0.8082 (OUTLIER) cc_final: 0.7097 (t0) REVERT: C 226 GLN cc_start: 0.7964 (mm110) cc_final: 0.7543 (mm110) REVERT: C 269 GLU cc_start: 0.8051 (pm20) cc_final: 0.7621 (pt0) REVERT: C 271 ARG cc_start: 0.7251 (mtp-110) cc_final: 0.6858 (mtp-110) REVERT: C 320 SER cc_start: 0.8209 (m) cc_final: 0.7885 (t) REVERT: C 490 GLU cc_start: 0.5797 (mp0) cc_final: 0.5556 (mp0) REVERT: C 498 GLN cc_start: 0.7583 (mt0) cc_final: 0.7275 (mt0) REVERT: C 590 ASP cc_start: 0.7215 (p0) cc_final: 0.5977 (t0) REVERT: C 604 MET cc_start: 0.4492 (mmt) cc_final: 0.3798 (mpp) REVERT: D 204 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7235 (t0) REVERT: D 226 GLN cc_start: 0.7988 (mm110) cc_final: 0.7536 (mm110) REVERT: D 269 GLU cc_start: 0.8094 (pm20) cc_final: 0.7656 (pt0) REVERT: D 271 ARG cc_start: 0.7272 (mtp-110) cc_final: 0.6860 (mtp-110) REVERT: D 320 SER cc_start: 0.8220 (m) cc_final: 0.7872 (t) REVERT: D 540 ASP cc_start: 0.5599 (m-30) cc_final: 0.5367 (m-30) REVERT: D 590 ASP cc_start: 0.7180 (p0) cc_final: 0.5982 (t0) REVERT: D 604 MET cc_start: 0.4486 (mmt) cc_final: 0.3793 (mpp) outliers start: 39 outliers final: 32 residues processed: 230 average time/residue: 0.2646 time to fit residues: 90.8671 Evaluate side-chains 238 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 202 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 542 SER Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 568 ILE Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 260 TYR Chi-restraints excluded: chain D residue 302 ASN Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 465 ILE Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 542 SER Chi-restraints excluded: chain D residue 568 ILE Chi-restraints excluded: chain D residue 593 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 161 optimal weight: 0.6980 chunk 97 optimal weight: 0.0980 chunk 70 optimal weight: 5.9990 chunk 126 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 146 optimal weight: 0.9990 chunk 152 optimal weight: 0.2980 chunk 106 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN B 302 ASN C 302 ASN D 302 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 15196 Z= 0.166 Angle : 0.472 7.772 20608 Z= 0.244 Chirality : 0.039 0.142 2312 Planarity : 0.003 0.032 2540 Dihedral : 4.032 18.093 2032 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.02 % Allowed : 14.01 % 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: 0.88 (0.20), residues: 1792 helix: 1.26 (0.16), residues: 1092 sheet: -0.55 (0.81), residues: 48 loop : -0.37 (0.26), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 168 HIS 0.001 0.001 HIS D 422 PHE 0.008 0.001 PHE A 574 TYR 0.015 0.001 TYR C 196 ARG 0.003 0.000 ARG D 271 *********************** 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 261 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 212 time to evaluate : 1.894 Fit side-chains REVERT: A 204 ASP cc_start: 0.8090 (OUTLIER) cc_final: 0.7245 (t0) REVERT: A 226 GLN cc_start: 0.7818 (mm110) cc_final: 0.7476 (mm-40) REVERT: A 238 ASN cc_start: 0.7881 (m-40) cc_final: 0.7664 (m110) REVERT: A 269 GLU cc_start: 0.8083 (pm20) cc_final: 0.7635 (pt0) REVERT: A 271 ARG cc_start: 0.7247 (mtp-110) cc_final: 0.6946 (mtp-110) REVERT: A 320 SER cc_start: 0.8264 (m) cc_final: 0.7902 (t) REVERT: A 490 GLU cc_start: 0.5861 (mp0) cc_final: 0.5625 (mp0) REVERT: A 590 ASP cc_start: 0.7300 (p0) cc_final: 0.6128 (t0) REVERT: A 604 MET cc_start: 0.4540 (mmt) cc_final: 0.3809 (mpp) REVERT: B 172 ILE cc_start: 0.9113 (tp) cc_final: 0.8846 (tp) REVERT: B 204 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7048 (t0) REVERT: B 226 GLN cc_start: 0.7787 (mm110) cc_final: 0.7538 (mm-40) REVERT: B 269 GLU cc_start: 0.8007 (pm20) cc_final: 0.7540 (pt0) REVERT: B 271 ARG cc_start: 0.7254 (mtp-110) cc_final: 0.6912 (mtp-110) REVERT: B 320 SER cc_start: 0.8238 (m) cc_final: 0.7899 (t) REVERT: B 490 GLU cc_start: 0.5884 (mp0) cc_final: 0.5644 (mp0) REVERT: B 498 GLN cc_start: 0.7590 (mt0) cc_final: 0.7282 (mt0) REVERT: B 578 LYS cc_start: 0.4872 (tttm) cc_final: 0.4617 (pttm) REVERT: B 590 ASP cc_start: 0.7313 (p0) cc_final: 0.6113 (t0) REVERT: B 604 MET cc_start: 0.4523 (mmt) cc_final: 0.3793 (mpp) REVERT: C 171 CYS cc_start: 0.7317 (m) cc_final: 0.7067 (m) REVERT: C 204 ASP cc_start: 0.8075 (OUTLIER) cc_final: 0.7136 (t0) REVERT: C 226 GLN cc_start: 0.7961 (mm110) cc_final: 0.7596 (mm110) REVERT: C 246 PHE cc_start: 0.8414 (t80) cc_final: 0.8185 (t80) REVERT: C 269 GLU cc_start: 0.8073 (pm20) cc_final: 0.7628 (pt0) REVERT: C 271 ARG cc_start: 0.7223 (mtp-110) cc_final: 0.6913 (mtp-110) REVERT: C 320 SER cc_start: 0.8232 (m) cc_final: 0.7902 (t) REVERT: C 498 GLN cc_start: 0.7583 (mt0) cc_final: 0.7277 (mt0) REVERT: C 590 ASP cc_start: 0.7317 (p0) cc_final: 0.6134 (t0) REVERT: C 604 MET cc_start: 0.4490 (mmt) cc_final: 0.3776 (mpp) REVERT: D 204 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7239 (t0) REVERT: D 226 GLN cc_start: 0.7978 (mm110) cc_final: 0.7600 (mm110) REVERT: D 269 GLU cc_start: 0.8084 (pm20) cc_final: 0.7644 (pt0) REVERT: D 271 ARG cc_start: 0.7258 (mtp-110) cc_final: 0.6922 (mtp-110) REVERT: D 320 SER cc_start: 0.8250 (m) cc_final: 0.7897 (t) REVERT: D 498 GLN cc_start: 0.7568 (mt0) cc_final: 0.7253 (mt0) REVERT: D 540 ASP cc_start: 0.5618 (m-30) cc_final: 0.5372 (m-30) REVERT: D 578 LYS cc_start: 0.4450 (tptm) cc_final: 0.4171 (tptm) REVERT: D 590 ASP cc_start: 0.7334 (p0) cc_final: 0.6132 (t0) REVERT: D 604 MET cc_start: 0.4477 (mmt) cc_final: 0.3758 (mpp) outliers start: 49 outliers final: 40 residues processed: 239 average time/residue: 0.2592 time to fit residues: 92.2174 Evaluate side-chains 247 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 203 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 542 SER Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 338 ASN Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 540 ASP Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 568 ILE Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 260 TYR Chi-restraints excluded: chain D residue 302 ASN Chi-restraints excluded: chain D residue 373 SER Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 465 ILE Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 542 SER Chi-restraints excluded: chain D residue 568 ILE Chi-restraints excluded: chain D residue 593 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 10.0000 chunk 104 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 179 optimal weight: 5.9990 chunk 165 optimal weight: 0.6980 chunk 142 optimal weight: 10.0000 chunk 14 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 113 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN B 302 ASN C 302 ASN D 302 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 15196 Z= 0.153 Angle : 0.468 7.699 20608 Z= 0.242 Chirality : 0.039 0.143 2312 Planarity : 0.003 0.034 2540 Dihedral : 4.001 17.751 2032 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.78 % Allowed : 14.32 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.20), residues: 1792 helix: 1.25 (0.16), residues: 1092 sheet: -0.56 (0.81), residues: 48 loop : -0.36 (0.26), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 168 HIS 0.001 0.001 HIS D 422 PHE 0.008 0.001 PHE B 298 TYR 0.015 0.001 TYR A 196 ARG 0.002 0.000 ARG D 271 ********************** 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 253 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 208 time to evaluate : 1.740 Fit side-chains REVERT: A 204 ASP cc_start: 0.8070 (OUTLIER) cc_final: 0.6997 (t0) REVERT: A 226 GLN cc_start: 0.7783 (mm110) cc_final: 0.7477 (mm-40) REVERT: A 238 ASN cc_start: 0.7887 (m-40) cc_final: 0.7652 (m110) REVERT: A 269 GLU cc_start: 0.8079 (pm20) cc_final: 0.7585 (pt0) REVERT: A 320 SER cc_start: 0.8247 (m) cc_final: 0.7886 (t) REVERT: A 490 GLU cc_start: 0.5789 (mp0) cc_final: 0.5563 (mp0) REVERT: A 498 GLN cc_start: 0.7622 (mt0) cc_final: 0.7300 (mt0) REVERT: A 604 MET cc_start: 0.4550 (mmt) cc_final: 0.3822 (mpp) REVERT: B 172 ILE cc_start: 0.9115 (tp) cc_final: 0.8849 (tp) REVERT: B 204 ASP cc_start: 0.7973 (OUTLIER) cc_final: 0.6950 (t0) REVERT: B 226 GLN cc_start: 0.7728 (mm110) cc_final: 0.7513 (mm-40) REVERT: B 269 GLU cc_start: 0.7999 (pm20) cc_final: 0.7540 (pt0) REVERT: B 271 ARG cc_start: 0.7160 (mtp-110) cc_final: 0.6933 (mtp-110) REVERT: B 320 SER cc_start: 0.8222 (m) cc_final: 0.7883 (t) REVERT: B 498 GLN cc_start: 0.7581 (mt0) cc_final: 0.7277 (mt0) REVERT: B 578 LYS cc_start: 0.4938 (tttm) cc_final: 0.4639 (pttm) REVERT: B 590 ASP cc_start: 0.7340 (p0) cc_final: 0.6978 (p0) REVERT: B 604 MET cc_start: 0.4538 (mmt) cc_final: 0.3817 (mpp) REVERT: C 171 CYS cc_start: 0.7323 (m) cc_final: 0.7068 (m) REVERT: C 204 ASP cc_start: 0.8064 (OUTLIER) cc_final: 0.7003 (t0) REVERT: C 226 GLN cc_start: 0.7943 (mm110) cc_final: 0.7600 (mm110) REVERT: C 269 GLU cc_start: 0.7998 (pm20) cc_final: 0.7505 (pt0) REVERT: C 320 SER cc_start: 0.8213 (m) cc_final: 0.7886 (t) REVERT: C 498 GLN cc_start: 0.7582 (mt0) cc_final: 0.7286 (mt0) REVERT: C 521 GLU cc_start: 0.7018 (tm-30) cc_final: 0.6801 (tm-30) REVERT: C 604 MET cc_start: 0.4507 (mmt) cc_final: 0.3780 (mpp) REVERT: D 204 ASP cc_start: 0.8094 (OUTLIER) cc_final: 0.7008 (t0) REVERT: D 226 GLN cc_start: 0.7940 (mm110) cc_final: 0.7555 (mm110) REVERT: D 269 GLU cc_start: 0.8079 (pm20) cc_final: 0.7591 (pt0) REVERT: D 320 SER cc_start: 0.8228 (m) cc_final: 0.7882 (t) REVERT: D 498 GLN cc_start: 0.7557 (mt0) cc_final: 0.7259 (mt0) REVERT: D 540 ASP cc_start: 0.5605 (m-30) cc_final: 0.5370 (m-30) REVERT: D 590 ASP cc_start: 0.7310 (p0) cc_final: 0.6955 (p0) REVERT: D 604 MET cc_start: 0.4485 (mmt) cc_final: 0.3768 (mpp) outliers start: 45 outliers final: 41 residues processed: 236 average time/residue: 0.2566 time to fit residues: 90.9607 Evaluate side-chains 242 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 197 time to evaluate : 1.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 542 SER Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 540 ASP Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 568 ILE Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 260 TYR Chi-restraints excluded: chain D residue 302 ASN Chi-restraints excluded: chain D residue 338 ASN Chi-restraints excluded: chain D residue 373 SER Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 465 ILE Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 542 SER Chi-restraints excluded: chain D residue 568 ILE Chi-restraints excluded: chain D residue 593 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 0.9980 chunk 43 optimal weight: 0.3980 chunk 131 optimal weight: 9.9990 chunk 21 optimal weight: 0.0570 chunk 39 optimal weight: 8.9990 chunk 143 optimal weight: 0.0980 chunk 59 optimal weight: 4.9990 chunk 146 optimal weight: 0.9990 chunk 18 optimal weight: 0.0020 chunk 26 optimal weight: 4.9990 chunk 125 optimal weight: 10.0000 overall best weight: 0.3106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN B 302 ASN C 302 ASN D 302 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.149320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.121378 restraints weight = 21076.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.120018 restraints weight = 18770.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.120988 restraints weight = 14563.252| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15196 Z= 0.132 Angle : 0.470 7.633 20608 Z= 0.244 Chirality : 0.039 0.144 2312 Planarity : 0.003 0.034 2540 Dihedral : 3.918 17.079 2032 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.47 % Allowed : 14.57 % 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: 0.93 (0.21), residues: 1792 helix: 1.29 (0.16), residues: 1092 sheet: -0.51 (0.82), residues: 48 loop : -0.35 (0.26), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 168 HIS 0.001 0.001 HIS D 422 PHE 0.012 0.001 PHE C 246 TYR 0.015 0.001 TYR C 306 ARG 0.003 0.000 ARG C 271 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2918.85 seconds wall clock time: 54 minutes 37.49 seconds (3277.49 seconds total)