Starting phenix.real_space_refine on Sat Feb 17 04:07:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v00_20966/02_2024/6v00_20966.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v00_20966/02_2024/6v00_20966.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v00_20966/02_2024/6v00_20966.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v00_20966/02_2024/6v00_20966.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v00_20966/02_2024/6v00_20966.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v00_20966/02_2024/6v00_20966.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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: 5 Type Number sf(0) Gaussians Ca 8 9.91 5 S 88 5.16 5 C 11264 2.51 5 N 2988 2.21 5 O 3112 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 174": "NH1" <-> "NH2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A ARG 243": "NH1" <-> "NH2" Residue "A ARG 249": "NH1" <-> "NH2" Residue "A ARG 293": "NH1" <-> "NH2" Residue "A ARG 360": "NH1" <-> "NH2" Residue "A ARG 507": "NH1" <-> "NH2" Residue "A ARG 511": "NH1" <-> "NH2" Residue "A ARG 539": "NH1" <-> "NH2" Residue "B ARG 75": "NH1" <-> "NH2" Residue "B TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 53": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C ARG 99": "NH1" <-> "NH2" Residue "D ARG 174": "NH1" <-> "NH2" Residue "D ARG 228": "NH1" <-> "NH2" Residue "D ARG 237": "NH1" <-> "NH2" Residue "D ARG 243": "NH1" <-> "NH2" Residue "D ARG 249": "NH1" <-> "NH2" Residue "D ARG 293": "NH1" <-> "NH2" Residue "D ARG 360": "NH1" <-> "NH2" Residue "D ARG 507": "NH1" <-> "NH2" Residue "D ARG 511": "NH1" <-> "NH2" Residue "D ARG 539": "NH1" <-> "NH2" Residue "E ARG 75": "NH1" <-> "NH2" Residue "E TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 53": "NH1" <-> "NH2" Residue "F ARG 88": "NH1" <-> "NH2" Residue "F ARG 99": "NH1" <-> "NH2" Residue "G ARG 174": "NH1" <-> "NH2" Residue "G ARG 228": "NH1" <-> "NH2" Residue "G ARG 237": "NH1" <-> "NH2" Residue "G ARG 243": "NH1" <-> "NH2" Residue "G ARG 249": "NH1" <-> "NH2" Residue "G ARG 293": "NH1" <-> "NH2" Residue "G ARG 360": "NH1" <-> "NH2" Residue "G ARG 507": "NH1" <-> "NH2" Residue "G ARG 511": "NH1" <-> "NH2" Residue "G ARG 539": "NH1" <-> "NH2" Residue "H ARG 75": "NH1" <-> "NH2" Residue "H TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 53": "NH1" <-> "NH2" Residue "I ARG 88": "NH1" <-> "NH2" Residue "I ARG 99": "NH1" <-> "NH2" Residue "J ARG 174": "NH1" <-> "NH2" Residue "J ARG 228": "NH1" <-> "NH2" Residue "J ARG 237": "NH1" <-> "NH2" Residue "J ARG 243": "NH1" <-> "NH2" Residue "J ARG 249": "NH1" <-> "NH2" Residue "J ARG 293": "NH1" <-> "NH2" Residue "J ARG 360": "NH1" <-> "NH2" Residue "J ARG 507": "NH1" <-> "NH2" Residue "J ARG 511": "NH1" <-> "NH2" Residue "J ARG 539": "NH1" <-> "NH2" Residue "K ARG 75": "NH1" <-> "NH2" Residue "K TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 53": "NH1" <-> "NH2" Residue "L ARG 88": "NH1" <-> "NH2" Residue "L ARG 99": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17460 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2864 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 346} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1105 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ASP:plan': 6} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 394 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 45} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 2864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2864 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 346} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1105 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ASP:plan': 6} Unresolved non-hydrogen planarities: 18 Chain: "F" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 394 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 45} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 2864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2864 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 346} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1105 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ASP:plan': 6} Unresolved non-hydrogen planarities: 18 Chain: "I" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 394 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 45} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "J" Number of atoms: 2864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2864 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 346} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1105 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ASP:plan': 6} Unresolved non-hydrogen planarities: 18 Chain: "L" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 394 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 45} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb="CA CA B 202 " occ=0.83 residue: pdb="CA CA E 202 " occ=0.83 residue: pdb="CA CA H 202 " occ=0.83 residue: pdb="CA CA K 202 " occ=0.83 Time building chain proxies: 9.55, per 1000 atoms: 0.55 Number of scatterers: 17460 At special positions: 0 Unit cell: (110.21, 110.21, 125.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 8 19.99 S 88 16.00 O 3112 8.00 N 2988 7.00 C 11264 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: 6.73 Conformation dependent library (CDL) restraints added in 3.4 seconds 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4056 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 4 sheets defined 77.7% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 104 through 115 Processing helix chain 'A' and resid 120 through 142 Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 148 through 152 removed outlier: 3.684A pdb=" N ALA A 152 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 178 removed outlier: 3.769A pdb=" N TYR A 171 " --> pdb=" O PHE A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 194 removed outlier: 3.741A pdb=" N GLY A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 216 Processing helix chain 'A' and resid 223 through 237 Processing helix chain 'A' and resid 238 through 241 removed outlier: 3.625A pdb=" N VAL A 241 " --> pdb=" O MET A 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 238 through 241' Processing helix chain 'A' and resid 242 through 244 No H-bonds generated for 'chain 'A' and resid 242 through 244' Processing helix chain 'A' and resid 245 through 258 removed outlier: 3.705A pdb=" N LEU A 250 " --> pdb=" O GLY A 246 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 284 removed outlier: 3.837A pdb=" N THR A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 311 removed outlier: 3.821A pdb=" N THR A 311 " --> pdb=" O VAL A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 358 removed outlier: 4.109A pdb=" N PHE A 335 " --> pdb=" O CYS A 331 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N SER A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE A 339 " --> pdb=" O PHE A 335 " (cutoff:3.500A) Proline residue: A 343 - end of helix Processing helix chain 'A' and resid 363 through 366 Processing helix chain 'A' and resid 367 through 385 removed outlier: 3.904A pdb=" N THR A 377 " --> pdb=" O SER A 373 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU A 385 " --> pdb=" O CYS A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 394 removed outlier: 3.620A pdb=" N LYS A 393 " --> pdb=" O SER A 390 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE A 394 " --> pdb=" O THR A 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 390 through 394' Processing helix chain 'A' and resid 509 through 532 removed outlier: 3.588A pdb=" N THR A 513 " --> pdb=" O HIS A 509 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 564 removed outlier: 3.786A pdb=" N VAL A 541 " --> pdb=" O ASP A 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 22 removed outlier: 3.695A pdb=" N GLU B 12 " --> pdb=" O GLU B 8 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS B 22 " --> pdb=" O SER B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 40 removed outlier: 3.837A pdb=" N VAL B 36 " --> pdb=" O GLU B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 54 removed outlier: 3.518A pdb=" N ILE B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 75 removed outlier: 3.695A pdb=" N MET B 72 " --> pdb=" O GLU B 68 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET B 73 " --> pdb=" O PHE B 69 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 91 removed outlier: 3.714A pdb=" N ILE B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG B 91 " --> pdb=" O ARG B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 98 removed outlier: 5.583A pdb=" N LYS B 95 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ASP B 96 " --> pdb=" O PHE B 93 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY B 97 " --> pdb=" O ASP B 94 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ASN B 98 " --> pdb=" O LYS B 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 92 through 98' Processing helix chain 'B' and resid 103 through 111 Processing helix chain 'B' and resid 118 through 129 removed outlier: 3.767A pdb=" N ARG B 127 " --> pdb=" O ASP B 123 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU B 128 " --> pdb=" O GLU B 124 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ALA B 129 " --> pdb=" O MET B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 149 removed outlier: 3.740A pdb=" N MET B 146 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS B 149 " --> pdb=" O MET B 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 81 removed outlier: 4.381A pdb=" N TYR C 60 " --> pdb=" O ASN C 56 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE C 61 " --> pdb=" O SER C 57 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU C 67 " --> pdb=" O PHE C 63 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG C 81 " --> pdb=" O LEU C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 99 Processing helix chain 'D' and resid 105 through 115 Processing helix chain 'D' and resid 120 through 142 Processing helix chain 'D' and resid 143 through 145 No H-bonds generated for 'chain 'D' and resid 143 through 145' Processing helix chain 'D' and resid 148 through 152 removed outlier: 3.684A pdb=" N ALA D 152 " --> pdb=" O ALA D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 178 removed outlier: 3.769A pdb=" N TYR D 171 " --> pdb=" O PHE D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 194 removed outlier: 3.742A pdb=" N GLY D 189 " --> pdb=" O VAL D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 216 Processing helix chain 'D' and resid 223 through 237 Processing helix chain 'D' and resid 238 through 241 removed outlier: 3.625A pdb=" N VAL D 241 " --> pdb=" O MET D 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 238 through 241' Processing helix chain 'D' and resid 242 through 244 No H-bonds generated for 'chain 'D' and resid 242 through 244' Processing helix chain 'D' and resid 245 through 258 removed outlier: 3.705A pdb=" N LEU D 250 " --> pdb=" O GLY D 246 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL D 254 " --> pdb=" O LEU D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 284 removed outlier: 3.837A pdb=" N THR D 265 " --> pdb=" O GLU D 261 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU D 266 " --> pdb=" O LEU D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 311 removed outlier: 3.821A pdb=" N THR D 311 " --> pdb=" O VAL D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 358 removed outlier: 4.109A pdb=" N PHE D 335 " --> pdb=" O CYS D 331 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N SER D 338 " --> pdb=" O VAL D 334 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE D 339 " --> pdb=" O PHE D 335 " (cutoff:3.500A) Proline residue: D 343 - end of helix Processing helix chain 'D' and resid 363 through 366 Processing helix chain 'D' and resid 367 through 385 removed outlier: 3.903A pdb=" N THR D 377 " --> pdb=" O SER D 373 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU D 385 " --> pdb=" O CYS D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 394 removed outlier: 3.619A pdb=" N LYS D 393 " --> pdb=" O SER D 390 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE D 394 " --> pdb=" O THR D 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 390 through 394' Processing helix chain 'D' and resid 509 through 532 removed outlier: 3.589A pdb=" N THR D 513 " --> pdb=" O HIS D 509 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL D 516 " --> pdb=" O ALA D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 564 removed outlier: 3.786A pdb=" N VAL D 541 " --> pdb=" O ASP D 537 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 22 removed outlier: 3.695A pdb=" N GLU E 12 " --> pdb=" O GLU E 8 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE E 20 " --> pdb=" O ALA E 16 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS E 22 " --> pdb=" O SER E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 40 removed outlier: 3.837A pdb=" N VAL E 36 " --> pdb=" O GLU E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 54 removed outlier: 3.519A pdb=" N ILE E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 75 removed outlier: 3.696A pdb=" N MET E 72 " --> pdb=" O GLU E 68 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET E 73 " --> pdb=" O PHE E 69 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG E 75 " --> pdb=" O THR E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 91 removed outlier: 3.714A pdb=" N ILE E 86 " --> pdb=" O SER E 82 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG E 91 " --> pdb=" O ARG E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 98 removed outlier: 5.583A pdb=" N LYS E 95 " --> pdb=" O VAL E 92 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ASP E 96 " --> pdb=" O PHE E 93 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY E 97 " --> pdb=" O ASP E 94 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ASN E 98 " --> pdb=" O LYS E 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 92 through 98' Processing helix chain 'E' and resid 103 through 111 Processing helix chain 'E' and resid 118 through 129 removed outlier: 3.768A pdb=" N ARG E 127 " --> pdb=" O ASP E 123 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU E 128 " --> pdb=" O GLU E 124 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA E 129 " --> pdb=" O MET E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 149 removed outlier: 3.741A pdb=" N MET E 146 " --> pdb=" O PHE E 142 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS E 149 " --> pdb=" O MET E 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 81 removed outlier: 4.381A pdb=" N TYR F 60 " --> pdb=" O ASN F 56 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE F 61 " --> pdb=" O SER F 57 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU F 67 " --> pdb=" O PHE F 63 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG F 81 " --> pdb=" O LEU F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 99 Processing helix chain 'G' and resid 105 through 115 Processing helix chain 'G' and resid 120 through 142 Processing helix chain 'G' and resid 143 through 145 No H-bonds generated for 'chain 'G' and resid 143 through 145' Processing helix chain 'G' and resid 148 through 152 removed outlier: 3.684A pdb=" N ALA G 152 " --> pdb=" O ALA G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 178 removed outlier: 3.769A pdb=" N TYR G 171 " --> pdb=" O PHE G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 194 removed outlier: 3.742A pdb=" N GLY G 189 " --> pdb=" O VAL G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 216 Processing helix chain 'G' and resid 223 through 237 Processing helix chain 'G' and resid 238 through 241 removed outlier: 3.625A pdb=" N VAL G 241 " --> pdb=" O MET G 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 238 through 241' Processing helix chain 'G' and resid 242 through 244 No H-bonds generated for 'chain 'G' and resid 242 through 244' Processing helix chain 'G' and resid 245 through 258 removed outlier: 3.705A pdb=" N LEU G 250 " --> pdb=" O GLY G 246 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL G 254 " --> pdb=" O LEU G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 284 removed outlier: 3.837A pdb=" N THR G 265 " --> pdb=" O GLU G 261 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU G 266 " --> pdb=" O LEU G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 311 removed outlier: 3.821A pdb=" N THR G 311 " --> pdb=" O VAL G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 322 through 358 removed outlier: 4.109A pdb=" N PHE G 335 " --> pdb=" O CYS G 331 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N SER G 338 " --> pdb=" O VAL G 334 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE G 339 " --> pdb=" O PHE G 335 " (cutoff:3.500A) Proline residue: G 343 - end of helix Processing helix chain 'G' and resid 363 through 366 Processing helix chain 'G' and resid 367 through 385 removed outlier: 3.903A pdb=" N THR G 377 " --> pdb=" O SER G 373 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU G 385 " --> pdb=" O CYS G 381 " (cutoff:3.500A) Processing helix chain 'G' and resid 390 through 394 removed outlier: 3.619A pdb=" N LYS G 393 " --> pdb=" O SER G 390 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE G 394 " --> pdb=" O THR G 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 390 through 394' Processing helix chain 'G' and resid 509 through 532 removed outlier: 3.589A pdb=" N THR G 513 " --> pdb=" O HIS G 509 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL G 516 " --> pdb=" O ALA G 512 " (cutoff:3.500A) Processing helix chain 'G' and resid 537 through 564 removed outlier: 3.786A pdb=" N VAL G 541 " --> pdb=" O ASP G 537 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 22 removed outlier: 3.695A pdb=" N GLU H 12 " --> pdb=" O GLU H 8 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE H 20 " --> pdb=" O ALA H 16 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS H 22 " --> pdb=" O SER H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 40 removed outlier: 3.837A pdb=" N VAL H 36 " --> pdb=" O GLU H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 54 removed outlier: 3.519A pdb=" N ILE H 53 " --> pdb=" O LEU H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 75 removed outlier: 3.697A pdb=" N MET H 72 " --> pdb=" O GLU H 68 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET H 73 " --> pdb=" O PHE H 69 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG H 75 " --> pdb=" O THR H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 91 removed outlier: 3.714A pdb=" N ILE H 86 " --> pdb=" O SER H 82 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG H 91 " --> pdb=" O ARG H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 98 removed outlier: 5.583A pdb=" N LYS H 95 " --> pdb=" O VAL H 92 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ASP H 96 " --> pdb=" O PHE H 93 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY H 97 " --> pdb=" O ASP H 94 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ASN H 98 " --> pdb=" O LYS H 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 92 through 98' Processing helix chain 'H' and resid 103 through 111 Processing helix chain 'H' and resid 118 through 129 removed outlier: 3.768A pdb=" N ARG H 127 " --> pdb=" O ASP H 123 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU H 128 " --> pdb=" O GLU H 124 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA H 129 " --> pdb=" O MET H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 149 removed outlier: 3.741A pdb=" N MET H 146 " --> pdb=" O PHE H 142 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS H 149 " --> pdb=" O MET H 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 56 through 81 removed outlier: 4.381A pdb=" N TYR I 60 " --> pdb=" O ASN I 56 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE I 61 " --> pdb=" O SER I 57 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU I 67 " --> pdb=" O PHE I 63 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG I 81 " --> pdb=" O LEU I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 99 Processing helix chain 'J' and resid 105 through 115 Processing helix chain 'J' and resid 120 through 142 Processing helix chain 'J' and resid 143 through 145 No H-bonds generated for 'chain 'J' and resid 143 through 145' Processing helix chain 'J' and resid 148 through 152 removed outlier: 3.684A pdb=" N ALA J 152 " --> pdb=" O ALA J 149 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 178 removed outlier: 3.768A pdb=" N TYR J 171 " --> pdb=" O PHE J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 185 through 194 removed outlier: 3.742A pdb=" N GLY J 189 " --> pdb=" O VAL J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 196 through 216 Processing helix chain 'J' and resid 223 through 237 Processing helix chain 'J' and resid 238 through 241 removed outlier: 3.625A pdb=" N VAL J 241 " --> pdb=" O MET J 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 238 through 241' Processing helix chain 'J' and resid 242 through 244 No H-bonds generated for 'chain 'J' and resid 242 through 244' Processing helix chain 'J' and resid 245 through 258 removed outlier: 3.705A pdb=" N LEU J 250 " --> pdb=" O GLY J 246 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL J 254 " --> pdb=" O LEU J 250 " (cutoff:3.500A) Processing helix chain 'J' and resid 258 through 284 removed outlier: 3.837A pdb=" N THR J 265 " --> pdb=" O GLU J 261 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU J 266 " --> pdb=" O LEU J 262 " (cutoff:3.500A) Processing helix chain 'J' and resid 298 through 311 removed outlier: 3.821A pdb=" N THR J 311 " --> pdb=" O VAL J 307 " (cutoff:3.500A) Processing helix chain 'J' and resid 322 through 358 removed outlier: 4.109A pdb=" N PHE J 335 " --> pdb=" O CYS J 331 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N SER J 338 " --> pdb=" O VAL J 334 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE J 339 " --> pdb=" O PHE J 335 " (cutoff:3.500A) Proline residue: J 343 - end of helix Processing helix chain 'J' and resid 363 through 366 Processing helix chain 'J' and resid 367 through 385 removed outlier: 3.903A pdb=" N THR J 377 " --> pdb=" O SER J 373 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU J 385 " --> pdb=" O CYS J 381 " (cutoff:3.500A) Processing helix chain 'J' and resid 390 through 394 removed outlier: 3.620A pdb=" N LYS J 393 " --> pdb=" O SER J 390 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ILE J 394 " --> pdb=" O THR J 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 390 through 394' Processing helix chain 'J' and resid 509 through 532 removed outlier: 3.588A pdb=" N THR J 513 " --> pdb=" O HIS J 509 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL J 516 " --> pdb=" O ALA J 512 " (cutoff:3.500A) Processing helix chain 'J' and resid 537 through 564 removed outlier: 3.786A pdb=" N VAL J 541 " --> pdb=" O ASP J 537 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 22 removed outlier: 3.695A pdb=" N GLU K 12 " --> pdb=" O GLU K 8 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE K 20 " --> pdb=" O ALA K 16 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS K 22 " --> pdb=" O SER K 18 " (cutoff:3.500A) Processing helix chain 'K' and resid 29 through 40 removed outlier: 3.837A pdb=" N VAL K 36 " --> pdb=" O GLU K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 54 removed outlier: 3.518A pdb=" N ILE K 53 " --> pdb=" O LEU K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 65 through 75 removed outlier: 3.695A pdb=" N MET K 72 " --> pdb=" O GLU K 68 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET K 73 " --> pdb=" O PHE K 69 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 91 removed outlier: 3.714A pdb=" N ILE K 86 " --> pdb=" O SER K 82 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG K 91 " --> pdb=" O ARG K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 98 removed outlier: 5.583A pdb=" N LYS K 95 " --> pdb=" O VAL K 92 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ASP K 96 " --> pdb=" O PHE K 93 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY K 97 " --> pdb=" O ASP K 94 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ASN K 98 " --> pdb=" O LYS K 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 92 through 98' Processing helix chain 'K' and resid 103 through 111 Processing helix chain 'K' and resid 118 through 129 removed outlier: 3.767A pdb=" N ARG K 127 " --> pdb=" O ASP K 123 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU K 128 " --> pdb=" O GLU K 124 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA K 129 " --> pdb=" O MET K 125 " (cutoff:3.500A) Processing helix chain 'K' and resid 139 through 149 removed outlier: 3.741A pdb=" N MET K 146 " --> pdb=" O PHE K 142 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS K 149 " --> pdb=" O MET K 145 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 81 removed outlier: 4.381A pdb=" N TYR L 60 " --> pdb=" O ASN L 56 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE L 61 " --> pdb=" O SER L 57 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU L 67 " --> pdb=" O PHE L 63 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG L 81 " --> pdb=" O LEU L 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 90 through 99 Processing sheet with id=AA1, first strand: chain 'B' and resid 100 through 102 Processing sheet with id=AA2, first strand: chain 'E' and resid 100 through 102 Processing sheet with id=AA3, first strand: chain 'H' and resid 100 through 102 Processing sheet with id=AA4, first strand: chain 'K' and resid 100 through 102 1069 hydrogen bonds defined for protein. 3183 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: 5.13 Time building geometry restraints manager: 7.35 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: 5360 1.34 - 1.46: 3419 1.46 - 1.57: 8889 1.57 - 1.69: 0 1.69 - 1.81: 152 Bond restraints: 17820 Sorted by residual: bond pdb=" CB VAL A 310 " pdb=" CG1 VAL A 310 " ideal model delta sigma weight residual 1.521 1.419 0.102 3.30e-02 9.18e+02 9.51e+00 bond pdb=" CB VAL J 310 " pdb=" CG1 VAL J 310 " ideal model delta sigma weight residual 1.521 1.419 0.102 3.30e-02 9.18e+02 9.48e+00 bond pdb=" CB VAL D 310 " pdb=" CG1 VAL D 310 " ideal model delta sigma weight residual 1.521 1.420 0.101 3.30e-02 9.18e+02 9.43e+00 bond pdb=" CB VAL G 310 " pdb=" CG1 VAL G 310 " ideal model delta sigma weight residual 1.521 1.420 0.101 3.30e-02 9.18e+02 9.43e+00 bond pdb=" CB CYS A 122 " pdb=" SG CYS A 122 " ideal model delta sigma weight residual 1.808 1.752 0.056 3.30e-02 9.18e+02 2.89e+00 ... (remaining 17815 not shown) Histogram of bond angle deviations from ideal: 99.19 - 106.18: 261 106.18 - 113.17: 9469 113.17 - 120.16: 7432 120.16 - 127.16: 6714 127.16 - 134.15: 196 Bond angle restraints: 24072 Sorted by residual: angle pdb=" C LYS K 95 " pdb=" N ASP K 96 " pdb=" CA ASP K 96 " ideal model delta sigma weight residual 121.54 129.23 -7.69 1.91e+00 2.74e-01 1.62e+01 angle pdb=" C LYS B 95 " pdb=" N ASP B 96 " pdb=" CA ASP B 96 " ideal model delta sigma weight residual 121.54 129.20 -7.66 1.91e+00 2.74e-01 1.61e+01 angle pdb=" C LYS E 95 " pdb=" N ASP E 96 " pdb=" CA ASP E 96 " ideal model delta sigma weight residual 121.54 129.20 -7.66 1.91e+00 2.74e-01 1.61e+01 angle pdb=" C LYS H 95 " pdb=" N ASP H 96 " pdb=" CA ASP H 96 " ideal model delta sigma weight residual 121.54 129.20 -7.66 1.91e+00 2.74e-01 1.61e+01 angle pdb=" C ARG J 243 " pdb=" N GLN J 244 " pdb=" CA GLN J 244 " ideal model delta sigma weight residual 121.54 129.17 -7.63 1.91e+00 2.74e-01 1.60e+01 ... (remaining 24067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.40: 9843 14.40 - 28.80: 465 28.80 - 43.20: 125 43.20 - 57.60: 15 57.60 - 72.00: 20 Dihedral angle restraints: 10468 sinusoidal: 4164 harmonic: 6304 Sorted by residual: dihedral pdb=" CA HIS J 363 " pdb=" C HIS J 363 " pdb=" N PHE J 364 " pdb=" CA PHE J 364 " ideal model delta harmonic sigma weight residual -180.00 -152.17 -27.83 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA HIS A 363 " pdb=" C HIS A 363 " pdb=" N PHE A 364 " pdb=" CA PHE A 364 " ideal model delta harmonic sigma weight residual -180.00 -152.18 -27.82 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA HIS G 363 " pdb=" C HIS G 363 " pdb=" N PHE G 364 " pdb=" CA PHE G 364 " ideal model delta harmonic sigma weight residual 180.00 -152.21 -27.79 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 10465 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1459 0.039 - 0.077: 879 0.077 - 0.116: 226 0.116 - 0.154: 106 0.154 - 0.193: 18 Chirality restraints: 2688 Sorted by residual: chirality pdb=" CA ARG A 116 " pdb=" N ARG A 116 " pdb=" C ARG A 116 " pdb=" CB ARG A 116 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.29e-01 chirality pdb=" CA ARG J 116 " pdb=" N ARG J 116 " pdb=" C ARG J 116 " pdb=" CB ARG J 116 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.20e-01 chirality pdb=" CA ARG D 116 " pdb=" N ARG D 116 " pdb=" C ARG D 116 " pdb=" CB ARG D 116 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.20e-01 ... (remaining 2685 not shown) Planarity restraints: 3028 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE G 332 " -0.032 2.00e-02 2.50e+03 2.30e-02 9.24e+00 pdb=" CG PHE G 332 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE G 332 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE G 332 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE G 332 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE G 332 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE G 332 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 332 " -0.032 2.00e-02 2.50e+03 2.30e-02 9.24e+00 pdb=" CG PHE D 332 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE D 332 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE D 332 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE D 332 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE D 332 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE D 332 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 332 " 0.032 2.00e-02 2.50e+03 2.29e-02 9.14e+00 pdb=" CG PHE A 332 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE A 332 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 332 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 332 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 332 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 332 " 0.022 2.00e-02 2.50e+03 ... (remaining 3025 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 5479 2.83 - 3.35: 16710 3.35 - 3.87: 28038 3.87 - 4.38: 31098 4.38 - 4.90: 55323 Nonbonded interactions: 136648 Sorted by model distance: nonbonded pdb=" OE2 GLU A 284 " pdb=" OG1 THR A 322 " model vdw 2.315 2.440 nonbonded pdb=" OE2 GLU D 284 " pdb=" OG1 THR D 322 " model vdw 2.315 2.440 nonbonded pdb=" OE2 GLU G 284 " pdb=" OG1 THR G 322 " model vdw 2.315 2.440 nonbonded pdb=" OE2 GLU J 284 " pdb=" OG1 THR J 322 " model vdw 2.315 2.440 nonbonded pdb=" O LYS A 183 " pdb=" NH2 ARG A 192 " model vdw 2.359 2.520 ... (remaining 136643 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' selection = chain 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' } 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=0.83 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.840 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: 6.960 Check model and map are aligned: 0.270 Set scattering table: 0.150 Process input model: 48.200 Find NCS groups from input model: 1.070 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 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 : 0.007 0.102 17820 Z= 0.460 Angle : 0.954 8.521 24072 Z= 0.545 Chirality : 0.053 0.193 2688 Planarity : 0.007 0.048 3028 Dihedral : 10.226 72.001 6412 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.30 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % 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: -3.43 (0.14), residues: 2140 helix: -2.24 (0.09), residues: 1616 sheet: None (None), residues: 0 loop : -1.56 (0.25), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP D 305 HIS 0.013 0.002 HIS A 363 PHE 0.046 0.003 PHE G 332 TYR 0.021 0.003 TYR G 315 ARG 0.008 0.001 ARG G 243 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 480 time to evaluate : 2.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 LEU cc_start: 0.8401 (tp) cc_final: 0.7913 (mm) REVERT: A 507 ARG cc_start: 0.7501 (mmt-90) cc_final: 0.7100 (mpt180) REVERT: B 18 SER cc_start: 0.8995 (t) cc_final: 0.8666 (p) REVERT: B 19 LEU cc_start: 0.9032 (mp) cc_final: 0.8809 (mt) REVERT: B 123 ASP cc_start: 0.8390 (m-30) cc_final: 0.7878 (m-30) REVERT: C 65 MET cc_start: 0.8697 (mmt) cc_final: 0.8249 (mmt) REVERT: C 81 ARG cc_start: 0.7839 (mtp180) cc_final: 0.7181 (mmt180) REVERT: D 191 LEU cc_start: 0.8395 (tp) cc_final: 0.7927 (mm) REVERT: D 507 ARG cc_start: 0.7541 (mmt-90) cc_final: 0.7086 (mpt180) REVERT: E 18 SER cc_start: 0.9001 (t) cc_final: 0.8673 (p) REVERT: E 123 ASP cc_start: 0.8392 (m-30) cc_final: 0.7842 (m-30) REVERT: F 65 MET cc_start: 0.8695 (mmt) cc_final: 0.8220 (mmt) REVERT: F 81 ARG cc_start: 0.7823 (mtp180) cc_final: 0.7130 (mmt180) REVERT: G 191 LEU cc_start: 0.8394 (tp) cc_final: 0.7924 (mm) REVERT: G 507 ARG cc_start: 0.7541 (mmt-90) cc_final: 0.7085 (mpt180) REVERT: H 18 SER cc_start: 0.9002 (t) cc_final: 0.8674 (p) REVERT: H 123 ASP cc_start: 0.8391 (m-30) cc_final: 0.7842 (m-30) REVERT: I 81 ARG cc_start: 0.7833 (mtp180) cc_final: 0.7058 (mmt180) REVERT: J 191 LEU cc_start: 0.8392 (tp) cc_final: 0.7914 (mm) REVERT: J 507 ARG cc_start: 0.7513 (mmt-90) cc_final: 0.7066 (mpt180) REVERT: K 18 SER cc_start: 0.9004 (t) cc_final: 0.8664 (p) REVERT: K 19 LEU cc_start: 0.9009 (mp) cc_final: 0.8798 (mt) REVERT: K 123 ASP cc_start: 0.8391 (m-30) cc_final: 0.7873 (m-30) REVERT: L 81 ARG cc_start: 0.7817 (mtp180) cc_final: 0.7089 (mmt180) outliers start: 0 outliers final: 0 residues processed: 480 average time/residue: 0.4102 time to fit residues: 266.1503 Evaluate side-chains 304 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 304 time to evaluate : 2.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 0.9990 chunk 160 optimal weight: 0.7980 chunk 89 optimal weight: 7.9990 chunk 54 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 chunk 192 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 GLN A 386 ASN A 560 GLN ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 HIS D 376 GLN D 386 ASN D 560 GLN ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 HIS G 376 GLN G 386 ASN G 560 GLN ** H 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 93 HIS J 376 GLN J 386 ASN J 560 GLN ** K 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 ASN L 93 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17820 Z= 0.178 Angle : 0.511 6.273 24072 Z= 0.276 Chirality : 0.038 0.125 2688 Planarity : 0.004 0.029 3028 Dihedral : 4.426 23.088 2396 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.91 % Allowed : 8.08 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.17), residues: 2140 helix: -0.23 (0.12), residues: 1620 sheet: None (None), residues: 0 loop : -1.11 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 379 HIS 0.004 0.001 HIS A 240 PHE 0.021 0.001 PHE K 17 TYR 0.015 0.001 TYR D 545 ARG 0.007 0.000 ARG E 127 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 302 time to evaluate : 2.237 Fit side-chains revert: symmetry clash REVERT: A 191 LEU cc_start: 0.8390 (tp) cc_final: 0.7820 (mm) REVERT: A 286 ASP cc_start: 0.7948 (t0) cc_final: 0.7620 (t0) REVERT: A 562 ARG cc_start: 0.7923 (ttp80) cc_final: 0.7291 (tpt90) REVERT: B 22 LYS cc_start: 0.6340 (mtmm) cc_final: 0.5851 (mttp) REVERT: B 123 ASP cc_start: 0.8235 (m-30) cc_final: 0.7898 (m-30) REVERT: C 65 MET cc_start: 0.8746 (mmt) cc_final: 0.8453 (mmt) REVERT: C 81 ARG cc_start: 0.7586 (mtp180) cc_final: 0.7241 (mpt180) REVERT: D 191 LEU cc_start: 0.8382 (tp) cc_final: 0.7828 (mm) REVERT: D 286 ASP cc_start: 0.7936 (t0) cc_final: 0.7560 (t0) REVERT: D 562 ARG cc_start: 0.7935 (ttp80) cc_final: 0.7288 (tpt90) REVERT: E 22 LYS cc_start: 0.6260 (mtmm) cc_final: 0.5756 (mttp) REVERT: E 123 ASP cc_start: 0.8236 (m-30) cc_final: 0.7870 (m-30) REVERT: F 65 MET cc_start: 0.8756 (mmt) cc_final: 0.8466 (mmt) REVERT: F 81 ARG cc_start: 0.7538 (mtp180) cc_final: 0.7307 (mpt180) REVERT: G 191 LEU cc_start: 0.8380 (tp) cc_final: 0.7826 (mm) REVERT: G 286 ASP cc_start: 0.7937 (t0) cc_final: 0.7560 (t0) REVERT: G 562 ARG cc_start: 0.7935 (ttp80) cc_final: 0.7229 (tpt90) REVERT: H 22 LYS cc_start: 0.6256 (mtmm) cc_final: 0.5752 (mttp) REVERT: H 123 ASP cc_start: 0.8238 (m-30) cc_final: 0.7870 (m-30) REVERT: I 65 MET cc_start: 0.8777 (mmt) cc_final: 0.8354 (mmt) REVERT: I 81 ARG cc_start: 0.7570 (mtp180) cc_final: 0.7172 (mpt180) REVERT: J 191 LEU cc_start: 0.8382 (tp) cc_final: 0.7826 (mm) REVERT: J 286 ASP cc_start: 0.7936 (t0) cc_final: 0.7557 (t0) REVERT: J 562 ARG cc_start: 0.7924 (ttp80) cc_final: 0.7220 (tpt90) REVERT: K 18 SER cc_start: 0.8991 (t) cc_final: 0.8633 (p) REVERT: K 22 LYS cc_start: 0.6296 (mtmm) cc_final: 0.5784 (mttp) REVERT: K 123 ASP cc_start: 0.8232 (m-30) cc_final: 0.7929 (m-30) REVERT: L 65 MET cc_start: 0.8784 (mmt) cc_final: 0.8374 (mmt) REVERT: L 81 ARG cc_start: 0.7559 (mtp180) cc_final: 0.7257 (mpt180) outliers start: 35 outliers final: 31 residues processed: 329 average time/residue: 0.3939 time to fit residues: 179.4792 Evaluate side-chains 284 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 253 time to evaluate : 2.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 214 CYS Chi-restraints excluded: chain G residue 290 GLU Chi-restraints excluded: chain G residue 301 ASP Chi-restraints excluded: chain G residue 514 ILE Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 214 CYS Chi-restraints excluded: chain J residue 290 GLU Chi-restraints excluded: chain J residue 301 ASP Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 145 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 160 optimal weight: 0.7980 chunk 131 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 192 optimal weight: 4.9990 chunk 208 optimal weight: 2.9990 chunk 171 optimal weight: 0.9980 chunk 191 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 HIS ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 GLN D 510 HIS E 54 ASN E 144 GLN G 510 HIS ** H 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 144 GLN J 510 HIS ** K 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 144 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 17820 Z= 0.219 Angle : 0.502 5.765 24072 Z= 0.268 Chirality : 0.039 0.149 2688 Planarity : 0.003 0.028 3028 Dihedral : 4.057 19.619 2396 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.35 % Allowed : 9.33 % Favored : 88.32 % 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 (0.17), residues: 2140 helix: 0.72 (0.12), residues: 1616 sheet: None (None), residues: 0 loop : -0.99 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 379 HIS 0.004 0.001 HIS J 240 PHE 0.020 0.002 PHE A 332 TYR 0.017 0.001 TYR J 545 ARG 0.008 0.000 ARG K 127 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 290 time to evaluate : 1.982 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 TRP cc_start: 0.7008 (m-90) cc_final: 0.6412 (m100) REVERT: A 191 LEU cc_start: 0.8468 (tp) cc_final: 0.7889 (mm) REVERT: A 286 ASP cc_start: 0.7949 (t0) cc_final: 0.7567 (t0) REVERT: A 553 MET cc_start: 0.8711 (tpp) cc_final: 0.8312 (tpp) REVERT: A 562 ARG cc_start: 0.8058 (ttp80) cc_final: 0.7727 (ttp80) REVERT: B 18 SER cc_start: 0.8974 (t) cc_final: 0.8658 (p) REVERT: B 119 ASP cc_start: 0.7524 (t0) cc_final: 0.7193 (t0) REVERT: B 123 ASP cc_start: 0.8262 (m-30) cc_final: 0.7811 (m-30) REVERT: C 65 MET cc_start: 0.8759 (mmt) cc_final: 0.8320 (mmt) REVERT: D 158 TRP cc_start: 0.6999 (m-90) cc_final: 0.6396 (m100) REVERT: D 188 TRP cc_start: 0.8332 (m100) cc_final: 0.8052 (m-90) REVERT: D 191 LEU cc_start: 0.8436 (tp) cc_final: 0.7847 (mm) REVERT: D 286 ASP cc_start: 0.7967 (t0) cc_final: 0.7581 (t0) REVERT: D 507 ARG cc_start: 0.7803 (mmt-90) cc_final: 0.7121 (mpt180) REVERT: D 553 MET cc_start: 0.8731 (tpp) cc_final: 0.8299 (tpp) REVERT: D 562 ARG cc_start: 0.8101 (ttp80) cc_final: 0.7761 (ttp80) REVERT: E 18 SER cc_start: 0.8983 (t) cc_final: 0.8655 (p) REVERT: E 119 ASP cc_start: 0.7551 (t0) cc_final: 0.7186 (t0) REVERT: E 123 ASP cc_start: 0.8265 (m-30) cc_final: 0.7776 (m-30) REVERT: F 65 MET cc_start: 0.8759 (mmt) cc_final: 0.8326 (mmt) REVERT: G 158 TRP cc_start: 0.6998 (m-90) cc_final: 0.6398 (m100) REVERT: G 188 TRP cc_start: 0.8332 (m100) cc_final: 0.8051 (m-90) REVERT: G 191 LEU cc_start: 0.8436 (tp) cc_final: 0.7848 (mm) REVERT: G 286 ASP cc_start: 0.7967 (t0) cc_final: 0.7580 (t0) REVERT: G 507 ARG cc_start: 0.7802 (mmt-90) cc_final: 0.7120 (mpt180) REVERT: G 553 MET cc_start: 0.8717 (tpp) cc_final: 0.8310 (tpp) REVERT: G 562 ARG cc_start: 0.8022 (ttp80) cc_final: 0.7731 (ttp80) REVERT: H 18 SER cc_start: 0.8984 (t) cc_final: 0.8657 (p) REVERT: H 119 ASP cc_start: 0.7548 (t0) cc_final: 0.7186 (t0) REVERT: H 123 ASP cc_start: 0.8265 (m-30) cc_final: 0.7775 (m-30) REVERT: I 65 MET cc_start: 0.8752 (mmt) cc_final: 0.8235 (mmt) REVERT: J 158 TRP cc_start: 0.7002 (m-90) cc_final: 0.6405 (m100) REVERT: J 188 TRP cc_start: 0.8320 (m100) cc_final: 0.8048 (m-90) REVERT: J 191 LEU cc_start: 0.8436 (tp) cc_final: 0.7847 (mm) REVERT: J 286 ASP cc_start: 0.7964 (t0) cc_final: 0.7577 (t0) REVERT: J 553 MET cc_start: 0.8724 (tpp) cc_final: 0.8302 (tpp) REVERT: J 562 ARG cc_start: 0.8050 (ttp80) cc_final: 0.7727 (ttp80) REVERT: K 18 SER cc_start: 0.8969 (t) cc_final: 0.8637 (p) REVERT: K 119 ASP cc_start: 0.7518 (t0) cc_final: 0.7155 (t0) REVERT: K 123 ASP cc_start: 0.8259 (m-30) cc_final: 0.7767 (m-30) REVERT: L 65 MET cc_start: 0.8762 (mmt) cc_final: 0.8262 (mmt) outliers start: 43 outliers final: 28 residues processed: 314 average time/residue: 0.3865 time to fit residues: 171.2399 Evaluate side-chains 293 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 265 time to evaluate : 2.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 332 PHE Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 214 CYS Chi-restraints excluded: chain G residue 301 ASP Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain G residue 514 ILE Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 140 GLU Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 214 CYS Chi-restraints excluded: chain J residue 301 ASP Chi-restraints excluded: chain J residue 332 PHE Chi-restraints excluded: chain K residue 29 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 129 optimal weight: 0.3980 chunk 193 optimal weight: 4.9990 chunk 204 optimal weight: 3.9990 chunk 101 optimal weight: 0.5980 chunk 183 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 HIS D 258 HIS G 258 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 17820 Z= 0.277 Angle : 0.514 5.020 24072 Z= 0.275 Chirality : 0.040 0.145 2688 Planarity : 0.003 0.024 3028 Dihedral : 3.992 17.161 2396 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.17 % Allowed : 10.81 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.18), residues: 2140 helix: 1.09 (0.13), residues: 1616 sheet: None (None), residues: 0 loop : -0.82 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 379 HIS 0.005 0.001 HIS A 240 PHE 0.020 0.002 PHE J 332 TYR 0.019 0.002 TYR D 545 ARG 0.004 0.000 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 289 time to evaluate : 2.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 TRP cc_start: 0.7059 (m-90) cc_final: 0.6510 (m100) REVERT: A 286 ASP cc_start: 0.8040 (t0) cc_final: 0.7683 (t0) REVERT: A 366 ARG cc_start: 0.9150 (tpp80) cc_final: 0.8843 (tpp-160) REVERT: A 507 ARG cc_start: 0.7915 (mmt-90) cc_final: 0.7012 (mpt180) REVERT: B 18 SER cc_start: 0.8988 (t) cc_final: 0.8669 (p) REVERT: B 119 ASP cc_start: 0.7710 (t0) cc_final: 0.7388 (t0) REVERT: B 123 ASP cc_start: 0.8267 (m-30) cc_final: 0.7767 (m-30) REVERT: D 158 TRP cc_start: 0.7053 (m-90) cc_final: 0.6500 (m100) REVERT: D 286 ASP cc_start: 0.8038 (t0) cc_final: 0.7685 (t0) REVERT: D 366 ARG cc_start: 0.9149 (tpp80) cc_final: 0.8841 (tpp-160) REVERT: D 507 ARG cc_start: 0.7909 (mmt-90) cc_final: 0.7001 (mpt180) REVERT: E 18 SER cc_start: 0.8993 (t) cc_final: 0.8676 (p) REVERT: E 123 ASP cc_start: 0.8274 (m-30) cc_final: 0.7771 (m-30) REVERT: G 158 TRP cc_start: 0.7053 (m-90) cc_final: 0.6499 (m100) REVERT: G 286 ASP cc_start: 0.8041 (t0) cc_final: 0.7685 (t0) REVERT: G 366 ARG cc_start: 0.9147 (tpp80) cc_final: 0.8843 (tpp-160) REVERT: G 507 ARG cc_start: 0.7911 (mmt-90) cc_final: 0.7002 (mpt180) REVERT: H 18 SER cc_start: 0.8994 (t) cc_final: 0.8674 (p) REVERT: H 123 ASP cc_start: 0.8273 (m-30) cc_final: 0.7770 (m-30) REVERT: J 158 TRP cc_start: 0.7056 (m-90) cc_final: 0.6505 (m100) REVERT: J 286 ASP cc_start: 0.8041 (t0) cc_final: 0.7683 (t0) REVERT: J 366 ARG cc_start: 0.9144 (tpp80) cc_final: 0.8845 (tpp-160) REVERT: J 507 ARG cc_start: 0.7909 (mmt-90) cc_final: 0.7006 (mpt180) REVERT: K 18 SER cc_start: 0.8998 (t) cc_final: 0.8672 (p) REVERT: K 119 ASP cc_start: 0.7706 (t0) cc_final: 0.7382 (t0) REVERT: K 123 ASP cc_start: 0.8267 (m-30) cc_final: 0.7767 (m-30) outliers start: 58 outliers final: 31 residues processed: 331 average time/residue: 0.3744 time to fit residues: 172.9323 Evaluate side-chains 293 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 262 time to evaluate : 2.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 376 GLN Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 214 CYS Chi-restraints excluded: chain G residue 301 ASP Chi-restraints excluded: chain G residue 376 GLN Chi-restraints excluded: chain G residue 514 ILE Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 213 LEU Chi-restraints excluded: chain J residue 214 CYS Chi-restraints excluded: chain J residue 301 ASP Chi-restraints excluded: chain J residue 376 GLN Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 140 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 8.9990 chunk 116 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 183 optimal weight: 0.5980 chunk 51 optimal weight: 0.0970 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN E 54 ASN H 54 ASN K 54 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17820 Z= 0.216 Angle : 0.476 5.292 24072 Z= 0.254 Chirality : 0.039 0.131 2688 Planarity : 0.003 0.029 3028 Dihedral : 3.776 14.645 2396 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.73 % Allowed : 11.68 % Favored : 85.59 % 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: 1.36 (0.18), residues: 2140 helix: 1.44 (0.13), residues: 1624 sheet: None (None), residues: 0 loop : -0.72 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 379 HIS 0.004 0.001 HIS J 240 PHE 0.017 0.001 PHE A 332 TYR 0.015 0.001 TYR A 545 ARG 0.009 0.000 ARG H 127 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 298 time to evaluate : 2.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 TRP cc_start: 0.7007 (m-90) cc_final: 0.6441 (m100) REVERT: A 286 ASP cc_start: 0.8040 (t0) cc_final: 0.7662 (t0) REVERT: A 507 ARG cc_start: 0.7948 (mmt-90) cc_final: 0.7036 (mpt180) REVERT: A 562 ARG cc_start: 0.8252 (ttp80) cc_final: 0.7938 (ttp80) REVERT: B 18 SER cc_start: 0.9005 (t) cc_final: 0.8700 (p) REVERT: B 119 ASP cc_start: 0.7739 (t0) cc_final: 0.7419 (t0) REVERT: B 123 ASP cc_start: 0.8281 (m-30) cc_final: 0.7786 (m-30) REVERT: C 65 MET cc_start: 0.8758 (mmt) cc_final: 0.8293 (mmt) REVERT: D 158 TRP cc_start: 0.7005 (m-90) cc_final: 0.6433 (m100) REVERT: D 286 ASP cc_start: 0.8031 (t0) cc_final: 0.7658 (t0) REVERT: D 507 ARG cc_start: 0.7962 (mmt-90) cc_final: 0.6983 (mpt180) REVERT: D 562 ARG cc_start: 0.8251 (ttp80) cc_final: 0.7943 (ttp80) REVERT: E 18 SER cc_start: 0.9035 (t) cc_final: 0.8750 (p) REVERT: E 123 ASP cc_start: 0.8301 (m-30) cc_final: 0.7792 (m-30) REVERT: F 65 MET cc_start: 0.8757 (mmt) cc_final: 0.8291 (mmt) REVERT: G 158 TRP cc_start: 0.7005 (m-90) cc_final: 0.6434 (m100) REVERT: G 286 ASP cc_start: 0.8033 (t0) cc_final: 0.7658 (t0) REVERT: G 507 ARG cc_start: 0.7963 (mmt-90) cc_final: 0.6985 (mpt180) REVERT: G 562 ARG cc_start: 0.8260 (ttp80) cc_final: 0.7946 (ttp80) REVERT: H 18 SER cc_start: 0.9031 (t) cc_final: 0.8753 (p) REVERT: H 54 ASN cc_start: 0.8622 (m110) cc_final: 0.8324 (m-40) REVERT: H 123 ASP cc_start: 0.8302 (m-30) cc_final: 0.7791 (m-30) REVERT: I 65 MET cc_start: 0.8753 (mmt) cc_final: 0.8293 (mmt) REVERT: J 158 TRP cc_start: 0.7006 (m-90) cc_final: 0.6440 (m100) REVERT: J 286 ASP cc_start: 0.8032 (t0) cc_final: 0.7655 (t0) REVERT: J 507 ARG cc_start: 0.7904 (mmt-90) cc_final: 0.6993 (mpt180) REVERT: J 562 ARG cc_start: 0.8302 (ttp80) cc_final: 0.7983 (ttp80) REVERT: K 18 SER cc_start: 0.9015 (t) cc_final: 0.8711 (p) REVERT: K 119 ASP cc_start: 0.7734 (t0) cc_final: 0.7427 (t0) REVERT: K 123 ASP cc_start: 0.8279 (m-30) cc_final: 0.7788 (m-30) REVERT: L 65 MET cc_start: 0.8761 (mmt) cc_final: 0.8305 (mmt) outliers start: 50 outliers final: 30 residues processed: 332 average time/residue: 0.3735 time to fit residues: 172.2981 Evaluate side-chains 296 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 266 time to evaluate : 2.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 376 GLN Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 214 CYS Chi-restraints excluded: chain G residue 376 GLN Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 140 GLU Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 213 LEU Chi-restraints excluded: chain J residue 214 CYS Chi-restraints excluded: chain J residue 363 HIS Chi-restraints excluded: chain J residue 376 GLN Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 140 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 chunk 40 optimal weight: 0.2980 chunk 120 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 205 optimal weight: 6.9990 chunk 170 optimal weight: 9.9990 chunk 94 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 98 ASN J 258 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17820 Z= 0.153 Angle : 0.446 5.354 24072 Z= 0.238 Chirality : 0.037 0.121 2688 Planarity : 0.003 0.032 3028 Dihedral : 3.584 14.222 2396 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.40 % Allowed : 13.16 % Favored : 84.44 % 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: 1.84 (0.18), residues: 2140 helix: 1.80 (0.13), residues: 1616 sheet: None (None), residues: 0 loop : -0.56 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 379 HIS 0.004 0.001 HIS A 363 PHE 0.015 0.001 PHE A 332 TYR 0.011 0.001 TYR J 545 ARG 0.010 0.000 ARG H 127 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 276 time to evaluate : 2.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 TRP cc_start: 0.6942 (m-90) cc_final: 0.6424 (m100) REVERT: A 286 ASP cc_start: 0.8012 (t0) cc_final: 0.7633 (t0) REVERT: A 507 ARG cc_start: 0.7993 (mmt-90) cc_final: 0.6994 (mpt180) REVERT: A 562 ARG cc_start: 0.8296 (ttp80) cc_final: 0.8001 (ttp80) REVERT: C 65 MET cc_start: 0.8737 (mmt) cc_final: 0.8233 (mmt) REVERT: D 158 TRP cc_start: 0.6935 (m-90) cc_final: 0.6416 (m100) REVERT: D 286 ASP cc_start: 0.8011 (t0) cc_final: 0.7633 (t0) REVERT: D 507 ARG cc_start: 0.7993 (mmt-90) cc_final: 0.6995 (mpt180) REVERT: D 562 ARG cc_start: 0.8315 (ttp80) cc_final: 0.8017 (ttp80) REVERT: E 18 SER cc_start: 0.9005 (t) cc_final: 0.8730 (p) REVERT: E 123 ASP cc_start: 0.8269 (m-30) cc_final: 0.7748 (m-30) REVERT: F 65 MET cc_start: 0.8731 (mmt) cc_final: 0.8257 (mmt) REVERT: G 158 TRP cc_start: 0.6937 (m-90) cc_final: 0.6417 (m100) REVERT: G 286 ASP cc_start: 0.8010 (t0) cc_final: 0.7634 (t0) REVERT: G 507 ARG cc_start: 0.7995 (mmt-90) cc_final: 0.6999 (mpt180) REVERT: G 528 LYS cc_start: 0.8269 (mttp) cc_final: 0.7986 (mmtm) REVERT: G 562 ARG cc_start: 0.8298 (ttp80) cc_final: 0.8006 (ttp80) REVERT: H 18 SER cc_start: 0.9005 (t) cc_final: 0.8731 (p) REVERT: H 38 ARG cc_start: 0.8814 (mtm110) cc_final: 0.8531 (mtm110) REVERT: H 54 ASN cc_start: 0.8681 (m110) cc_final: 0.8337 (m-40) REVERT: H 123 ASP cc_start: 0.8270 (m-30) cc_final: 0.7747 (m-30) REVERT: I 65 MET cc_start: 0.8728 (mmt) cc_final: 0.8270 (mmt) REVERT: J 158 TRP cc_start: 0.6938 (m-90) cc_final: 0.6422 (m100) REVERT: J 286 ASP cc_start: 0.8012 (t0) cc_final: 0.7629 (t0) REVERT: J 507 ARG cc_start: 0.7993 (mmt-90) cc_final: 0.7019 (mpt180) REVERT: J 562 ARG cc_start: 0.8292 (ttp80) cc_final: 0.7991 (ttp80) REVERT: K 119 ASP cc_start: 0.7721 (t0) cc_final: 0.7425 (t0) REVERT: K 123 ASP cc_start: 0.8258 (m-30) cc_final: 0.7760 (m-30) REVERT: L 65 MET cc_start: 0.8741 (mmt) cc_final: 0.8266 (mmt) outliers start: 44 outliers final: 30 residues processed: 305 average time/residue: 0.3892 time to fit residues: 164.5093 Evaluate side-chains 297 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 267 time to evaluate : 1.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 363 HIS Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 376 GLN Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 214 CYS Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 376 GLN Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 140 GLU Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 214 CYS Chi-restraints excluded: chain J residue 264 THR Chi-restraints excluded: chain J residue 363 HIS Chi-restraints excluded: chain J residue 376 GLN Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 140 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 149 optimal weight: 4.9990 chunk 172 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 204 optimal weight: 4.9990 chunk 127 optimal weight: 0.9980 chunk 124 optimal weight: 0.7980 chunk 94 optimal weight: 0.3980 chunk 126 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17820 Z= 0.180 Angle : 0.458 5.317 24072 Z= 0.244 Chirality : 0.038 0.128 2688 Planarity : 0.003 0.043 3028 Dihedral : 3.512 13.750 2396 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.18 % Allowed : 13.21 % Favored : 84.61 % 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: 1.97 (0.18), residues: 2140 helix: 1.90 (0.13), residues: 1620 sheet: None (None), residues: 0 loop : -0.56 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 379 HIS 0.003 0.001 HIS D 240 PHE 0.014 0.001 PHE D 332 TYR 0.014 0.001 TYR J 545 ARG 0.011 0.000 ARG K 127 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 271 time to evaluate : 2.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 TRP cc_start: 0.6992 (m-90) cc_final: 0.6452 (m100) REVERT: A 286 ASP cc_start: 0.8047 (t0) cc_final: 0.7672 (t0) REVERT: A 507 ARG cc_start: 0.8044 (mmt-90) cc_final: 0.7004 (mpt180) REVERT: A 528 LYS cc_start: 0.8242 (mttp) cc_final: 0.7976 (mmtm) REVERT: A 562 ARG cc_start: 0.8324 (ttp80) cc_final: 0.8032 (ttp80) REVERT: B 51 ASP cc_start: 0.8314 (m-30) cc_final: 0.8100 (m-30) REVERT: B 123 ASP cc_start: 0.8278 (m-30) cc_final: 0.7764 (m-30) REVERT: C 65 MET cc_start: 0.8740 (mmt) cc_final: 0.8275 (mmt) REVERT: D 158 TRP cc_start: 0.6990 (m-90) cc_final: 0.6446 (m100) REVERT: D 286 ASP cc_start: 0.8055 (t0) cc_final: 0.7674 (t0) REVERT: D 507 ARG cc_start: 0.8040 (mmt-90) cc_final: 0.6993 (mpt180) REVERT: D 528 LYS cc_start: 0.8270 (mttp) cc_final: 0.8012 (mmtm) REVERT: D 562 ARG cc_start: 0.8289 (ttp80) cc_final: 0.7997 (ttp80) REVERT: E 38 ARG cc_start: 0.8729 (mtm110) cc_final: 0.8470 (mtm110) REVERT: E 123 ASP cc_start: 0.8280 (m-30) cc_final: 0.7762 (m-30) REVERT: F 82 SER cc_start: 0.8142 (t) cc_final: 0.7939 (p) REVERT: G 158 TRP cc_start: 0.6990 (m-90) cc_final: 0.6446 (m100) REVERT: G 286 ASP cc_start: 0.8056 (t0) cc_final: 0.7673 (t0) REVERT: G 507 ARG cc_start: 0.8040 (mmt-90) cc_final: 0.6992 (mpt180) REVERT: G 528 LYS cc_start: 0.8276 (mttp) cc_final: 0.8007 (mmtm) REVERT: G 562 ARG cc_start: 0.8308 (ttp80) cc_final: 0.8019 (ttp80) REVERT: H 54 ASN cc_start: 0.8631 (m110) cc_final: 0.8290 (m-40) REVERT: H 123 ASP cc_start: 0.8277 (m-30) cc_final: 0.7763 (m-30) REVERT: J 158 TRP cc_start: 0.6989 (m-90) cc_final: 0.6448 (m100) REVERT: J 286 ASP cc_start: 0.8053 (t0) cc_final: 0.7672 (t0) REVERT: J 507 ARG cc_start: 0.8046 (mmt-90) cc_final: 0.6997 (mpt180) REVERT: J 528 LYS cc_start: 0.8239 (mttp) cc_final: 0.7986 (mmtm) REVERT: J 562 ARG cc_start: 0.8304 (ttp80) cc_final: 0.8009 (ttp80) REVERT: K 119 ASP cc_start: 0.7766 (t0) cc_final: 0.7476 (t0) REVERT: K 123 ASP cc_start: 0.8264 (m-30) cc_final: 0.7769 (m-30) REVERT: L 65 MET cc_start: 0.8743 (mmt) cc_final: 0.8279 (mmt) REVERT: L 82 SER cc_start: 0.8144 (t) cc_final: 0.7943 (p) outliers start: 40 outliers final: 27 residues processed: 297 average time/residue: 0.4030 time to fit residues: 165.8385 Evaluate side-chains 293 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 266 time to evaluate : 2.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 363 HIS Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 376 GLN Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 214 CYS Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 376 GLN Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 140 GLU Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 214 CYS Chi-restraints excluded: chain J residue 363 HIS Chi-restraints excluded: chain J residue 376 GLN Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 140 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 10.0000 chunk 122 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 40 optimal weight: 0.0770 chunk 39 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 139 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 160 optimal weight: 0.9990 chunk 185 optimal weight: 0.8980 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 98 ASN ** K 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17820 Z= 0.152 Angle : 0.443 5.654 24072 Z= 0.235 Chirality : 0.037 0.123 2688 Planarity : 0.003 0.045 3028 Dihedral : 3.430 14.010 2396 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.24 % Allowed : 13.59 % Favored : 84.17 % 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: 2.12 (0.18), residues: 2140 helix: 2.00 (0.13), residues: 1628 sheet: None (None), residues: 0 loop : -0.51 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 379 HIS 0.003 0.001 HIS G 363 PHE 0.014 0.001 PHE D 332 TYR 0.010 0.001 TYR J 545 ARG 0.012 0.000 ARG E 127 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 278 time to evaluate : 1.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 TRP cc_start: 0.6836 (m-90) cc_final: 0.6384 (m100) REVERT: A 286 ASP cc_start: 0.8006 (t0) cc_final: 0.7646 (t0) REVERT: A 507 ARG cc_start: 0.8060 (mmt-90) cc_final: 0.6983 (mpt180) REVERT: A 528 LYS cc_start: 0.8221 (mttp) cc_final: 0.7996 (mmtm) REVERT: A 562 ARG cc_start: 0.8302 (ttp80) cc_final: 0.8029 (ttp80) REVERT: B 123 ASP cc_start: 0.8268 (m-30) cc_final: 0.7784 (m-30) REVERT: C 65 MET cc_start: 0.8741 (mmt) cc_final: 0.8255 (mmt) REVERT: D 158 TRP cc_start: 0.6880 (m-90) cc_final: 0.6376 (m100) REVERT: D 286 ASP cc_start: 0.8029 (t0) cc_final: 0.7668 (t0) REVERT: D 507 ARG cc_start: 0.8055 (mmt-90) cc_final: 0.6970 (mpt180) REVERT: D 528 LYS cc_start: 0.8250 (mttp) cc_final: 0.8029 (mmtm) REVERT: D 562 ARG cc_start: 0.8329 (ttp80) cc_final: 0.8056 (ttp80) REVERT: E 38 ARG cc_start: 0.8699 (mtm110) cc_final: 0.8419 (mtm110) REVERT: E 123 ASP cc_start: 0.8268 (m-30) cc_final: 0.7748 (m-30) REVERT: F 65 MET cc_start: 0.8723 (mmt) cc_final: 0.8263 (mmt) REVERT: G 158 TRP cc_start: 0.6879 (m-90) cc_final: 0.6376 (m100) REVERT: G 286 ASP cc_start: 0.8007 (t0) cc_final: 0.7644 (t0) REVERT: G 507 ARG cc_start: 0.8054 (mmt-90) cc_final: 0.6971 (mpt180) REVERT: G 528 LYS cc_start: 0.8257 (mttp) cc_final: 0.8025 (mmtm) REVERT: G 562 ARG cc_start: 0.8298 (ttp80) cc_final: 0.8023 (ttp80) REVERT: H 38 ARG cc_start: 0.8709 (mtm110) cc_final: 0.8441 (mtm110) REVERT: H 54 ASN cc_start: 0.8629 (m110) cc_final: 0.8293 (m-40) REVERT: H 123 ASP cc_start: 0.8269 (m-30) cc_final: 0.7748 (m-30) REVERT: I 65 MET cc_start: 0.8720 (mmt) cc_final: 0.8234 (mmt) REVERT: J 158 TRP cc_start: 0.6834 (m-90) cc_final: 0.6380 (m100) REVERT: J 286 ASP cc_start: 0.8031 (t0) cc_final: 0.7669 (t0) REVERT: J 507 ARG cc_start: 0.8063 (mmt-90) cc_final: 0.6980 (mpt180) REVERT: J 528 LYS cc_start: 0.8225 (mttp) cc_final: 0.7990 (mmtm) REVERT: J 562 ARG cc_start: 0.8273 (ttp80) cc_final: 0.7993 (ttp80) REVERT: K 119 ASP cc_start: 0.7772 (t0) cc_final: 0.7513 (t0) REVERT: K 123 ASP cc_start: 0.8246 (m-30) cc_final: 0.7747 (m-30) REVERT: L 65 MET cc_start: 0.8730 (mmt) cc_final: 0.8275 (mmt) outliers start: 41 outliers final: 26 residues processed: 306 average time/residue: 0.3904 time to fit residues: 164.4045 Evaluate side-chains 297 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 271 time to evaluate : 2.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 376 GLN Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 214 CYS Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 376 GLN Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 140 GLU Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 214 CYS Chi-restraints excluded: chain J residue 264 THR Chi-restraints excluded: chain J residue 363 HIS Chi-restraints excluded: chain J residue 376 GLN Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 140 GLU Chi-restraints excluded: chain K residue 145 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 0.8980 chunk 178 optimal weight: 2.9990 chunk 190 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 chunk 149 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 172 optimal weight: 6.9990 chunk 180 optimal weight: 0.2980 chunk 189 optimal weight: 0.6980 chunk 125 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 56 ASN ** K 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17820 Z= 0.152 Angle : 0.445 5.749 24072 Z= 0.236 Chirality : 0.037 0.123 2688 Planarity : 0.003 0.054 3028 Dihedral : 3.381 13.298 2396 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.69 % Allowed : 14.47 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.18), residues: 2140 helix: 2.05 (0.13), residues: 1628 sheet: None (None), residues: 0 loop : -0.53 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 379 HIS 0.003 0.001 HIS J 240 PHE 0.014 0.001 PHE G 332 TYR 0.011 0.001 TYR J 545 ARG 0.013 0.000 ARG K 127 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 282 time to evaluate : 2.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 TRP cc_start: 0.6830 (m-90) cc_final: 0.6392 (m100) REVERT: A 286 ASP cc_start: 0.8007 (t0) cc_final: 0.7669 (t0) REVERT: A 507 ARG cc_start: 0.8091 (mmt-90) cc_final: 0.6979 (mpt180) REVERT: A 528 LYS cc_start: 0.8220 (mttp) cc_final: 0.8000 (mmtm) REVERT: A 562 ARG cc_start: 0.8308 (ttp80) cc_final: 0.8045 (ttp80) REVERT: C 65 MET cc_start: 0.8727 (mmt) cc_final: 0.8254 (mmt) REVERT: D 158 TRP cc_start: 0.6831 (m-90) cc_final: 0.6389 (m100) REVERT: D 286 ASP cc_start: 0.8010 (t0) cc_final: 0.7650 (t0) REVERT: D 507 ARG cc_start: 0.8136 (mmt-90) cc_final: 0.7013 (mpt180) REVERT: D 528 LYS cc_start: 0.8246 (mttp) cc_final: 0.8033 (mmtm) REVERT: D 562 ARG cc_start: 0.8312 (ttp80) cc_final: 0.8036 (ttp80) REVERT: E 38 ARG cc_start: 0.8700 (mtm110) cc_final: 0.8429 (mtm110) REVERT: E 123 ASP cc_start: 0.8264 (m-30) cc_final: 0.7744 (m-30) REVERT: G 158 TRP cc_start: 0.6829 (m-90) cc_final: 0.6389 (m100) REVERT: G 286 ASP cc_start: 0.8010 (t0) cc_final: 0.7665 (t0) REVERT: G 507 ARG cc_start: 0.8137 (mmt-90) cc_final: 0.7014 (mpt180) REVERT: G 528 LYS cc_start: 0.8254 (mttp) cc_final: 0.8032 (mmtm) REVERT: G 562 ARG cc_start: 0.8314 (ttp80) cc_final: 0.8045 (ttp80) REVERT: H 38 ARG cc_start: 0.8697 (mtm110) cc_final: 0.8439 (mtm110) REVERT: H 54 ASN cc_start: 0.8585 (m110) cc_final: 0.8259 (m-40) REVERT: H 123 ASP cc_start: 0.8266 (m-30) cc_final: 0.7745 (m-30) REVERT: J 158 TRP cc_start: 0.6831 (m-90) cc_final: 0.6392 (m100) REVERT: J 286 ASP cc_start: 0.8012 (t0) cc_final: 0.7668 (t0) REVERT: J 376 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.8018 (mt0) REVERT: J 507 ARG cc_start: 0.8144 (mmt-90) cc_final: 0.7020 (mpt180) REVERT: J 528 LYS cc_start: 0.8221 (mttp) cc_final: 0.8006 (mmtm) REVERT: J 562 ARG cc_start: 0.8290 (ttp80) cc_final: 0.8012 (ttp80) REVERT: K 119 ASP cc_start: 0.7817 (t0) cc_final: 0.7577 (t0) REVERT: K 123 ASP cc_start: 0.8244 (m-30) cc_final: 0.7747 (m-30) REVERT: L 65 MET cc_start: 0.8719 (mmt) cc_final: 0.8247 (mmt) outliers start: 31 outliers final: 22 residues processed: 302 average time/residue: 0.4027 time to fit residues: 167.6308 Evaluate side-chains 297 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 274 time to evaluate : 2.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 376 GLN Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 214 CYS Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 376 GLN Chi-restraints excluded: chain H residue 140 GLU Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 214 CYS Chi-restraints excluded: chain J residue 264 THR Chi-restraints excluded: chain J residue 363 HIS Chi-restraints excluded: chain J residue 376 GLN Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 140 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 211 optimal weight: 0.0040 chunk 194 optimal weight: 0.9980 chunk 168 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 129 optimal weight: 0.1980 chunk 103 optimal weight: 0.6980 chunk 133 optimal weight: 3.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 56 ASN ** K 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17820 Z= 0.139 Angle : 0.446 7.672 24072 Z= 0.234 Chirality : 0.037 0.120 2688 Planarity : 0.003 0.056 3028 Dihedral : 3.320 13.229 2396 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.69 % Allowed : 14.74 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.18), residues: 2140 helix: 2.08 (0.13), residues: 1640 sheet: None (None), residues: 0 loop : -0.48 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 379 HIS 0.002 0.001 HIS G 240 PHE 0.013 0.001 PHE A 332 TYR 0.010 0.001 TYR J 545 ARG 0.014 0.000 ARG H 127 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 285 time to evaluate : 2.113 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 TRP cc_start: 0.6807 (m-90) cc_final: 0.6305 (m100) REVERT: A 286 ASP cc_start: 0.7992 (t0) cc_final: 0.7658 (t0) REVERT: A 507 ARG cc_start: 0.8101 (mmt-90) cc_final: 0.6956 (mpt180) REVERT: A 562 ARG cc_start: 0.8243 (ttp80) cc_final: 0.7983 (ttp80) REVERT: B 123 ASP cc_start: 0.8235 (m-30) cc_final: 0.7747 (m-30) REVERT: C 65 MET cc_start: 0.8717 (mmt) cc_final: 0.8259 (mmt) REVERT: D 158 TRP cc_start: 0.6804 (m-90) cc_final: 0.6301 (m100) REVERT: D 191 LEU cc_start: 0.8327 (tp) cc_final: 0.7918 (mm) REVERT: D 286 ASP cc_start: 0.7997 (t0) cc_final: 0.7656 (t0) REVERT: D 507 ARG cc_start: 0.8155 (mmt-90) cc_final: 0.6977 (mpt180) REVERT: D 562 ARG cc_start: 0.8306 (ttp80) cc_final: 0.8046 (ttp80) REVERT: E 38 ARG cc_start: 0.8676 (mtm110) cc_final: 0.8410 (mtm110) REVERT: F 65 MET cc_start: 0.8710 (mmt) cc_final: 0.8246 (mmt) REVERT: G 158 TRP cc_start: 0.6805 (m-90) cc_final: 0.6300 (m100) REVERT: G 286 ASP cc_start: 0.7997 (t0) cc_final: 0.7657 (t0) REVERT: G 376 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7953 (mt0) REVERT: G 507 ARG cc_start: 0.8157 (mmt-90) cc_final: 0.6979 (mpt180) REVERT: G 562 ARG cc_start: 0.8308 (ttp80) cc_final: 0.8048 (ttp80) REVERT: H 38 ARG cc_start: 0.8691 (mtm110) cc_final: 0.8433 (mtm110) REVERT: H 54 ASN cc_start: 0.8609 (m110) cc_final: 0.8296 (m-40) REVERT: I 65 MET cc_start: 0.8714 (mmt) cc_final: 0.8254 (mmt) REVERT: J 158 TRP cc_start: 0.6805 (m-90) cc_final: 0.6303 (m100) REVERT: J 286 ASP cc_start: 0.7996 (t0) cc_final: 0.7657 (t0) REVERT: J 507 ARG cc_start: 0.8162 (mmt-90) cc_final: 0.6986 (mpt180) REVERT: J 527 LYS cc_start: 0.8364 (ttmt) cc_final: 0.8113 (ttmt) REVERT: J 562 ARG cc_start: 0.8265 (ttp80) cc_final: 0.8036 (ttp80) REVERT: L 65 MET cc_start: 0.8721 (mmt) cc_final: 0.8264 (mmt) outliers start: 31 outliers final: 23 residues processed: 310 average time/residue: 0.4041 time to fit residues: 172.1581 Evaluate side-chains 296 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 272 time to evaluate : 2.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 376 GLN Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 214 CYS Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 376 GLN Chi-restraints excluded: chain H residue 10 ILE Chi-restraints excluded: chain H residue 140 GLU Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 214 CYS Chi-restraints excluded: chain J residue 264 THR Chi-restraints excluded: chain J residue 301 ASP Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 140 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 155 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 172 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 147 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.131726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.098583 restraints weight = 24486.922| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.40 r_work: 0.3113 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17820 Z= 0.191 Angle : 0.488 10.213 24072 Z= 0.254 Chirality : 0.038 0.128 2688 Planarity : 0.003 0.058 3028 Dihedral : 3.376 12.331 2396 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.86 % Allowed : 14.41 % Favored : 83.73 % 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: 2.22 (0.18), residues: 2140 helix: 2.02 (0.13), residues: 1648 sheet: None (None), residues: 0 loop : -0.37 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 379 HIS 0.003 0.001 HIS J 363 PHE 0.014 0.001 PHE J 332 TYR 0.014 0.001 TYR G 545 ARG 0.014 0.001 ARG B 127 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4349.72 seconds wall clock time: 79 minutes 7.26 seconds (4747.26 seconds total)