Starting phenix.real_space_refine on Fri Feb 16 09:57:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lg1_23310/02_2024/7lg1_23310_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lg1_23310/02_2024/7lg1_23310.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lg1_23310/02_2024/7lg1_23310_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lg1_23310/02_2024/7lg1_23310_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lg1_23310/02_2024/7lg1_23310_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lg1_23310/02_2024/7lg1_23310.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lg1_23310/02_2024/7lg1_23310.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lg1_23310/02_2024/7lg1_23310_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lg1_23310/02_2024/7lg1_23310_updated.pdb" } resolution = 2.7 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 4 5.49 5 S 76 5.16 5 C 9788 2.51 5 N 2428 2.21 5 O 2720 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 GLU 341": "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: 15017 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3730 Number of conformers: 2 Conformer: "A" 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 Conformer: "B" 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 bond proxies already assigned to first conformer: 3729 Chain: "B" Number of atoms: 3730 Number of conformers: 2 Conformer: "A" 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 Conformer: "B" 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 bond proxies already assigned to first conformer: 3729 Chain: "C" Number of atoms: 3730 Number of conformers: 2 Conformer: "A" 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 Conformer: "B" 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 bond proxies already assigned to first conformer: 3729 Chain: "D" Number of atoms: 3730 Number of conformers: 2 Conformer: "A" 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 Conformer: "B" 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 bond proxies already assigned to first conformer: 3729 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {' CA': 1, 'PCG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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} Residues with excluded nonbonded symmetry interactions: 24 residue: pdb=" N ATHR A 362 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BTHR A 362 " occ=0.50 residue: pdb=" N AILE A 363 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE A 363 " occ=0.50 residue: pdb=" N AGLY A 364 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 364 " occ=0.50 residue: pdb=" N AGLN A 365 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A 365 " occ=0.50 residue: pdb=" N ATHR A 366 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BTHR A 366 " occ=0.50 residue: pdb=" N APRO A 367 " occ=0.50 ... (12 atoms not shown) pdb=" CD BPRO A 367 " occ=0.50 residue: pdb=" N ATHR B 362 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BTHR B 362 " occ=0.50 residue: pdb=" N AILE B 363 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE B 363 " occ=0.50 residue: pdb=" N AGLY B 364 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY B 364 " occ=0.50 residue: pdb=" N AGLN B 365 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN B 365 " occ=0.50 residue: pdb=" N ATHR B 366 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BTHR B 366 " occ=0.50 residue: pdb=" N APRO B 367 " occ=0.50 ... (12 atoms not shown) pdb=" CD BPRO B 367 " occ=0.50 ... (remaining 12 not shown) Time building chain proxies: 14.32, per 1000 atoms: 0.95 Number of scatterers: 15017 At special positions: 0 Unit cell: (95.589, 95.589, 114.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 76 16.00 P 4 15.00 O 2720 8.00 N 2428 7.00 C 9788 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.10 Conformation dependent library (CDL) restraints added in 5.0 seconds 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3448 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: 3.10 Creating SS restraints... Processing helix chain 'A' and resid 163 through 188 Proline residue: A 175 - end of helix removed outlier: 5.268A 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: 3.587A 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: 4.056A pdb=" N ASN A 273 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG A 277 " --> pdb=" O ARG A 274 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N SER A 279 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 4.199A 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: 5.741A pdb=" N THR A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 492 removed outlier: 3.724A 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: 5.268A pdb=" N ILE B 184 " --> pdb=" O TRP B 180 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA B 185 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 195 Processing helix chain 'B' and resid 197 through 219 removed outlier: 3.588A pdb=" N ILE B 202 " --> pdb=" O GLU B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 241 Processing helix chain 'B' and resid 244 through 252 Processing helix chain 'B' and resid 256 through 263 removed outlier: 4.343A pdb=" N LEU B 263 " --> pdb=" O TYR B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 291 removed outlier: 4.056A 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: 4.726A 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: 3.518A 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: 4.906A pdb=" N TYR B 456 " --> pdb=" O GLU B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 474 removed outlier: 5.039A pdb=" N GLU B 464 " --> pdb=" O LYS B 460 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ASP B 472 " --> pdb=" O ASN B 468 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N THR B 473 " --> pdb=" O VAL B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 492 removed outlier: 3.724A 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: 5.268A pdb=" N ILE C 184 " --> pdb=" O TRP C 180 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA C 185 " --> pdb=" O THR C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 195 Processing helix chain 'C' and resid 197 through 219 removed outlier: 3.588A pdb=" N ILE C 202 " --> pdb=" O GLU C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 241 Processing helix chain 'C' and resid 244 through 252 Processing helix chain 'C' and resid 256 through 263 removed outlier: 4.343A pdb=" N LEU C 263 " --> pdb=" O TYR C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 291 removed outlier: 4.055A pdb=" N ASN C 273 " --> pdb=" O ILE C 270 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG C 277 " --> pdb=" O ARG C 274 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N SER C 279 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 4.199A 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: 4.904A pdb=" N TYR C 456 " --> pdb=" O GLU C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 474 removed outlier: 5.039A pdb=" N GLU C 464 " --> pdb=" O LYS C 460 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ASP C 472 " --> pdb=" O ASN C 468 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N THR C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 492 removed outlier: 3.724A 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: 5.267A pdb=" N ILE D 184 " --> pdb=" O TRP D 180 " (cutoff:3.500A) removed outlier: 3.827A 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: 3.587A pdb=" N ILE D 202 " --> pdb=" O GLU D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 241 Processing helix chain 'D' and resid 244 through 252 Processing helix chain 'D' and resid 256 through 263 removed outlier: 4.343A pdb=" N LEU D 263 " --> pdb=" O TYR D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 291 removed outlier: 4.056A pdb=" N ASN D 273 " --> pdb=" O ILE D 270 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG D 277 " --> pdb=" O ARG D 274 " (cutoff:3.500A) removed outlier: 4.726A 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: 3.518A 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: 5.039A pdb=" N GLU D 464 " --> pdb=" O LYS D 460 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ASP D 472 " --> pdb=" O ASN D 468 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N THR D 473 " --> pdb=" O VAL D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 492 removed outlier: 3.725A pdb=" N LEU D 491 " --> pdb=" O LEU D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 549 No H-bonds generated for 'chain 'D' and resid 547 through 549' Processing helix chain 'D' and resid 578 through 585 Processing helix chain 'D' and resid 592 through 604 Processing sheet with id= A, first strand: chain 'A' and resid 496 through 500 removed outlier: 6.563A pdb=" N PHE A 574 " --> pdb=" O ILE A 519 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ILE A 519 " --> pdb=" O PHE A 574 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU A 576 " --> pdb=" O TYR A 517 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N TYR A 517 " --> pdb=" O LEU A 576 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 564 through 568 removed outlier: 4.434A pdb=" N ASN A 564 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS A 523 " --> pdb=" O ILE A 568 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 496 through 500 removed outlier: 6.562A pdb=" N PHE B 574 " --> pdb=" O ILE B 519 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ILE B 519 " --> pdb=" O PHE B 574 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU B 576 " --> pdb=" O TYR B 517 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N TYR B 517 " --> pdb=" O LEU B 576 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 564 through 568 removed outlier: 4.434A pdb=" N ASN B 564 " --> pdb=" O VAL B 527 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS B 523 " --> pdb=" O ILE B 568 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 496 through 500 removed outlier: 6.563A 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: 6.583A pdb=" N LEU C 576 " --> pdb=" O TYR C 517 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N TYR C 517 " --> pdb=" O LEU C 576 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 564 through 568 removed outlier: 4.435A 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: 6.563A pdb=" N PHE D 574 " --> pdb=" O ILE D 519 " (cutoff:3.500A) removed outlier: 5.863A 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: 5.010A 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: 3.983A 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: 5.17 Time building geometry restraints manager: 6.52 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: 4395 1.34 - 1.45: 2441 1.45 - 1.57: 8400 1.57 - 1.69: 8 1.69 - 1.81: 128 Bond restraints: 15372 Sorted by residual: bond pdb=" C3' PCG D 701 " pdb=" C4' PCG D 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 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 1.494 0.314 2.00e-02 2.50e+03 2.46e+02 bond pdb=" C3' PCG C 701 " pdb=" C4' PCG C 701 " ideal model delta sigma weight residual 1.808 1.494 0.314 2.00e-02 2.50e+03 2.46e+02 bond pdb=" C2' PCG D 701 " pdb=" C3' PCG D 701 " ideal model delta sigma weight residual 1.200 1.507 -0.307 2.00e-02 2.50e+03 2.35e+02 ... (remaining 15367 not shown) Histogram of bond angle deviations from ideal: 100.37 - 107.11: 369 107.11 - 113.86: 8660 113.86 - 120.60: 6233 120.60 - 127.35: 5474 127.35 - 134.09: 128 Bond angle restraints: 20864 Sorted by residual: angle pdb=" N BILE D 363 " pdb=" CA BILE D 363 " pdb=" C BILE D 363 " ideal model delta sigma weight residual 111.45 104.23 7.22 9.30e-01 1.16e+00 6.03e+01 angle pdb=" N BILE A 363 " pdb=" CA BILE A 363 " pdb=" C BILE A 363 " ideal model delta sigma weight residual 111.45 104.24 7.21 9.30e-01 1.16e+00 6.01e+01 angle pdb=" N BILE C 363 " pdb=" CA BILE C 363 " pdb=" C BILE C 363 " ideal model delta sigma weight residual 111.45 104.26 7.19 9.30e-01 1.16e+00 5.97e+01 angle pdb=" N BILE B 363 " pdb=" CA BILE B 363 " pdb=" C BILE B 363 " ideal model delta sigma weight residual 111.45 104.28 7.17 9.30e-01 1.16e+00 5.95e+01 angle pdb=" N AILE D 363 " pdb=" CA AILE D 363 " pdb=" C AILE D 363 " ideal model delta sigma weight residual 111.58 105.26 6.32 1.06e+00 8.90e-01 3.56e+01 ... (remaining 20859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.63: 8116 16.63 - 33.26: 854 33.26 - 49.88: 122 49.88 - 66.51: 28 66.51 - 83.14: 4 Dihedral angle restraints: 9124 sinusoidal: 3740 harmonic: 5384 Sorted by residual: 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 180.00 158.89 21.11 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA GLU D 596 " pdb=" C GLU D 596 " pdb=" N GLU D 597 " pdb=" CA GLU D 597 " ideal model delta harmonic sigma weight residual 180.00 158.89 21.11 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA GLU C 596 " pdb=" C GLU C 596 " pdb=" N GLU C 597 " pdb=" CA GLU C 597 " ideal model delta harmonic sigma weight residual 180.00 158.89 21.11 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 9121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 2191 0.087 - 0.174: 121 0.174 - 0.261: 16 0.261 - 0.348: 8 0.348 - 0.435: 8 Chirality restraints: 2344 Sorted by residual: 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 0.43 2.00e-01 2.50e+01 4.72e+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 0.43 2.00e-01 2.50e+01 4.72e+00 chirality pdb=" C3' PCG D 701 " pdb=" C2' PCG D 701 " pdb=" C4' PCG D 701 " pdb=" O3' PCG D 701 " both_signs ideal model delta sigma weight residual False -2.10 -2.54 0.43 2.00e-01 2.50e+01 4.72e+00 ... (remaining 2341 not shown) Planarity restraints: 2580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ATHR A 366 " -0.011 2.00e-02 2.50e+03 2.17e-02 4.72e+00 pdb=" C ATHR A 366 " 0.038 2.00e-02 2.50e+03 pdb=" O ATHR A 366 " -0.014 2.00e-02 2.50e+03 pdb=" N APRO A 367 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ATHR B 366 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.72e+00 pdb=" C ATHR B 366 " -0.038 2.00e-02 2.50e+03 pdb=" O ATHR B 366 " 0.014 2.00e-02 2.50e+03 pdb=" N APRO B 367 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ATHR D 366 " -0.011 2.00e-02 2.50e+03 2.17e-02 4.72e+00 pdb=" C ATHR D 366 " 0.038 2.00e-02 2.50e+03 pdb=" O ATHR D 366 " -0.014 2.00e-02 2.50e+03 pdb=" N APRO D 367 " -0.013 2.00e-02 2.50e+03 ... (remaining 2577 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2732 2.76 - 3.30: 15974 3.30 - 3.83: 27475 3.83 - 4.37: 33173 4.37 - 4.90: 54463 Nonbonded interactions: 133817 Sorted by model distance: nonbonded pdb=" O PHE C 216 " pdb=" OG1 THR C 219 " model vdw 2.226 2.440 nonbonded pdb=" O PHE B 216 " pdb=" OG1 THR B 219 " model vdw 2.226 2.440 nonbonded pdb=" O PHE D 216 " pdb=" OG1 THR D 219 " model vdw 2.226 2.440 nonbonded pdb=" O PHE A 216 " pdb=" OG1 THR A 219 " model vdw 2.226 2.440 nonbonded pdb=" O THR C 357 " pdb=" OG1 THR C 361 " model vdw 2.267 2.440 ... (remaining 133812 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 361 or resid 368 through 605 or resid 701)) selection = (chain 'B' and (resid 156 through 361 or resid 368 through 605 or resid 701)) selection = (chain 'C' and (resid 156 through 361 or resid 368 through 605 or resid 701)) selection = (chain 'D' and (resid 156 through 361 or resid 368 through 605 or resid 701)) } 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=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 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: 6.000 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 52.160 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.130 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:12.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 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 15372 Z= 0.745 Angle : 0.706 10.175 20864 Z= 0.437 Chirality : 0.054 0.435 2344 Planarity : 0.005 0.049 2580 Dihedral : 13.204 83.136 5676 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.24 % Allowed : 2.93 % Favored : 96.83 % 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: -1.33 (0.19), residues: 1824 helix: -0.53 (0.14), residues: 1080 sheet: -1.26 (0.82), residues: 56 loop : -1.23 (0.26), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 168 HIS 0.003 0.001 HIS C 312 PHE 0.015 0.002 PHE C 389 TYR 0.014 0.001 TYR B 349 ARG 0.003 0.000 ARG B 561 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 330 time to evaluate : 1.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 LYS cc_start: 0.7574 (tppt) cc_final: 0.7369 (tptp) REVERT: A 281 MET cc_start: 0.8286 (ttp) cc_final: 0.8039 (ttm) REVERT: A 286 GLN cc_start: 0.7563 (pp30) cc_final: 0.7112 (tm130) REVERT: A 293 ASN cc_start: 0.7245 (m-40) cc_final: 0.6786 (m-40) REVERT: A 415 ASP cc_start: 0.7232 (m-30) cc_final: 0.7020 (m-30) REVERT: A 431 GLU cc_start: 0.7096 (tt0) cc_final: 0.6836 (mt-10) REVERT: A 432 LYS cc_start: 0.7138 (mttm) cc_final: 0.6630 (ttpt) REVERT: A 459 ASP cc_start: 0.6236 (m-30) cc_final: 0.5867 (t0) REVERT: A 505 TYR cc_start: 0.7652 (m-80) cc_final: 0.7432 (m-80) REVERT: A 520 LYS cc_start: 0.7071 (tttm) cc_final: 0.6726 (ttpt) REVERT: A 521 GLU cc_start: 0.6931 (tt0) cc_final: 0.6127 (tp30) REVERT: A 566 LYS cc_start: 0.7943 (ptmt) cc_final: 0.7709 (ptmm) REVERT: B 239 LYS cc_start: 0.7576 (tppt) cc_final: 0.7372 (tptp) REVERT: B 281 MET cc_start: 0.8290 (ttp) cc_final: 0.8043 (ttm) REVERT: B 286 GLN cc_start: 0.7563 (pp30) cc_final: 0.7119 (tm130) REVERT: B 293 ASN cc_start: 0.7245 (m-40) cc_final: 0.6784 (m-40) REVERT: B 415 ASP cc_start: 0.7230 (m-30) cc_final: 0.7017 (m-30) REVERT: B 431 GLU cc_start: 0.7093 (tt0) cc_final: 0.6835 (mt-10) REVERT: B 432 LYS cc_start: 0.7098 (mttm) cc_final: 0.6583 (ttpt) REVERT: B 459 ASP cc_start: 0.6237 (m-30) cc_final: 0.5866 (t0) REVERT: B 505 TYR cc_start: 0.7674 (m-80) cc_final: 0.7444 (m-80) REVERT: B 520 LYS cc_start: 0.7066 (tttm) cc_final: 0.6718 (ttpt) REVERT: B 521 GLU cc_start: 0.6961 (tt0) cc_final: 0.6150 (tp30) REVERT: B 566 LYS cc_start: 0.7945 (ptmt) cc_final: 0.7713 (ptmm) REVERT: C 226 GLN cc_start: 0.6516 (mm110) cc_final: 0.5997 (mm-40) REVERT: C 281 MET cc_start: 0.8284 (ttp) cc_final: 0.8036 (ttm) REVERT: C 293 ASN cc_start: 0.7226 (m-40) cc_final: 0.6757 (m-40) REVERT: C 415 ASP cc_start: 0.7230 (m-30) cc_final: 0.7025 (m-30) REVERT: C 431 GLU cc_start: 0.7090 (tt0) cc_final: 0.6829 (mt-10) REVERT: C 432 LYS cc_start: 0.7097 (mttm) cc_final: 0.6581 (ttpt) REVERT: C 459 ASP cc_start: 0.6238 (m-30) cc_final: 0.5867 (t0) REVERT: C 505 TYR cc_start: 0.7680 (m-80) cc_final: 0.7422 (m-80) REVERT: C 520 LYS cc_start: 0.7062 (tttm) cc_final: 0.6710 (ttpt) REVERT: C 566 LYS cc_start: 0.7944 (ptmt) cc_final: 0.7711 (ptmm) REVERT: D 226 GLN cc_start: 0.6519 (mm110) cc_final: 0.5996 (mm-40) REVERT: D 281 MET cc_start: 0.8287 (ttp) cc_final: 0.8041 (ttm) REVERT: D 293 ASN cc_start: 0.7226 (m-40) cc_final: 0.6759 (m-40) REVERT: D 415 ASP cc_start: 0.7236 (m-30) cc_final: 0.7030 (m-30) REVERT: D 431 GLU cc_start: 0.7104 (tt0) cc_final: 0.6838 (mt-10) REVERT: D 432 LYS cc_start: 0.7100 (mttm) cc_final: 0.6609 (ttpt) REVERT: D 459 ASP cc_start: 0.6239 (m-30) cc_final: 0.5873 (t0) REVERT: D 505 TYR cc_start: 0.7652 (m-80) cc_final: 0.7438 (m-80) REVERT: D 520 LYS cc_start: 0.7068 (tttm) cc_final: 0.6724 (ttpt) REVERT: D 566 LYS cc_start: 0.7942 (ptmt) cc_final: 0.7709 (ptmm) outliers start: 4 outliers final: 4 residues processed: 334 average time/residue: 1.3042 time to fit residues: 477.7169 Evaluate side-chains 215 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 211 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain D residue 518 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 0.9980 chunk 136 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 141 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 chunk 105 optimal weight: 0.6980 chunk 163 optimal weight: 0.9990 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 402 ASN A 468 ASN A 496 GLN A 534 GLN B 402 ASN B 468 ASN B 496 GLN B 534 GLN C 226 GLN C 402 ASN C 468 ASN C 496 GLN C 534 GLN D 226 GLN D 402 ASN D 468 ASN D 496 GLN D 498 GLN D 534 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15372 Z= 0.209 Angle : 0.588 8.156 20864 Z= 0.299 Chirality : 0.041 0.183 2344 Planarity : 0.005 0.051 2580 Dihedral : 4.842 22.094 2068 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.10 % Allowed : 13.35 % Favored : 85.55 % 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: -0.22 (0.20), residues: 1824 helix: 0.37 (0.15), residues: 1084 sheet: -0.59 (0.90), residues: 48 loop : -0.80 (0.26), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 168 HIS 0.002 0.001 HIS D 312 PHE 0.014 0.001 PHE C 389 TYR 0.017 0.002 TYR A 199 ARG 0.002 0.000 ARG C 478 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 218 time to evaluate : 1.569 Fit side-chains REVERT: A 221 THR cc_start: 0.8020 (t) cc_final: 0.7778 (m) REVERT: A 281 MET cc_start: 0.8338 (ttp) cc_final: 0.8068 (ttm) REVERT: A 286 GLN cc_start: 0.7572 (pp30) cc_final: 0.7139 (tm130) REVERT: A 293 ASN cc_start: 0.7213 (m-40) cc_final: 0.6779 (m-40) REVERT: A 415 ASP cc_start: 0.7222 (m-30) cc_final: 0.6914 (m-30) REVERT: A 431 GLU cc_start: 0.7063 (tt0) cc_final: 0.6781 (mt-10) REVERT: A 432 LYS cc_start: 0.7147 (mttm) cc_final: 0.6616 (ttpt) REVERT: A 505 TYR cc_start: 0.7641 (m-80) cc_final: 0.7430 (m-80) REVERT: A 520 LYS cc_start: 0.7106 (tttm) cc_final: 0.6733 (ttpt) REVERT: A 566 LYS cc_start: 0.7979 (ptmt) cc_final: 0.7733 (ttmm) REVERT: B 212 LEU cc_start: 0.8479 (tp) cc_final: 0.8140 (mt) REVERT: B 221 THR cc_start: 0.8027 (t) cc_final: 0.7787 (m) REVERT: B 281 MET cc_start: 0.8350 (ttp) cc_final: 0.8081 (ttm) REVERT: B 286 GLN cc_start: 0.7573 (pp30) cc_final: 0.7142 (tm130) REVERT: B 293 ASN cc_start: 0.7213 (m-40) cc_final: 0.6792 (m-40) REVERT: B 413 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7191 (mtp85) REVERT: B 415 ASP cc_start: 0.7218 (m-30) cc_final: 0.6877 (m-30) REVERT: B 431 GLU cc_start: 0.7061 (tt0) cc_final: 0.6771 (mt-10) REVERT: B 432 LYS cc_start: 0.7138 (mttm) cc_final: 0.6608 (ttpt) REVERT: B 505 TYR cc_start: 0.7663 (m-80) cc_final: 0.7443 (m-80) REVERT: B 520 LYS cc_start: 0.7098 (tttm) cc_final: 0.6724 (ttpt) REVERT: B 566 LYS cc_start: 0.7968 (ptmt) cc_final: 0.7747 (ttmm) REVERT: C 212 LEU cc_start: 0.8481 (tp) cc_final: 0.8137 (mt) REVERT: C 221 THR cc_start: 0.8045 (t) cc_final: 0.7798 (m) REVERT: C 281 MET cc_start: 0.8344 (ttp) cc_final: 0.8079 (ttm) REVERT: C 286 GLN cc_start: 0.7634 (pp30) cc_final: 0.7196 (tm130) REVERT: C 293 ASN cc_start: 0.7217 (m-40) cc_final: 0.6792 (m-40) REVERT: C 415 ASP cc_start: 0.7224 (m-30) cc_final: 0.6889 (m-30) REVERT: C 431 GLU cc_start: 0.7086 (tt0) cc_final: 0.6800 (mt-10) REVERT: C 432 LYS cc_start: 0.7133 (mttm) cc_final: 0.6604 (ttpt) REVERT: C 505 TYR cc_start: 0.7659 (m-80) cc_final: 0.7437 (m-80) REVERT: C 520 LYS cc_start: 0.7093 (tttm) cc_final: 0.6734 (ttpt) REVERT: C 521 GLU cc_start: 0.7192 (tt0) cc_final: 0.6694 (tm-30) REVERT: C 566 LYS cc_start: 0.7966 (ptmt) cc_final: 0.7744 (ttmm) REVERT: D 212 LEU cc_start: 0.8479 (tp) cc_final: 0.8137 (mt) REVERT: D 221 THR cc_start: 0.8049 (t) cc_final: 0.7801 (m) REVERT: D 281 MET cc_start: 0.8339 (ttp) cc_final: 0.8066 (ttm) REVERT: D 286 GLN cc_start: 0.7632 (pp30) cc_final: 0.7197 (tm130) REVERT: D 293 ASN cc_start: 0.7216 (m-40) cc_final: 0.6784 (m-40) REVERT: D 413 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7209 (mtp85) REVERT: D 415 ASP cc_start: 0.7227 (m-30) cc_final: 0.6895 (m-30) REVERT: D 431 GLU cc_start: 0.7058 (tt0) cc_final: 0.6769 (mt-10) REVERT: D 432 LYS cc_start: 0.7147 (mttm) cc_final: 0.6617 (ttpt) REVERT: D 505 TYR cc_start: 0.7623 (m-80) cc_final: 0.7414 (m-80) REVERT: D 520 LYS cc_start: 0.7101 (tttm) cc_final: 0.6740 (ttpt) REVERT: D 521 GLU cc_start: 0.7194 (tt0) cc_final: 0.6694 (tm-30) REVERT: D 566 LYS cc_start: 0.7974 (ptmt) cc_final: 0.7746 (ttmm) outliers start: 18 outliers final: 0 residues processed: 227 average time/residue: 1.1708 time to fit residues: 295.0230 Evaluate side-chains 192 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 190 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 413 ARG Chi-restraints excluded: chain D residue 413 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 136 optimal weight: 0.7980 chunk 111 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 chunk 163 optimal weight: 6.9990 chunk 176 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 chunk 162 optimal weight: 0.5980 chunk 55 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN B 395 ASN C 395 ASN D 395 ASN D 498 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15372 Z= 0.275 Angle : 0.604 7.353 20864 Z= 0.313 Chirality : 0.043 0.194 2344 Planarity : 0.005 0.049 2580 Dihedral : 4.709 23.533 2060 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.89 % Allowed : 15.30 % Favored : 82.80 % 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: -0.10 (0.20), residues: 1824 helix: 0.45 (0.15), residues: 1096 sheet: -0.74 (0.82), residues: 48 loop : -0.72 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 168 HIS 0.003 0.001 HIS D 422 PHE 0.018 0.002 PHE C 389 TYR 0.021 0.002 TYR B 351 ARG 0.003 0.000 ARG C 218 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 207 time to evaluate : 1.884 Fit side-chains REVERT: A 212 LEU cc_start: 0.8495 (tp) cc_final: 0.8165 (mt) REVERT: A 221 THR cc_start: 0.8016 (t) cc_final: 0.7756 (m) REVERT: A 281 MET cc_start: 0.8479 (ttp) cc_final: 0.8221 (ttm) REVERT: A 286 GLN cc_start: 0.7677 (pp30) cc_final: 0.7264 (tm130) REVERT: A 293 ASN cc_start: 0.7192 (m-40) cc_final: 0.6777 (m-40) REVERT: A 395 ASN cc_start: 0.6664 (m-40) cc_final: 0.5952 (t0) REVERT: A 413 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7210 (mtp85) REVERT: A 415 ASP cc_start: 0.7195 (m-30) cc_final: 0.6872 (m-30) REVERT: A 431 GLU cc_start: 0.7033 (tt0) cc_final: 0.6775 (mt-10) REVERT: A 432 LYS cc_start: 0.7190 (mttm) cc_final: 0.6664 (ttpt) REVERT: A 505 TYR cc_start: 0.7818 (m-80) cc_final: 0.7523 (m-80) REVERT: A 520 LYS cc_start: 0.7280 (tttm) cc_final: 0.6960 (ttmt) REVERT: A 564 ASN cc_start: 0.6212 (OUTLIER) cc_final: 0.5972 (m110) REVERT: A 575 CYS cc_start: 0.6828 (OUTLIER) cc_final: 0.6430 (t) REVERT: B 221 THR cc_start: 0.8017 (t) cc_final: 0.7763 (m) REVERT: B 281 MET cc_start: 0.8479 (ttp) cc_final: 0.8221 (ttm) REVERT: B 286 GLN cc_start: 0.7672 (pp30) cc_final: 0.7253 (tm130) REVERT: B 293 ASN cc_start: 0.7194 (m-40) cc_final: 0.6778 (m-40) REVERT: B 395 ASN cc_start: 0.6665 (m-40) cc_final: 0.5949 (t0) REVERT: B 413 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7184 (mtp85) REVERT: B 415 ASP cc_start: 0.7196 (m-30) cc_final: 0.6873 (m-30) REVERT: B 431 GLU cc_start: 0.7034 (tt0) cc_final: 0.6774 (mt-10) REVERT: B 432 LYS cc_start: 0.7204 (mttm) cc_final: 0.6683 (ttpt) REVERT: B 505 TYR cc_start: 0.7820 (m-80) cc_final: 0.7517 (m-80) REVERT: B 520 LYS cc_start: 0.7259 (tttm) cc_final: 0.6939 (ttmt) REVERT: B 564 ASN cc_start: 0.6225 (OUTLIER) cc_final: 0.5991 (m110) REVERT: B 566 LYS cc_start: 0.8066 (ptmt) cc_final: 0.7846 (ttmm) REVERT: B 575 CYS cc_start: 0.6800 (OUTLIER) cc_final: 0.6396 (t) REVERT: B 604 MET cc_start: 0.3737 (mpm) cc_final: 0.3519 (mpm) REVERT: C 221 THR cc_start: 0.8027 (t) cc_final: 0.7774 (m) REVERT: C 281 MET cc_start: 0.8477 (ttp) cc_final: 0.8225 (ttm) REVERT: C 286 GLN cc_start: 0.7680 (pp30) cc_final: 0.7289 (tm130) REVERT: C 293 ASN cc_start: 0.7196 (m-40) cc_final: 0.6789 (m-40) REVERT: C 395 ASN cc_start: 0.6661 (m-40) cc_final: 0.5949 (t0) REVERT: C 413 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.7208 (mtp85) REVERT: C 415 ASP cc_start: 0.7194 (m-30) cc_final: 0.6887 (m-30) REVERT: C 431 GLU cc_start: 0.7035 (tt0) cc_final: 0.6777 (mt-10) REVERT: C 432 LYS cc_start: 0.7201 (mttm) cc_final: 0.6686 (ttpt) REVERT: C 474 LEU cc_start: 0.6613 (mt) cc_final: 0.6189 (mt) REVERT: C 505 TYR cc_start: 0.7819 (m-80) cc_final: 0.7515 (m-80) REVERT: C 520 LYS cc_start: 0.7221 (tttm) cc_final: 0.6923 (ttmt) REVERT: C 521 GLU cc_start: 0.7301 (tt0) cc_final: 0.6688 (tm-30) REVERT: C 564 ASN cc_start: 0.6224 (OUTLIER) cc_final: 0.5992 (m110) REVERT: C 566 LYS cc_start: 0.8059 (ptmt) cc_final: 0.7848 (ttmm) REVERT: C 575 CYS cc_start: 0.6778 (OUTLIER) cc_final: 0.6324 (t) REVERT: C 604 MET cc_start: 0.3732 (mpm) cc_final: 0.3517 (mpm) REVERT: D 221 THR cc_start: 0.8028 (t) cc_final: 0.7775 (m) REVERT: D 281 MET cc_start: 0.8480 (ttp) cc_final: 0.8221 (ttm) REVERT: D 286 GLN cc_start: 0.7681 (pp30) cc_final: 0.7294 (tm130) REVERT: D 293 ASN cc_start: 0.7195 (m-40) cc_final: 0.6786 (m-40) REVERT: D 395 ASN cc_start: 0.6661 (m-40) cc_final: 0.5954 (t0) REVERT: D 413 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.7178 (mtp85) REVERT: D 415 ASP cc_start: 0.7197 (m-30) cc_final: 0.6902 (m-30) REVERT: D 431 GLU cc_start: 0.7034 (tt0) cc_final: 0.6777 (mt-10) REVERT: D 432 LYS cc_start: 0.7204 (mttm) cc_final: 0.6683 (ttpt) REVERT: D 505 TYR cc_start: 0.7815 (m-80) cc_final: 0.7521 (m-80) REVERT: D 520 LYS cc_start: 0.7253 (tttm) cc_final: 0.6955 (ttmt) REVERT: D 521 GLU cc_start: 0.7283 (tt0) cc_final: 0.6675 (tm-30) REVERT: D 564 ASN cc_start: 0.6228 (OUTLIER) cc_final: 0.5998 (m110) REVERT: D 566 LYS cc_start: 0.8070 (ptmt) cc_final: 0.7850 (ttmm) REVERT: D 575 CYS cc_start: 0.6764 (OUTLIER) cc_final: 0.6336 (t) outliers start: 31 outliers final: 0 residues processed: 224 average time/residue: 1.2850 time to fit residues: 317.0116 Evaluate side-chains 196 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 184 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 ARG Chi-restraints excluded: chain A residue 564 ASN Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain B residue 413 ARG Chi-restraints excluded: chain B residue 564 ASN Chi-restraints excluded: chain B residue 575 CYS Chi-restraints excluded: chain C residue 413 ARG Chi-restraints excluded: chain C residue 564 ASN Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain D residue 413 ARG Chi-restraints excluded: chain D residue 564 ASN Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 chunk 84 optimal weight: 0.5980 chunk 18 optimal weight: 0.4980 chunk 78 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 173 optimal weight: 10.0000 chunk 85 optimal weight: 0.9980 chunk 155 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 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 C 226 GLN C 498 GLN C 534 GLN D 226 GLN D 302 ASN D 498 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15372 Z= 0.192 Angle : 0.560 7.009 20864 Z= 0.286 Chirality : 0.041 0.190 2344 Planarity : 0.005 0.050 2580 Dihedral : 4.683 23.226 2060 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.20 % Allowed : 15.18 % Favored : 82.62 % 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: 0.14 (0.20), residues: 1824 helix: 0.63 (0.16), residues: 1080 sheet: -0.84 (0.81), residues: 48 loop : -0.56 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 168 HIS 0.002 0.001 HIS D 312 PHE 0.012 0.001 PHE D 389 TYR 0.019 0.001 TYR D 199 ARG 0.002 0.000 ARG D 218 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 205 time to evaluate : 1.694 Fit side-chains REVERT: A 212 LEU cc_start: 0.8455 (tp) cc_final: 0.8156 (mt) REVERT: A 221 THR cc_start: 0.8007 (t) cc_final: 0.7759 (m) REVERT: A 281 MET cc_start: 0.8472 (ttp) cc_final: 0.8220 (ttm) REVERT: A 286 GLN cc_start: 0.7524 (pp30) cc_final: 0.7119 (tm130) REVERT: A 293 ASN cc_start: 0.7218 (m-40) cc_final: 0.6622 (m-40) REVERT: A 413 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7194 (mtp85) REVERT: A 415 ASP cc_start: 0.7173 (m-30) cc_final: 0.6855 (m-30) REVERT: A 431 GLU cc_start: 0.7015 (tt0) cc_final: 0.6776 (mt-10) REVERT: A 432 LYS cc_start: 0.7125 (mttm) cc_final: 0.6588 (ttpt) REVERT: A 505 TYR cc_start: 0.7769 (m-80) cc_final: 0.7497 (m-80) REVERT: A 520 LYS cc_start: 0.7270 (tttm) cc_final: 0.6925 (ttmt) REVERT: A 521 GLU cc_start: 0.7382 (tt0) cc_final: 0.6719 (tm-30) REVERT: A 575 CYS cc_start: 0.6786 (OUTLIER) cc_final: 0.6421 (t) REVERT: B 212 LEU cc_start: 0.8482 (tp) cc_final: 0.8172 (mt) REVERT: B 221 THR cc_start: 0.7986 (t) cc_final: 0.7745 (m) REVERT: B 281 MET cc_start: 0.8471 (ttp) cc_final: 0.8222 (ttm) REVERT: B 286 GLN cc_start: 0.7497 (pp30) cc_final: 0.7088 (tm130) REVERT: B 293 ASN cc_start: 0.7217 (m-40) cc_final: 0.6632 (m-40) REVERT: B 409 GLU cc_start: 0.6781 (tp30) cc_final: 0.6379 (tp30) REVERT: B 413 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7157 (mtp85) REVERT: B 415 ASP cc_start: 0.7173 (m-30) cc_final: 0.6872 (m-30) REVERT: B 431 GLU cc_start: 0.7011 (tt0) cc_final: 0.6766 (mt-10) REVERT: B 432 LYS cc_start: 0.7153 (mttm) cc_final: 0.6621 (ttpt) REVERT: B 505 TYR cc_start: 0.7817 (m-80) cc_final: 0.7513 (m-80) REVERT: B 520 LYS cc_start: 0.7275 (tttm) cc_final: 0.6915 (ttmt) REVERT: B 521 GLU cc_start: 0.7381 (tt0) cc_final: 0.6723 (tm-30) REVERT: B 564 ASN cc_start: 0.6265 (OUTLIER) cc_final: 0.6050 (m110) REVERT: B 575 CYS cc_start: 0.6792 (OUTLIER) cc_final: 0.6423 (t) REVERT: B 604 MET cc_start: 0.3638 (mpm) cc_final: 0.3426 (mpm) REVERT: C 212 LEU cc_start: 0.8483 (tp) cc_final: 0.8172 (mt) REVERT: C 221 THR cc_start: 0.8008 (t) cc_final: 0.7763 (m) REVERT: C 286 GLN cc_start: 0.7603 (pp30) cc_final: 0.7251 (tm130) REVERT: C 293 ASN cc_start: 0.7220 (m-40) cc_final: 0.6618 (m-40) REVERT: C 413 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7186 (mtp85) REVERT: C 415 ASP cc_start: 0.7143 (m-30) cc_final: 0.6847 (m-30) REVERT: C 431 GLU cc_start: 0.7013 (tt0) cc_final: 0.6772 (mt-10) REVERT: C 432 LYS cc_start: 0.7152 (mttm) cc_final: 0.6618 (ttpt) REVERT: C 505 TYR cc_start: 0.7819 (m-80) cc_final: 0.7510 (m-80) REVERT: C 520 LYS cc_start: 0.7247 (tttm) cc_final: 0.6803 (ttpt) REVERT: C 521 GLU cc_start: 0.7288 (tt0) cc_final: 0.6668 (tm-30) REVERT: C 564 ASN cc_start: 0.6264 (OUTLIER) cc_final: 0.6046 (m110) REVERT: C 575 CYS cc_start: 0.6739 (OUTLIER) cc_final: 0.6261 (t) REVERT: C 604 MET cc_start: 0.3635 (mpm) cc_final: 0.3422 (mpm) REVERT: D 212 LEU cc_start: 0.8486 (tp) cc_final: 0.8178 (mt) REVERT: D 221 THR cc_start: 0.8001 (t) cc_final: 0.7754 (m) REVERT: D 281 MET cc_start: 0.8474 (ttp) cc_final: 0.8225 (ttm) REVERT: D 286 GLN cc_start: 0.7602 (pp30) cc_final: 0.7253 (tm130) REVERT: D 293 ASN cc_start: 0.7222 (m-40) cc_final: 0.6621 (m-40) REVERT: D 409 GLU cc_start: 0.6779 (tp30) cc_final: 0.6377 (tp30) REVERT: D 413 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.7159 (mtp85) REVERT: D 415 ASP cc_start: 0.7148 (m-30) cc_final: 0.6863 (m-30) REVERT: D 431 GLU cc_start: 0.7016 (tt0) cc_final: 0.6773 (mt-10) REVERT: D 432 LYS cc_start: 0.7128 (mttm) cc_final: 0.6591 (ttpt) REVERT: D 505 TYR cc_start: 0.7812 (m-80) cc_final: 0.7511 (m-80) REVERT: D 520 LYS cc_start: 0.7274 (tttm) cc_final: 0.6811 (ttpt) REVERT: D 521 GLU cc_start: 0.7267 (tt0) cc_final: 0.6654 (tm-30) outliers start: 36 outliers final: 2 residues processed: 224 average time/residue: 1.2991 time to fit residues: 319.6525 Evaluate side-chains 195 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 184 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 ARG Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain B residue 413 ARG Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 564 ASN Chi-restraints excluded: chain B residue 575 CYS Chi-restraints excluded: chain C residue 413 ARG Chi-restraints excluded: chain C residue 564 ASN Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain D residue 413 ARG Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 0.8980 chunk 98 optimal weight: 7.9990 chunk 2 optimal weight: 0.6980 chunk 129 optimal weight: 0.0050 chunk 71 optimal weight: 0.8980 chunk 148 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 88 optimal weight: 9.9990 chunk 156 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN ** A 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 ASN C 395 ASN C 498 GLN D 395 ASN ** D 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15372 Z= 0.176 Angle : 0.541 7.908 20864 Z= 0.278 Chirality : 0.040 0.183 2344 Planarity : 0.004 0.049 2580 Dihedral : 4.512 22.528 2060 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.46 % Allowed : 16.77 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.31 (0.20), residues: 1824 helix: 0.70 (0.16), residues: 1092 sheet: -0.72 (0.83), residues: 48 loop : -0.38 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 168 HIS 0.002 0.001 HIS A 312 PHE 0.012 0.001 PHE A 389 TYR 0.019 0.001 TYR A 205 ARG 0.002 0.000 ARG D 478 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 206 time to evaluate : 1.840 Fit side-chains REVERT: A 212 LEU cc_start: 0.8432 (tp) cc_final: 0.8159 (mt) REVERT: A 221 THR cc_start: 0.7985 (t) cc_final: 0.7744 (m) REVERT: A 241 LYS cc_start: 0.7519 (mtmt) cc_final: 0.7274 (mtmm) REVERT: A 281 MET cc_start: 0.8439 (ttp) cc_final: 0.8186 (ttm) REVERT: A 286 GLN cc_start: 0.7487 (pp30) cc_final: 0.7084 (tm130) REVERT: A 293 ASN cc_start: 0.7179 (m-40) cc_final: 0.6871 (m-40) REVERT: A 409 GLU cc_start: 0.6847 (tp30) cc_final: 0.6421 (tp30) REVERT: A 413 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.7226 (mtp85) REVERT: A 415 ASP cc_start: 0.7134 (m-30) cc_final: 0.6807 (m-30) REVERT: A 431 GLU cc_start: 0.6971 (tt0) cc_final: 0.6739 (mt-10) REVERT: A 432 LYS cc_start: 0.7101 (mttm) cc_final: 0.6515 (ttpt) REVERT: A 505 TYR cc_start: 0.7781 (m-80) cc_final: 0.7498 (m-80) REVERT: A 520 LYS cc_start: 0.7297 (tttm) cc_final: 0.6685 (ttpt) REVERT: A 521 GLU cc_start: 0.7418 (tt0) cc_final: 0.6729 (tm-30) REVERT: A 575 CYS cc_start: 0.6861 (OUTLIER) cc_final: 0.6497 (t) REVERT: B 212 LEU cc_start: 0.8439 (tp) cc_final: 0.8159 (mt) REVERT: B 221 THR cc_start: 0.7975 (t) cc_final: 0.7735 (m) REVERT: B 281 MET cc_start: 0.8456 (ttp) cc_final: 0.8206 (ttm) REVERT: B 286 GLN cc_start: 0.7487 (pp30) cc_final: 0.7081 (tm130) REVERT: B 293 ASN cc_start: 0.7177 (m-40) cc_final: 0.6869 (m-40) REVERT: B 409 GLU cc_start: 0.6742 (tp30) cc_final: 0.6346 (tp30) REVERT: B 413 ARG cc_start: 0.7738 (OUTLIER) cc_final: 0.7227 (mtp85) REVERT: B 415 ASP cc_start: 0.7135 (m-30) cc_final: 0.6806 (m-30) REVERT: B 431 GLU cc_start: 0.6969 (tt0) cc_final: 0.6739 (mt-10) REVERT: B 432 LYS cc_start: 0.7102 (mttm) cc_final: 0.6517 (ttpt) REVERT: B 505 TYR cc_start: 0.7787 (m-80) cc_final: 0.7474 (m-80) REVERT: B 520 LYS cc_start: 0.7328 (tttm) cc_final: 0.6718 (ttpt) REVERT: B 521 GLU cc_start: 0.7419 (tt0) cc_final: 0.6735 (tm-30) REVERT: B 564 ASN cc_start: 0.6244 (OUTLIER) cc_final: 0.5986 (m-40) REVERT: B 575 CYS cc_start: 0.6833 (OUTLIER) cc_final: 0.6487 (t) REVERT: C 212 LEU cc_start: 0.8440 (tp) cc_final: 0.8158 (mt) REVERT: C 221 THR cc_start: 0.7987 (t) cc_final: 0.7750 (m) REVERT: C 281 MET cc_start: 0.8463 (ttp) cc_final: 0.8215 (ttm) REVERT: C 286 GLN cc_start: 0.7539 (pp30) cc_final: 0.7223 (tm130) REVERT: C 293 ASN cc_start: 0.7182 (m-40) cc_final: 0.6873 (m-40) REVERT: C 409 GLU cc_start: 0.6844 (tp30) cc_final: 0.6417 (tp30) REVERT: C 413 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.7228 (mtp85) REVERT: C 415 ASP cc_start: 0.7147 (m-30) cc_final: 0.6823 (m-30) REVERT: C 431 GLU cc_start: 0.7018 (tt0) cc_final: 0.6735 (mt-10) REVERT: C 432 LYS cc_start: 0.7079 (mttm) cc_final: 0.6508 (ttpt) REVERT: C 505 TYR cc_start: 0.7786 (m-80) cc_final: 0.7475 (m-80) REVERT: C 520 LYS cc_start: 0.7300 (tttm) cc_final: 0.6815 (ttpt) REVERT: C 521 GLU cc_start: 0.7335 (tt0) cc_final: 0.6708 (tm-30) REVERT: C 564 ASN cc_start: 0.6244 (OUTLIER) cc_final: 0.5990 (m-40) REVERT: C 575 CYS cc_start: 0.6868 (OUTLIER) cc_final: 0.6183 (t) REVERT: D 212 LEU cc_start: 0.8440 (tp) cc_final: 0.8160 (mt) REVERT: D 221 THR cc_start: 0.7979 (t) cc_final: 0.7735 (m) REVERT: D 241 LYS cc_start: 0.7521 (mtmt) cc_final: 0.7279 (mtmm) REVERT: D 281 MET cc_start: 0.8467 (ttp) cc_final: 0.8211 (ttm) REVERT: D 286 GLN cc_start: 0.7538 (pp30) cc_final: 0.7225 (tm130) REVERT: D 293 ASN cc_start: 0.7185 (m-40) cc_final: 0.6876 (m-40) REVERT: D 409 GLU cc_start: 0.6758 (tp30) cc_final: 0.6359 (tp30) REVERT: D 413 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7238 (mtp85) REVERT: D 415 ASP cc_start: 0.7140 (m-30) cc_final: 0.6811 (m-30) REVERT: D 431 GLU cc_start: 0.7009 (tt0) cc_final: 0.6723 (mt-10) REVERT: D 432 LYS cc_start: 0.7084 (mttm) cc_final: 0.6517 (ttpt) REVERT: D 505 TYR cc_start: 0.7782 (m-80) cc_final: 0.7495 (m-80) REVERT: D 520 LYS cc_start: 0.7299 (tttm) cc_final: 0.6820 (ttpt) REVERT: D 521 GLU cc_start: 0.7333 (tt0) cc_final: 0.6742 (tm-30) outliers start: 24 outliers final: 1 residues processed: 218 average time/residue: 1.3199 time to fit residues: 317.1895 Evaluate side-chains 205 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 195 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 ARG Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain B residue 413 ARG Chi-restraints excluded: chain B residue 564 ASN Chi-restraints excluded: chain B residue 575 CYS Chi-restraints excluded: chain C residue 413 ARG Chi-restraints excluded: chain C residue 564 ASN Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain D residue 413 ARG Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 7.9990 chunk 156 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 174 optimal weight: 0.0000 chunk 144 optimal weight: 0.8980 chunk 80 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 91 optimal weight: 0.4980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15372 Z= 0.168 Angle : 0.535 9.810 20864 Z= 0.273 Chirality : 0.040 0.178 2344 Planarity : 0.004 0.050 2580 Dihedral : 4.499 22.132 2060 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.40 % Allowed : 16.89 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.32 (0.20), residues: 1824 helix: 0.66 (0.15), residues: 1116 sheet: -0.43 (0.83), residues: 48 loop : -0.33 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 168 HIS 0.001 0.001 HIS B 312 PHE 0.011 0.001 PHE C 389 TYR 0.020 0.001 TYR B 205 ARG 0.002 0.000 ARG C 413 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 213 time to evaluate : 1.766 Fit side-chains REVERT: A 212 LEU cc_start: 0.8409 (tp) cc_final: 0.8147 (mt) REVERT: A 221 THR cc_start: 0.7957 (t) cc_final: 0.7725 (m) REVERT: A 241 LYS cc_start: 0.7505 (mtmt) cc_final: 0.7257 (mtmm) REVERT: A 281 MET cc_start: 0.8448 (ttp) cc_final: 0.8185 (ttm) REVERT: A 286 GLN cc_start: 0.7461 (pp30) cc_final: 0.7085 (tm130) REVERT: A 293 ASN cc_start: 0.7154 (m-40) cc_final: 0.6815 (m-40) REVERT: A 413 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.7203 (mtp85) REVERT: A 415 ASP cc_start: 0.7123 (m-30) cc_final: 0.6798 (m-30) REVERT: A 431 GLU cc_start: 0.7005 (tt0) cc_final: 0.6734 (mt-10) REVERT: A 432 LYS cc_start: 0.7100 (mttm) cc_final: 0.6502 (ttpt) REVERT: A 505 TYR cc_start: 0.7777 (m-80) cc_final: 0.7493 (m-80) REVERT: A 520 LYS cc_start: 0.7353 (tttm) cc_final: 0.6856 (ttpt) REVERT: A 521 GLU cc_start: 0.7509 (tt0) cc_final: 0.6823 (tm-30) REVERT: A 575 CYS cc_start: 0.6903 (OUTLIER) cc_final: 0.6209 (t) REVERT: A 596 GLU cc_start: 0.5326 (OUTLIER) cc_final: 0.3651 (pt0) REVERT: B 212 LEU cc_start: 0.8406 (tp) cc_final: 0.8148 (mt) REVERT: B 221 THR cc_start: 0.7953 (t) cc_final: 0.7712 (m) REVERT: B 281 MET cc_start: 0.8436 (ttp) cc_final: 0.8187 (ttm) REVERT: B 286 GLN cc_start: 0.7457 (pp30) cc_final: 0.7080 (tm130) REVERT: B 293 ASN cc_start: 0.7146 (m-40) cc_final: 0.6798 (m-40) REVERT: B 413 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7199 (mtp85) REVERT: B 415 ASP cc_start: 0.7121 (m-30) cc_final: 0.6795 (m-30) REVERT: B 431 GLU cc_start: 0.7005 (tt0) cc_final: 0.6736 (mt-10) REVERT: B 432 LYS cc_start: 0.7101 (mttm) cc_final: 0.6502 (ttpt) REVERT: B 505 TYR cc_start: 0.7787 (m-80) cc_final: 0.7467 (m-80) REVERT: B 520 LYS cc_start: 0.7346 (tttm) cc_final: 0.6858 (ttpt) REVERT: B 521 GLU cc_start: 0.7485 (tt0) cc_final: 0.6806 (tm-30) REVERT: B 564 ASN cc_start: 0.6260 (OUTLIER) cc_final: 0.5966 (m-40) REVERT: B 575 CYS cc_start: 0.6894 (OUTLIER) cc_final: 0.6211 (t) REVERT: B 596 GLU cc_start: 0.5303 (OUTLIER) cc_final: 0.3649 (pt0) REVERT: C 212 LEU cc_start: 0.8406 (tp) cc_final: 0.8147 (mt) REVERT: C 221 THR cc_start: 0.7965 (t) cc_final: 0.7732 (m) REVERT: C 281 MET cc_start: 0.8465 (ttp) cc_final: 0.8209 (ttm) REVERT: C 286 GLN cc_start: 0.7538 (pp30) cc_final: 0.7215 (tm130) REVERT: C 293 ASN cc_start: 0.7156 (m-40) cc_final: 0.6818 (m-40) REVERT: C 413 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.7205 (mtp85) REVERT: C 415 ASP cc_start: 0.7133 (m-30) cc_final: 0.6813 (m-30) REVERT: C 431 GLU cc_start: 0.6993 (tt0) cc_final: 0.6721 (mt-10) REVERT: C 432 LYS cc_start: 0.7097 (mttm) cc_final: 0.6497 (ttpt) REVERT: C 505 TYR cc_start: 0.7782 (m-80) cc_final: 0.7458 (m-80) REVERT: C 520 LYS cc_start: 0.7332 (tttm) cc_final: 0.6839 (ttpt) REVERT: C 521 GLU cc_start: 0.7325 (tt0) cc_final: 0.6733 (tm-30) REVERT: C 564 ASN cc_start: 0.6259 (OUTLIER) cc_final: 0.5966 (m-40) REVERT: C 575 CYS cc_start: 0.6537 (OUTLIER) cc_final: 0.6089 (t) REVERT: C 596 GLU cc_start: 0.5303 (OUTLIER) cc_final: 0.3641 (pt0) REVERT: D 212 LEU cc_start: 0.8404 (tp) cc_final: 0.8147 (mt) REVERT: D 221 THR cc_start: 0.7961 (t) cc_final: 0.7730 (m) REVERT: D 241 LYS cc_start: 0.7521 (mtmt) cc_final: 0.7275 (mtmm) REVERT: D 281 MET cc_start: 0.8453 (ttp) cc_final: 0.8190 (ttm) REVERT: D 286 GLN cc_start: 0.7536 (pp30) cc_final: 0.7213 (tm130) REVERT: D 293 ASN cc_start: 0.7156 (m-40) cc_final: 0.6819 (m-40) REVERT: D 413 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.7203 (mtp85) REVERT: D 415 ASP cc_start: 0.7127 (m-30) cc_final: 0.6803 (m-30) REVERT: D 431 GLU cc_start: 0.6992 (tt0) cc_final: 0.6726 (mt-10) REVERT: D 432 LYS cc_start: 0.7103 (mttm) cc_final: 0.6505 (ttpt) REVERT: D 505 TYR cc_start: 0.7776 (m-80) cc_final: 0.7487 (m-80) REVERT: D 520 LYS cc_start: 0.7336 (tttm) cc_final: 0.6851 (ttpt) REVERT: D 521 GLU cc_start: 0.7315 (tt0) cc_final: 0.6718 (tm-30) REVERT: D 565 ILE cc_start: 0.7915 (mm) cc_final: 0.7623 (mm) REVERT: D 575 CYS cc_start: 0.6481 (OUTLIER) cc_final: 0.6026 (t) REVERT: D 596 GLU cc_start: 0.5268 (OUTLIER) cc_final: 0.3620 (pt0) outliers start: 23 outliers final: 4 residues processed: 225 average time/residue: 1.3123 time to fit residues: 325.3858 Evaluate side-chains 215 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 197 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 ARG Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 596 GLU Chi-restraints excluded: chain B residue 413 ARG Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 564 ASN Chi-restraints excluded: chain B residue 575 CYS Chi-restraints excluded: chain B residue 596 GLU Chi-restraints excluded: chain C residue 413 ARG Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 564 ASN Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain C residue 596 GLU Chi-restraints excluded: chain D residue 413 ARG Chi-restraints excluded: chain D residue 518 ILE Chi-restraints excluded: chain D residue 575 CYS Chi-restraints excluded: chain D residue 596 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 chunk 127 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 173 optimal weight: 5.9990 chunk 108 optimal weight: 0.4980 chunk 105 optimal weight: 0.7980 chunk 80 optimal weight: 9.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 ASN ** A 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 ASN C 266 ASN D 266 ASN D 498 GLN ** D 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15372 Z= 0.176 Angle : 0.540 10.909 20864 Z= 0.276 Chirality : 0.040 0.176 2344 Planarity : 0.004 0.049 2580 Dihedral : 4.398 21.531 2060 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.07 % Allowed : 16.34 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.20), residues: 1824 helix: 0.68 (0.15), residues: 1116 sheet: -0.55 (0.81), residues: 48 loop : -0.26 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 442 HIS 0.002 0.001 HIS C 312 PHE 0.012 0.001 PHE A 389 TYR 0.019 0.001 TYR A 199 ARG 0.002 0.000 ARG B 413 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 214 time to evaluate : 1.714 Fit side-chains REVERT: A 212 LEU cc_start: 0.8403 (tp) cc_final: 0.8147 (mt) REVERT: A 221 THR cc_start: 0.7956 (t) cc_final: 0.7708 (m) REVERT: A 241 LYS cc_start: 0.7425 (mtmt) cc_final: 0.7161 (mtmm) REVERT: A 281 MET cc_start: 0.8442 (ttp) cc_final: 0.8193 (ttm) REVERT: A 286 GLN cc_start: 0.7390 (pp30) cc_final: 0.7027 (tm130) REVERT: A 293 ASN cc_start: 0.7121 (m-40) cc_final: 0.6796 (m-40) REVERT: A 409 GLU cc_start: 0.6735 (tp30) cc_final: 0.6489 (tp30) REVERT: A 413 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7199 (mtp85) REVERT: A 415 ASP cc_start: 0.7166 (m-30) cc_final: 0.6849 (m-30) REVERT: A 431 GLU cc_start: 0.6891 (tt0) cc_final: 0.6641 (mt-10) REVERT: A 432 LYS cc_start: 0.7126 (mttm) cc_final: 0.6527 (ttpt) REVERT: A 505 TYR cc_start: 0.7767 (m-80) cc_final: 0.7356 (m-80) REVERT: A 508 LYS cc_start: 0.5149 (mmtt) cc_final: 0.4723 (mmtt) REVERT: A 520 LYS cc_start: 0.7362 (tttm) cc_final: 0.6859 (ttpt) REVERT: A 521 GLU cc_start: 0.7515 (tt0) cc_final: 0.6823 (tm-30) REVERT: A 575 CYS cc_start: 0.6964 (OUTLIER) cc_final: 0.6294 (t) REVERT: A 596 GLU cc_start: 0.5368 (OUTLIER) cc_final: 0.3706 (pt0) REVERT: B 212 LEU cc_start: 0.8400 (tp) cc_final: 0.8149 (mt) REVERT: B 221 THR cc_start: 0.7965 (t) cc_final: 0.7722 (m) REVERT: B 281 MET cc_start: 0.8444 (ttp) cc_final: 0.8194 (ttm) REVERT: B 286 GLN cc_start: 0.7423 (pp30) cc_final: 0.7061 (tm130) REVERT: B 293 ASN cc_start: 0.7117 (m-40) cc_final: 0.6791 (m-40) REVERT: B 413 ARG cc_start: 0.7738 (OUTLIER) cc_final: 0.7187 (mtp85) REVERT: B 415 ASP cc_start: 0.7167 (m-30) cc_final: 0.6849 (m-30) REVERT: B 431 GLU cc_start: 0.6896 (tt0) cc_final: 0.6644 (mt-10) REVERT: B 432 LYS cc_start: 0.7126 (mttm) cc_final: 0.6524 (ttpt) REVERT: B 505 TYR cc_start: 0.7809 (m-80) cc_final: 0.7357 (m-80) REVERT: B 508 LYS cc_start: 0.4968 (mmtt) cc_final: 0.4660 (mmtt) REVERT: B 520 LYS cc_start: 0.7344 (tttm) cc_final: 0.6713 (ttpt) REVERT: B 521 GLU cc_start: 0.7514 (tt0) cc_final: 0.6823 (tm-30) REVERT: B 575 CYS cc_start: 0.6959 (OUTLIER) cc_final: 0.6301 (t) REVERT: B 596 GLU cc_start: 0.5368 (OUTLIER) cc_final: 0.3703 (pt0) REVERT: C 212 LEU cc_start: 0.8401 (tp) cc_final: 0.8148 (mt) REVERT: C 221 THR cc_start: 0.7959 (t) cc_final: 0.7707 (m) REVERT: C 281 MET cc_start: 0.8460 (ttp) cc_final: 0.8215 (ttm) REVERT: C 286 GLN cc_start: 0.7476 (pp30) cc_final: 0.7112 (tm130) REVERT: C 293 ASN cc_start: 0.7123 (m-40) cc_final: 0.6803 (m-40) REVERT: C 409 GLU cc_start: 0.6731 (tp30) cc_final: 0.6484 (tp30) REVERT: C 413 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.7193 (mtp85) REVERT: C 415 ASP cc_start: 0.7175 (m-30) cc_final: 0.6873 (m-30) REVERT: C 431 GLU cc_start: 0.6977 (tt0) cc_final: 0.6720 (mt-10) REVERT: C 432 LYS cc_start: 0.7096 (mttm) cc_final: 0.6477 (ttpt) REVERT: C 505 TYR cc_start: 0.7805 (m-80) cc_final: 0.7357 (m-80) REVERT: C 508 LYS cc_start: 0.4970 (mmtt) cc_final: 0.4665 (mmtt) REVERT: C 520 LYS cc_start: 0.7335 (tttm) cc_final: 0.6837 (ttpt) REVERT: C 521 GLU cc_start: 0.7314 (tt0) cc_final: 0.6718 (tm-30) REVERT: C 575 CYS cc_start: 0.6654 (OUTLIER) cc_final: 0.6151 (t) REVERT: C 596 GLU cc_start: 0.5362 (OUTLIER) cc_final: 0.3708 (pt0) REVERT: D 212 LEU cc_start: 0.8400 (tp) cc_final: 0.8148 (mt) REVERT: D 221 THR cc_start: 0.7956 (t) cc_final: 0.7704 (m) REVERT: D 241 LYS cc_start: 0.7485 (mtmt) cc_final: 0.7223 (mtmm) REVERT: D 281 MET cc_start: 0.8446 (ttp) cc_final: 0.8196 (ttm) REVERT: D 286 GLN cc_start: 0.7475 (pp30) cc_final: 0.7112 (tm130) REVERT: D 293 ASN cc_start: 0.7124 (m-40) cc_final: 0.6800 (m-40) REVERT: D 413 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7193 (mtp85) REVERT: D 415 ASP cc_start: 0.7133 (m-30) cc_final: 0.6815 (m-30) REVERT: D 431 GLU cc_start: 0.6955 (tt0) cc_final: 0.6709 (mt-10) REVERT: D 432 LYS cc_start: 0.7102 (mttm) cc_final: 0.6486 (ttpt) REVERT: D 505 TYR cc_start: 0.7797 (m-80) cc_final: 0.7406 (m-80) REVERT: D 508 LYS cc_start: 0.5123 (mmtt) cc_final: 0.4707 (mmtt) REVERT: D 520 LYS cc_start: 0.7345 (tttm) cc_final: 0.6834 (ttpt) REVERT: D 521 GLU cc_start: 0.7318 (tt0) cc_final: 0.6715 (tm-30) REVERT: D 565 ILE cc_start: 0.7903 (mm) cc_final: 0.7626 (mm) REVERT: D 575 CYS cc_start: 0.7017 (OUTLIER) cc_final: 0.6256 (t) REVERT: D 596 GLU cc_start: 0.5361 (OUTLIER) cc_final: 0.3714 (pt0) outliers start: 34 outliers final: 13 residues processed: 232 average time/residue: 1.2545 time to fit residues: 320.9587 Evaluate side-chains 229 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 204 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 413 ARG Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 596 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 413 ARG Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 575 CYS Chi-restraints excluded: chain B residue 596 GLU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 413 ARG Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 540 ASP Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain C residue 596 GLU Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 413 ARG Chi-restraints excluded: chain D residue 429 ASP Chi-restraints excluded: chain D residue 518 ILE Chi-restraints excluded: chain D residue 540 ASP Chi-restraints excluded: chain D residue 575 CYS Chi-restraints excluded: chain D residue 596 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 52 optimal weight: 0.0470 chunk 34 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 136 optimal weight: 0.5980 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 ASN ** A 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 ASN C 266 ASN C 498 GLN D 266 ASN ** D 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15372 Z= 0.167 Angle : 0.523 11.408 20864 Z= 0.269 Chirality : 0.040 0.184 2344 Planarity : 0.004 0.049 2580 Dihedral : 4.369 20.906 2060 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.65 % Allowed : 16.52 % Favored : 81.83 % 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: 0.45 (0.20), residues: 1824 helix: 0.72 (0.15), residues: 1116 sheet: -0.63 (0.78), residues: 48 loop : -0.15 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 442 HIS 0.001 0.001 HIS B 312 PHE 0.011 0.001 PHE A 389 TYR 0.018 0.001 TYR B 205 ARG 0.002 0.000 ARG B 413 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 216 time to evaluate : 1.736 Fit side-chains REVERT: A 212 LEU cc_start: 0.8377 (tp) cc_final: 0.8131 (mt) REVERT: A 221 THR cc_start: 0.7933 (t) cc_final: 0.7692 (m) REVERT: A 241 LYS cc_start: 0.7432 (mtmt) cc_final: 0.7168 (mtmm) REVERT: A 281 MET cc_start: 0.8438 (ttp) cc_final: 0.8181 (ttm) REVERT: A 293 ASN cc_start: 0.7043 (m-40) cc_final: 0.6717 (m-40) REVERT: A 409 GLU cc_start: 0.6718 (tp30) cc_final: 0.6479 (tp30) REVERT: A 413 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7201 (mtp85) REVERT: A 415 ASP cc_start: 0.7158 (m-30) cc_final: 0.6859 (m-30) REVERT: A 430 MET cc_start: 0.6947 (tpp) cc_final: 0.6651 (mtp) REVERT: A 431 GLU cc_start: 0.6872 (tt0) cc_final: 0.6652 (mt-10) REVERT: A 432 LYS cc_start: 0.7136 (mttm) cc_final: 0.6502 (ttpt) REVERT: A 505 TYR cc_start: 0.7763 (m-80) cc_final: 0.7345 (m-80) REVERT: A 508 LYS cc_start: 0.5153 (mmtt) cc_final: 0.4722 (mmtt) REVERT: A 520 LYS cc_start: 0.7344 (tttm) cc_final: 0.6841 (ttpt) REVERT: A 521 GLU cc_start: 0.7491 (tt0) cc_final: 0.6807 (tm-30) REVERT: A 575 CYS cc_start: 0.6958 (OUTLIER) cc_final: 0.6293 (t) REVERT: A 596 GLU cc_start: 0.5358 (OUTLIER) cc_final: 0.3713 (pt0) REVERT: B 212 LEU cc_start: 0.8369 (tp) cc_final: 0.8128 (mt) REVERT: B 221 THR cc_start: 0.7945 (t) cc_final: 0.7701 (m) REVERT: B 281 MET cc_start: 0.8440 (ttp) cc_final: 0.8182 (ttm) REVERT: B 293 ASN cc_start: 0.7037 (m-40) cc_final: 0.6701 (m-40) REVERT: B 296 ASN cc_start: 0.8058 (m-40) cc_final: 0.7700 (m-40) REVERT: B 409 GLU cc_start: 0.6801 (tp30) cc_final: 0.6542 (tp30) REVERT: B 413 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.7201 (mtp85) REVERT: B 415 ASP cc_start: 0.7169 (m-30) cc_final: 0.6867 (m-30) REVERT: B 430 MET cc_start: 0.6950 (tpp) cc_final: 0.6663 (mtp) REVERT: B 431 GLU cc_start: 0.6868 (tt0) cc_final: 0.6651 (mt-10) REVERT: B 432 LYS cc_start: 0.7133 (mttm) cc_final: 0.6514 (ttpt) REVERT: B 505 TYR cc_start: 0.7809 (m-80) cc_final: 0.7352 (m-80) REVERT: B 508 LYS cc_start: 0.4968 (mmtt) cc_final: 0.4663 (mmtt) REVERT: B 520 LYS cc_start: 0.7365 (tttm) cc_final: 0.6863 (ttpt) REVERT: B 521 GLU cc_start: 0.7502 (tt0) cc_final: 0.6822 (tm-30) REVERT: B 575 CYS cc_start: 0.6953 (OUTLIER) cc_final: 0.6293 (t) REVERT: B 596 GLU cc_start: 0.5374 (OUTLIER) cc_final: 0.3713 (pt0) REVERT: C 212 LEU cc_start: 0.8372 (tp) cc_final: 0.8126 (mt) REVERT: C 221 THR cc_start: 0.7942 (t) cc_final: 0.7693 (m) REVERT: C 281 MET cc_start: 0.8450 (ttp) cc_final: 0.8189 (ttm) REVERT: C 286 GLN cc_start: 0.7452 (pp30) cc_final: 0.7105 (tm130) REVERT: C 293 ASN cc_start: 0.7063 (m-40) cc_final: 0.6744 (m-40) REVERT: C 409 GLU cc_start: 0.6727 (tp30) cc_final: 0.6494 (tp30) REVERT: C 413 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7208 (mtp85) REVERT: C 415 ASP cc_start: 0.7175 (m-30) cc_final: 0.6863 (m-30) REVERT: C 430 MET cc_start: 0.7058 (tpp) cc_final: 0.6521 (mtp) REVERT: C 431 GLU cc_start: 0.6875 (tt0) cc_final: 0.6644 (mt-10) REVERT: C 432 LYS cc_start: 0.7122 (mttm) cc_final: 0.6510 (ttpt) REVERT: C 505 TYR cc_start: 0.7810 (m-80) cc_final: 0.7352 (m-80) REVERT: C 508 LYS cc_start: 0.4966 (mmtt) cc_final: 0.4663 (mmtt) REVERT: C 520 LYS cc_start: 0.7346 (tttm) cc_final: 0.6823 (ttpt) REVERT: C 521 GLU cc_start: 0.7314 (tt0) cc_final: 0.6722 (tm-30) REVERT: C 596 GLU cc_start: 0.5370 (OUTLIER) cc_final: 0.3719 (pt0) REVERT: D 212 LEU cc_start: 0.8371 (tp) cc_final: 0.8130 (mt) REVERT: D 221 THR cc_start: 0.7942 (t) cc_final: 0.7692 (m) REVERT: D 241 LYS cc_start: 0.7459 (mtmt) cc_final: 0.7192 (mtmm) REVERT: D 281 MET cc_start: 0.8451 (ttp) cc_final: 0.8188 (ttm) REVERT: D 286 GLN cc_start: 0.7453 (pp30) cc_final: 0.7108 (tm130) REVERT: D 293 ASN cc_start: 0.7063 (m-40) cc_final: 0.6742 (m-40) REVERT: D 409 GLU cc_start: 0.6798 (tp30) cc_final: 0.6544 (tp30) REVERT: D 413 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.7216 (mtp85) REVERT: D 415 ASP cc_start: 0.7170 (m-30) cc_final: 0.6879 (m-30) REVERT: D 430 MET cc_start: 0.7085 (tpp) cc_final: 0.6507 (mtp) REVERT: D 431 GLU cc_start: 0.6876 (tt0) cc_final: 0.6648 (mt-10) REVERT: D 432 LYS cc_start: 0.7127 (mttm) cc_final: 0.6511 (ttpt) REVERT: D 505 TYR cc_start: 0.7796 (m-80) cc_final: 0.7442 (m-80) REVERT: D 508 LYS cc_start: 0.5157 (mmtt) cc_final: 0.4827 (mmtt) REVERT: D 520 LYS cc_start: 0.7355 (tttm) cc_final: 0.6837 (ttpt) REVERT: D 521 GLU cc_start: 0.7293 (tt0) cc_final: 0.6693 (tm-30) REVERT: D 565 ILE cc_start: 0.7872 (mm) cc_final: 0.7591 (mm) REVERT: D 575 CYS cc_start: 0.6573 (OUTLIER) cc_final: 0.6114 (t) REVERT: D 596 GLU cc_start: 0.5365 (OUTLIER) cc_final: 0.3732 (pt0) outliers start: 27 outliers final: 11 residues processed: 225 average time/residue: 1.2981 time to fit residues: 321.3582 Evaluate side-chains 228 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 206 time to evaluate : 2.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 413 ARG Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 596 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 413 ARG Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 575 CYS Chi-restraints excluded: chain B residue 596 GLU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 413 ARG Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 540 ASP Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain C residue 596 GLU Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 413 ARG Chi-restraints excluded: chain D residue 518 ILE Chi-restraints excluded: chain D residue 540 ASP Chi-restraints excluded: chain D residue 575 CYS Chi-restraints excluded: chain D residue 596 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 0.6980 chunk 166 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 146 optimal weight: 4.9990 chunk 152 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15372 Z= 0.201 Angle : 0.558 11.913 20864 Z= 0.285 Chirality : 0.040 0.177 2344 Planarity : 0.004 0.048 2580 Dihedral : 4.387 20.765 2060 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.59 % Allowed : 16.59 % Favored : 81.83 % 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: 0.36 (0.20), residues: 1824 helix: 0.62 (0.15), residues: 1116 sheet: -0.73 (0.75), residues: 48 loop : -0.14 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 442 HIS 0.002 0.001 HIS C 312 PHE 0.013 0.001 PHE D 389 TYR 0.020 0.002 TYR A 199 ARG 0.002 0.000 ARG C 407 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 200 time to evaluate : 1.663 Fit side-chains REVERT: A 212 LEU cc_start: 0.8419 (tp) cc_final: 0.8150 (mt) REVERT: A 241 LYS cc_start: 0.7505 (mtmt) cc_final: 0.6709 (mtpp) REVERT: A 281 MET cc_start: 0.8458 (ttp) cc_final: 0.8203 (ttm) REVERT: A 286 GLN cc_start: 0.7425 (pp30) cc_final: 0.7002 (tm130) REVERT: A 293 ASN cc_start: 0.7104 (m-40) cc_final: 0.6777 (m-40) REVERT: A 413 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7190 (mtp85) REVERT: A 415 ASP cc_start: 0.7180 (m-30) cc_final: 0.6877 (m-30) REVERT: A 430 MET cc_start: 0.6984 (tpp) cc_final: 0.6584 (mtp) REVERT: A 431 GLU cc_start: 0.6876 (tt0) cc_final: 0.6663 (mt-10) REVERT: A 432 LYS cc_start: 0.7115 (mttm) cc_final: 0.6495 (ttpt) REVERT: A 505 TYR cc_start: 0.7824 (m-80) cc_final: 0.7374 (m-80) REVERT: A 508 LYS cc_start: 0.5136 (mmtt) cc_final: 0.4732 (mmtt) REVERT: A 520 LYS cc_start: 0.7442 (tttm) cc_final: 0.6957 (ttpt) REVERT: A 521 GLU cc_start: 0.7540 (tt0) cc_final: 0.6849 (tm-30) REVERT: A 575 CYS cc_start: 0.6992 (OUTLIER) cc_final: 0.6316 (t) REVERT: A 596 GLU cc_start: 0.5386 (OUTLIER) cc_final: 0.3747 (pt0) REVERT: B 212 LEU cc_start: 0.8411 (tp) cc_final: 0.8151 (mt) REVERT: B 281 MET cc_start: 0.8455 (ttp) cc_final: 0.8205 (ttm) REVERT: B 286 GLN cc_start: 0.7421 (pp30) cc_final: 0.6997 (tm130) REVERT: B 293 ASN cc_start: 0.7067 (m-40) cc_final: 0.6741 (m-40) REVERT: B 296 ASN cc_start: 0.8040 (m-40) cc_final: 0.7672 (m-40) REVERT: B 409 GLU cc_start: 0.6857 (tp30) cc_final: 0.6586 (tp30) REVERT: B 413 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7200 (mtp85) REVERT: B 415 ASP cc_start: 0.7174 (m-30) cc_final: 0.6870 (m-30) REVERT: B 430 MET cc_start: 0.6857 (tpp) cc_final: 0.6537 (mtp) REVERT: B 431 GLU cc_start: 0.6869 (tt0) cc_final: 0.6653 (mt-10) REVERT: B 432 LYS cc_start: 0.7115 (mttm) cc_final: 0.6497 (ttpt) REVERT: B 505 TYR cc_start: 0.7865 (m-80) cc_final: 0.7417 (m-80) REVERT: B 508 LYS cc_start: 0.4993 (mmtt) cc_final: 0.4687 (mmtt) REVERT: B 520 LYS cc_start: 0.7436 (tttm) cc_final: 0.6951 (ttpt) REVERT: B 521 GLU cc_start: 0.7517 (tt0) cc_final: 0.6835 (tm-30) REVERT: B 575 CYS cc_start: 0.6986 (OUTLIER) cc_final: 0.6313 (t) REVERT: B 596 GLU cc_start: 0.5411 (OUTLIER) cc_final: 0.3765 (pt0) REVERT: C 212 LEU cc_start: 0.8395 (tp) cc_final: 0.8150 (mt) REVERT: C 281 MET cc_start: 0.8480 (ttp) cc_final: 0.8225 (ttm) REVERT: C 286 GLN cc_start: 0.7471 (pp30) cc_final: 0.7107 (tm130) REVERT: C 293 ASN cc_start: 0.7100 (m-40) cc_final: 0.6779 (m-40) REVERT: C 409 GLU cc_start: 0.6735 (tp30) cc_final: 0.6500 (tp30) REVERT: C 413 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7209 (mtp85) REVERT: C 415 ASP cc_start: 0.7185 (m-30) cc_final: 0.6863 (m-30) REVERT: C 430 MET cc_start: 0.7035 (tpp) cc_final: 0.6474 (mtp) REVERT: C 431 GLU cc_start: 0.6885 (tt0) cc_final: 0.6666 (mt-10) REVERT: C 432 LYS cc_start: 0.7115 (mttm) cc_final: 0.6505 (ttpt) REVERT: C 505 TYR cc_start: 0.7854 (m-80) cc_final: 0.7407 (m-80) REVERT: C 508 LYS cc_start: 0.5128 (mmtt) cc_final: 0.4781 (mmtt) REVERT: C 520 LYS cc_start: 0.7347 (tttm) cc_final: 0.6863 (ttpt) REVERT: C 521 GLU cc_start: 0.7306 (tt0) cc_final: 0.6724 (tm-30) REVERT: C 596 GLU cc_start: 0.5376 (OUTLIER) cc_final: 0.3740 (pt0) REVERT: D 212 LEU cc_start: 0.8412 (tp) cc_final: 0.8152 (mt) REVERT: D 281 MET cc_start: 0.8476 (ttp) cc_final: 0.8223 (ttm) REVERT: D 286 GLN cc_start: 0.7473 (pp30) cc_final: 0.7110 (tm130) REVERT: D 293 ASN cc_start: 0.7103 (m-40) cc_final: 0.6780 (m-40) REVERT: D 409 GLU cc_start: 0.6851 (tp30) cc_final: 0.6575 (tp30) REVERT: D 413 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7211 (mtp85) REVERT: D 415 ASP cc_start: 0.7179 (m-30) cc_final: 0.6876 (m-30) REVERT: D 430 MET cc_start: 0.7053 (tpp) cc_final: 0.6505 (mtp) REVERT: D 431 GLU cc_start: 0.6855 (tt0) cc_final: 0.6641 (mt-10) REVERT: D 432 LYS cc_start: 0.7117 (mttm) cc_final: 0.6505 (ttpt) REVERT: D 505 TYR cc_start: 0.7835 (m-80) cc_final: 0.7394 (m-80) REVERT: D 508 LYS cc_start: 0.5120 (mmtt) cc_final: 0.4714 (mmtt) REVERT: D 520 LYS cc_start: 0.7418 (tttm) cc_final: 0.6937 (ttpt) REVERT: D 521 GLU cc_start: 0.7310 (tt0) cc_final: 0.6724 (tm-30) REVERT: D 565 ILE cc_start: 0.7889 (mm) cc_final: 0.7610 (mm) REVERT: D 596 GLU cc_start: 0.5400 (OUTLIER) cc_final: 0.3748 (pt0) outliers start: 26 outliers final: 6 residues processed: 204 average time/residue: 1.2810 time to fit residues: 287.8177 Evaluate side-chains 212 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 196 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 ARG Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 596 GLU Chi-restraints excluded: chain B residue 413 ARG Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 575 CYS Chi-restraints excluded: chain B residue 596 GLU Chi-restraints excluded: chain C residue 413 ARG Chi-restraints excluded: chain C residue 540 ASP Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain C residue 596 GLU Chi-restraints excluded: chain D residue 413 ARG Chi-restraints excluded: chain D residue 540 ASP Chi-restraints excluded: chain D residue 575 CYS Chi-restraints excluded: chain D residue 596 GLU 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: 0.9980 chunk 81 optimal weight: 10.0000 chunk 118 optimal weight: 0.6980 chunk 179 optimal weight: 8.9990 chunk 165 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 87 optimal weight: 0.5980 chunk 113 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 498 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15372 Z= 0.175 Angle : 0.534 12.373 20864 Z= 0.275 Chirality : 0.040 0.175 2344 Planarity : 0.004 0.048 2580 Dihedral : 4.359 20.132 2060 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.34 % Allowed : 16.95 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.44 (0.20), residues: 1824 helix: 0.64 (0.15), residues: 1116 sheet: -0.83 (0.73), residues: 48 loop : -0.00 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 442 HIS 0.001 0.001 HIS C 312 PHE 0.011 0.001 PHE D 389 TYR 0.018 0.001 TYR C 199 ARG 0.002 0.000 ARG C 407 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 210 time to evaluate : 1.814 Fit side-chains REVERT: A 212 LEU cc_start: 0.8387 (tp) cc_final: 0.8131 (mt) REVERT: A 241 LYS cc_start: 0.7485 (mtmt) cc_final: 0.6691 (mtpp) REVERT: A 281 MET cc_start: 0.8444 (ttp) cc_final: 0.8183 (ttm) REVERT: A 286 GLN cc_start: 0.7389 (pp30) cc_final: 0.7001 (tm130) REVERT: A 293 ASN cc_start: 0.7009 (m-40) cc_final: 0.6679 (m-40) REVERT: A 413 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.7192 (mtp85) REVERT: A 415 ASP cc_start: 0.7133 (m-30) cc_final: 0.6851 (m-30) REVERT: A 430 MET cc_start: 0.6849 (tpp) cc_final: 0.6537 (mtp) REVERT: A 432 LYS cc_start: 0.7110 (mttm) cc_final: 0.6492 (ttpt) REVERT: A 505 TYR cc_start: 0.7817 (m-80) cc_final: 0.7340 (m-80) REVERT: A 508 LYS cc_start: 0.5091 (mmtt) cc_final: 0.4665 (mmtt) REVERT: A 520 LYS cc_start: 0.7419 (tttm) cc_final: 0.6940 (ttpt) REVERT: A 521 GLU cc_start: 0.7510 (tt0) cc_final: 0.6833 (tm-30) REVERT: A 575 CYS cc_start: 0.7084 (OUTLIER) cc_final: 0.6365 (t) REVERT: A 596 GLU cc_start: 0.5331 (OUTLIER) cc_final: 0.3684 (pt0) REVERT: B 212 LEU cc_start: 0.8362 (tp) cc_final: 0.8132 (mt) REVERT: B 281 MET cc_start: 0.8445 (ttp) cc_final: 0.8184 (ttm) REVERT: B 286 GLN cc_start: 0.7385 (pp30) cc_final: 0.6999 (tm130) REVERT: B 293 ASN cc_start: 0.7013 (m-40) cc_final: 0.6684 (m-40) REVERT: B 409 GLU cc_start: 0.6816 (tp30) cc_final: 0.6553 (tp30) REVERT: B 413 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7201 (mtp85) REVERT: B 415 ASP cc_start: 0.7137 (m-30) cc_final: 0.6848 (m-30) REVERT: B 430 MET cc_start: 0.6798 (tpp) cc_final: 0.6513 (mtp) REVERT: B 432 LYS cc_start: 0.7108 (mttm) cc_final: 0.6489 (ttpt) REVERT: B 505 TYR cc_start: 0.7866 (m-80) cc_final: 0.7395 (m-80) REVERT: B 508 LYS cc_start: 0.5128 (mmtt) cc_final: 0.4810 (mmtt) REVERT: B 520 LYS cc_start: 0.7416 (tttm) cc_final: 0.6941 (ttpt) REVERT: B 521 GLU cc_start: 0.7492 (tt0) cc_final: 0.6820 (tm-30) REVERT: B 575 CYS cc_start: 0.7075 (OUTLIER) cc_final: 0.6364 (t) REVERT: B 596 GLU cc_start: 0.5346 (OUTLIER) cc_final: 0.3720 (pt0) REVERT: C 212 LEU cc_start: 0.8364 (tp) cc_final: 0.8129 (mt) REVERT: C 262 LYS cc_start: 0.7019 (OUTLIER) cc_final: 0.6711 (tttp) REVERT: C 281 MET cc_start: 0.8446 (ttp) cc_final: 0.8197 (ttm) REVERT: C 286 GLN cc_start: 0.7448 (pp30) cc_final: 0.7099 (tm130) REVERT: C 293 ASN cc_start: 0.7004 (m-40) cc_final: 0.6676 (m-40) REVERT: C 409 GLU cc_start: 0.6766 (tp30) cc_final: 0.6563 (tp30) REVERT: C 413 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7192 (mtp85) REVERT: C 415 ASP cc_start: 0.7158 (m-30) cc_final: 0.6868 (m-30) REVERT: C 430 MET cc_start: 0.6981 (tpp) cc_final: 0.6480 (mtp) REVERT: C 432 LYS cc_start: 0.7087 (mttm) cc_final: 0.6472 (ttpt) REVERT: C 505 TYR cc_start: 0.7858 (m-80) cc_final: 0.7391 (m-80) REVERT: C 508 LYS cc_start: 0.5124 (mmtt) cc_final: 0.4804 (mmtt) REVERT: C 520 LYS cc_start: 0.7367 (tttm) cc_final: 0.6890 (ttpt) REVERT: C 521 GLU cc_start: 0.7313 (tt0) cc_final: 0.6732 (tm-30) REVERT: C 596 GLU cc_start: 0.5399 (OUTLIER) cc_final: 0.3718 (pt0) REVERT: D 212 LEU cc_start: 0.8364 (tp) cc_final: 0.8133 (mt) REVERT: D 262 LYS cc_start: 0.7025 (OUTLIER) cc_final: 0.6710 (tttp) REVERT: D 281 MET cc_start: 0.8451 (ttp) cc_final: 0.8187 (ttm) REVERT: D 286 GLN cc_start: 0.7450 (pp30) cc_final: 0.7103 (tm130) REVERT: D 293 ASN cc_start: 0.7005 (m-40) cc_final: 0.6678 (m-40) REVERT: D 409 GLU cc_start: 0.6776 (tp30) cc_final: 0.6532 (tp30) REVERT: D 413 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7229 (mtp85) REVERT: D 415 ASP cc_start: 0.7143 (m-30) cc_final: 0.6851 (m-30) REVERT: D 430 MET cc_start: 0.6990 (tpp) cc_final: 0.6482 (mtp) REVERT: D 432 LYS cc_start: 0.7093 (mttm) cc_final: 0.6476 (ttpt) REVERT: D 505 TYR cc_start: 0.7844 (m-80) cc_final: 0.7386 (m-80) REVERT: D 508 LYS cc_start: 0.5104 (mmtt) cc_final: 0.4689 (mmtt) REVERT: D 520 LYS cc_start: 0.7380 (tttm) cc_final: 0.6895 (ttpt) REVERT: D 521 GLU cc_start: 0.7304 (tt0) cc_final: 0.6720 (tm-30) REVERT: D 565 ILE cc_start: 0.7859 (mm) cc_final: 0.7570 (mm) REVERT: D 596 GLU cc_start: 0.5391 (OUTLIER) cc_final: 0.3756 (pt0) outliers start: 22 outliers final: 9 residues processed: 219 average time/residue: 1.2934 time to fit residues: 311.8502 Evaluate side-chains 226 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 205 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 ARG Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 596 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 413 ARG Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 575 CYS Chi-restraints excluded: chain B residue 596 GLU Chi-restraints excluded: chain C residue 262 LYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 413 ARG Chi-restraints excluded: chain C residue 540 ASP Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain C residue 596 GLU Chi-restraints excluded: chain D residue 262 LYS Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 413 ARG Chi-restraints excluded: chain D residue 540 ASP Chi-restraints excluded: chain D residue 575 CYS Chi-restraints excluded: chain D residue 596 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 chunk 131 optimal weight: 6.9990 chunk 21 optimal weight: 0.0980 chunk 39 optimal weight: 20.0000 chunk 143 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 146 optimal weight: 0.0060 chunk 18 optimal weight: 0.0980 chunk 26 optimal weight: 0.9980 chunk 125 optimal weight: 8.9990 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 498 GLN D 468 ASN ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.193519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.151351 restraints weight = 92604.110| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 3.02 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3660 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3660 r_free = 0.3660 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3660 r_free = 0.3660 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3660 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15372 Z= 0.155 Angle : 0.524 12.340 20864 Z= 0.269 Chirality : 0.039 0.170 2344 Planarity : 0.004 0.048 2580 Dihedral : 4.273 19.485 2060 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.34 % Allowed : 16.89 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.60 (0.20), residues: 1824 helix: 0.75 (0.15), residues: 1116 sheet: -0.76 (0.73), residues: 48 loop : 0.10 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 442 HIS 0.001 0.001 HIS D 422 PHE 0.009 0.001 PHE D 389 TYR 0.017 0.001 TYR A 199 ARG 0.002 0.000 ARG A 413 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5392.90 seconds wall clock time: 97 minutes 24.22 seconds (5844.22 seconds total)