Starting phenix.real_space_refine on Tue Mar 19 13:26:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6x_28891/03_2024/8f6x_28891.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6x_28891/03_2024/8f6x_28891.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6x_28891/03_2024/8f6x_28891.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6x_28891/03_2024/8f6x_28891.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6x_28891/03_2024/8f6x_28891.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6x_28891/03_2024/8f6x_28891.pdb" } resolution = 3.25 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= 0.005 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9396 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 99 5.16 5 C 9336 2.51 5 N 2547 2.21 5 O 2970 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 336": "OD1" <-> "OD2" Residue "A GLU 349": "OE1" <-> "OE2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "B GLU 70": "OE1" <-> "OE2" Residue "B GLU 167": "OE1" <-> "OE2" Residue "B GLU 431": "OE1" <-> "OE2" Residue "C ASP 336": "OD1" <-> "OD2" Residue "C GLU 349": "OE1" <-> "OE2" Residue "C GLU 431": "OE1" <-> "OE2" Residue "E PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 112": "OD1" <-> "OD2" Residue "E GLU 229": "OE1" <-> "OE2" Residue "F ASP 59": "OD1" <-> "OD2" Residue "F ASP 112": "OD1" <-> "OD2" Residue "F GLU 229": "OE1" <-> "OE2" Residue "F TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 238": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14952 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3248 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 15, 'TRANS': 413} Chain: "B" Number of atoms: 3248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3248 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 15, 'TRANS': 413} Chain: "C" Number of atoms: 3248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3248 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 15, 'TRANS': 413} Chain: "D" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1722 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "E" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1722 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "F" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1722 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.87, per 1000 atoms: 0.53 Number of scatterers: 14952 At special positions: 0 Unit cell: (147.74, 141.1, 102.09, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 99 16.00 O 2970 8.00 N 2547 7.00 C 9336 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 28 " - pdb=" SG CYS A 407 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS B 249 " distance=2.03 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS A 249 " - pdb=" SG CYS C 84 " distance=2.03 Simple disulfide: pdb=" SG CYS A 283 " - pdb=" SG CYS A 311 " distance=2.03 Simple disulfide: pdb=" SG CYS A 292 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 335 " distance=2.03 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 390 " distance=2.03 Simple disulfide: pdb=" SG CYS A 454 " - pdb=" SG CYS A 458 " distance=2.03 Simple disulfide: pdb=" SG CYS B 28 " - pdb=" SG CYS B 407 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 182 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS C 249 " distance=2.03 Simple disulfide: pdb=" SG CYS B 140 " - pdb=" SG CYS B 147 " distance=2.03 Simple disulfide: pdb=" SG CYS B 283 " - pdb=" SG CYS B 311 " distance=2.03 Simple disulfide: pdb=" SG CYS B 292 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 326 " - pdb=" SG CYS B 335 " distance=2.03 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 384 " - pdb=" SG CYS B 390 " distance=2.03 Simple disulfide: pdb=" SG CYS B 454 " - pdb=" SG CYS B 458 " distance=2.03 Simple disulfide: pdb=" SG CYS C 28 " - pdb=" SG CYS C 407 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 182 " distance=2.03 Simple disulfide: pdb=" SG CYS C 140 " - pdb=" SG CYS C 147 " distance=2.03 Simple disulfide: pdb=" SG CYS C 283 " - pdb=" SG CYS C 311 " distance=2.03 Simple disulfide: pdb=" SG CYS C 292 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 326 " - pdb=" SG CYS C 335 " distance=2.03 Simple disulfide: pdb=" SG CYS C 350 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 384 " - pdb=" SG CYS C 390 " distance=2.03 Simple disulfide: pdb=" SG CYS C 454 " - pdb=" SG CYS C 458 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 166 " - pdb=" SG CYS D 234 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 166 " - pdb=" SG CYS E 234 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 166 " - pdb=" SG CYS F 234 " distance=2.03 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 Links applied NAG-ASN " NAG A 601 " - " ASN A 172 " " NAG B 601 " - " ASN B 172 " " NAG C 601 " - " ASN C 172 " Time building additional restraints: 5.45 Conformation dependent library (CDL) restraints added in 2.8 seconds 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3624 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 33 sheets defined 21.4% alpha, 32.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'A' and resid 67 through 84 removed outlier: 3.645A pdb=" N LYS A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N THR A 83 " --> pdb=" O ARG A 79 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N CYS A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 130 removed outlier: 3.618A pdb=" N ILE A 124 " --> pdb=" O ALA A 120 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 130 " --> pdb=" O LYS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 144 removed outlier: 4.368A pdb=" N THR A 143 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR A 144 " --> pdb=" O CYS A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 172 Processing helix chain 'A' and resid 172 through 177 Processing helix chain 'A' and resid 187 through 197 removed outlier: 3.730A pdb=" N VAL A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 210 Processing helix chain 'A' and resid 223 through 234 Processing helix chain 'A' and resid 237 through 247 Processing helix chain 'A' and resid 247 through 255 removed outlier: 3.666A pdb=" N VAL A 251 " --> pdb=" O ASN A 247 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG A 252 " --> pdb=" O ARG A 248 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ARG A 253 " --> pdb=" O CYS A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 352 Processing helix chain 'A' and resid 442 through 446 removed outlier: 3.776A pdb=" N PHE A 446 " --> pdb=" O SER A 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 81 Processing helix chain 'B' and resid 94 through 130 removed outlier: 3.638A pdb=" N ILE B 124 " --> pdb=" O ALA B 120 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR B 127 " --> pdb=" O ALA B 123 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU B 130 " --> pdb=" O LYS B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 144 removed outlier: 4.318A pdb=" N THR B 143 " --> pdb=" O GLY B 139 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR B 144 " --> pdb=" O CYS B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 172 Processing helix chain 'B' and resid 172 through 177 Processing helix chain 'B' and resid 187 through 197 removed outlier: 3.650A pdb=" N VAL B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 210 Processing helix chain 'B' and resid 223 through 234 Processing helix chain 'B' and resid 237 through 247 Processing helix chain 'B' and resid 247 through 255 removed outlier: 3.939A pdb=" N ARG B 253 " --> pdb=" O CYS B 249 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY B 255 " --> pdb=" O VAL B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 352 Processing helix chain 'B' and resid 442 through 446 removed outlier: 3.510A pdb=" N PHE B 446 " --> pdb=" O SER B 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 84 removed outlier: 3.708A pdb=" N LYS C 82 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR C 83 " --> pdb=" O ARG C 79 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N CYS C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 130 removed outlier: 3.610A pdb=" N ILE C 124 " --> pdb=" O ALA C 120 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR C 127 " --> pdb=" O ALA C 123 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU C 130 " --> pdb=" O LYS C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 144 removed outlier: 4.346A pdb=" N THR C 143 " --> pdb=" O GLY C 139 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR C 144 " --> pdb=" O CYS C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 172 removed outlier: 3.539A pdb=" N PHE C 168 " --> pdb=" O GLU C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 177 removed outlier: 3.880A pdb=" N ALA C 176 " --> pdb=" O LEU C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 197 removed outlier: 3.711A pdb=" N VAL C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 210 Processing helix chain 'C' and resid 223 through 234 Processing helix chain 'C' and resid 237 through 246 Processing helix chain 'C' and resid 247 through 255 removed outlier: 4.249A pdb=" N ARG C 253 " --> pdb=" O CYS C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 352 Processing helix chain 'C' and resid 442 through 446 removed outlier: 3.565A pdb=" N PHE C 446 " --> pdb=" O SER C 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 229 removed outlier: 3.664A pdb=" N ASP D 228 " --> pdb=" O GLN D 225 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU D 229 " --> pdb=" O ALA D 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 225 through 229' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.622A pdb=" N ASP E 90 " --> pdb=" O ARG E 87 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 91' Processing helix chain 'E' and resid 225 through 229 removed outlier: 3.859A pdb=" N GLU E 229 " --> pdb=" O ALA E 226 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 327 through 329 removed outlier: 3.790A pdb=" N HIS A 332 " --> pdb=" O ARG A 329 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N SER A 29 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA A 288 " --> pdb=" O SER A 29 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE A 31 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE A 286 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLU A 33 " --> pdb=" O TRP A 284 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TRP A 284 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N TYR A 35 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N SER A 37 " --> pdb=" O ASP A 280 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL A 278 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS A 312 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TRP A 309 " --> pdb=" O TYR A 320 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 327 through 329 removed outlier: 3.790A pdb=" N HIS A 332 " --> pdb=" O ARG A 329 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 146 through 150 removed outlier: 9.145A pdb=" N TRP A 43 " --> pdb=" O ARG A 156 " (cutoff:3.500A) removed outlier: 9.220A pdb=" N LEU A 158 " --> pdb=" O TRP A 43 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N THR A 45 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N THR A 160 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N VAL A 47 " --> pdb=" O THR A 160 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N SER A 266 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VAL A 262 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE A 268 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY A 257 " --> pdb=" O THR A 214 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 291 through 295 Processing sheet with id=AA5, first strand: chain 'A' and resid 372 through 374 Processing sheet with id=AA6, first strand: chain 'A' and resid 399 through 402 Processing sheet with id=AA7, first strand: chain 'B' and resid 327 through 329 removed outlier: 3.751A pdb=" N HIS B 332 " --> pdb=" O ARG B 329 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ILE B 31 " --> pdb=" O LYS B 287 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N LYS B 287 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N GLU B 33 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE B 285 " --> pdb=" O GLU B 33 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR B 35 " --> pdb=" O CYS B 283 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N THR B 281 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LEU B 39 " --> pdb=" O ILE B 279 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ILE B 279 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS B 312 " --> pdb=" O PRO B 282 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 327 through 329 removed outlier: 3.751A pdb=" N HIS B 332 " --> pdb=" O ARG B 329 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 146 through 150 removed outlier: 9.171A pdb=" N TRP B 43 " --> pdb=" O ARG B 156 " (cutoff:3.500A) removed outlier: 9.275A pdb=" N LEU B 158 " --> pdb=" O TRP B 43 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N THR B 45 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N THR B 160 " --> pdb=" O THR B 45 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N VAL B 47 " --> pdb=" O THR B 160 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N SER B 266 " --> pdb=" O VAL B 262 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL B 262 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE B 268 " --> pdb=" O ILE B 260 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY B 257 " --> pdb=" O THR B 214 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 291 through 295 Processing sheet with id=AB2, first strand: chain 'B' and resid 372 through 374 Processing sheet with id=AB3, first strand: chain 'B' and resid 398 through 402 removed outlier: 5.364A pdb=" N ILE B 399 " --> pdb=" O SER B 394 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N SER B 394 " --> pdb=" O ILE B 399 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 327 through 329 removed outlier: 3.728A pdb=" N HIS C 332 " --> pdb=" O ARG C 329 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N SER C 29 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ALA C 288 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE C 31 " --> pdb=" O ILE C 286 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE C 286 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLU C 33 " --> pdb=" O TRP C 284 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N TRP C 284 " --> pdb=" O GLU C 33 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N TYR C 35 " --> pdb=" O PRO C 282 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N SER C 37 " --> pdb=" O ASP C 280 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL C 278 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS C 312 " --> pdb=" O PRO C 282 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TRP C 309 " --> pdb=" O TYR C 320 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 327 through 329 removed outlier: 3.728A pdb=" N HIS C 332 " --> pdb=" O ARG C 329 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 146 through 150 removed outlier: 9.217A pdb=" N TRP C 43 " --> pdb=" O ARG C 156 " (cutoff:3.500A) removed outlier: 9.307A pdb=" N LEU C 158 " --> pdb=" O TRP C 43 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR C 45 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N THR C 160 " --> pdb=" O THR C 45 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N VAL C 47 " --> pdb=" O THR C 160 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N SER C 266 " --> pdb=" O VAL C 262 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL C 262 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE C 268 " --> pdb=" O ILE C 260 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE C 256 " --> pdb=" O GLN C 272 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY C 257 " --> pdb=" O THR C 214 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 291 through 295 removed outlier: 4.235A pdb=" N CYS C 458 " --> pdb=" O VAL C 363 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 372 through 374 Processing sheet with id=AB9, first strand: chain 'C' and resid 401 through 402 Processing sheet with id=AC1, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AC2, first strand: chain 'D' and resid 45 through 51 removed outlier: 6.558A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N SER D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N MET D 34 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER D 33 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 149 through 150 Processing sheet with id=AC4, first strand: chain 'D' and resid 153 through 154 removed outlier: 6.524A pdb=" N TRP D 181 " --> pdb=" O LEU D 193 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 153 through 154 Processing sheet with id=AC6, first strand: chain 'E' and resid 3 through 4 removed outlier: 3.513A pdb=" N GLN E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 45 through 51 removed outlier: 6.577A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N SER E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N MET E 34 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER E 33 " --> pdb=" O ALA E 99 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N CYS E 96 " --> pdb=" O TRP E 114 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N TRP E 114 " --> pdb=" O CYS E 96 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ARG E 98 " --> pdb=" O ASP E 112 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 45 through 51 removed outlier: 6.577A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N SER E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N MET E 34 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER E 33 " --> pdb=" O ALA E 99 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 149 through 150 removed outlier: 3.591A pdb=" N SER E 209 " --> pdb=" O ALA E 220 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 153 through 156 removed outlier: 6.879A pdb=" N VAL E 154 " --> pdb=" O THR E 252 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLN E 183 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N LEU E 192 " --> pdb=" O GLN E 183 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AD3, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.914A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 153 through 154 removed outlier: 6.568A pdb=" N TRP F 181 " --> pdb=" O LEU F 193 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 153 through 154 removed outlier: 3.613A pdb=" N SER F 236 " --> pdb=" O VAL F 244 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 162 through 165 668 hydrogen bonds defined for protein. 1692 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.98 Time building geometry restraints manager: 5.92 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: 4932 1.34 - 1.46: 3338 1.46 - 1.58: 6814 1.58 - 1.70: 0 1.70 - 1.81: 126 Bond restraints: 15210 Sorted by residual: bond pdb=" C1 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.406 1.470 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.43e+00 bond pdb=" C1 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.51e+00 bond pdb=" C5 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.35e+00 bond pdb=" C5 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.21e+00 ... (remaining 15205 not shown) Histogram of bond angle deviations from ideal: 99.76 - 106.60: 345 106.60 - 113.45: 8427 113.45 - 120.29: 5091 120.29 - 127.13: 6646 127.13 - 133.97: 119 Bond angle restraints: 20628 Sorted by residual: angle pdb=" C ASN C 172 " pdb=" CA ASN C 172 " pdb=" CB ASN C 172 " ideal model delta sigma weight residual 109.99 115.67 -5.68 1.74e+00 3.30e-01 1.06e+01 angle pdb=" CA VAL E 122 " pdb=" CB VAL E 122 " pdb=" CG1 VAL E 122 " ideal model delta sigma weight residual 110.40 114.14 -3.74 1.70e+00 3.46e-01 4.85e+00 angle pdb=" C SER C 170 " pdb=" N LYS C 171 " pdb=" CA LYS C 171 " ideal model delta sigma weight residual 122.60 118.48 4.12 1.88e+00 2.83e-01 4.81e+00 angle pdb=" CA LEU D 241 " pdb=" CB LEU D 241 " pdb=" CG LEU D 241 " ideal model delta sigma weight residual 116.30 123.90 -7.60 3.50e+00 8.16e-02 4.72e+00 angle pdb=" CA LEU B 381 " pdb=" CB LEU B 381 " pdb=" CG LEU B 381 " ideal model delta sigma weight residual 116.30 123.79 -7.49 3.50e+00 8.16e-02 4.58e+00 ... (remaining 20623 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 8354 17.97 - 35.95: 759 35.95 - 53.92: 119 53.92 - 71.90: 24 71.90 - 89.87: 17 Dihedral angle restraints: 9273 sinusoidal: 3600 harmonic: 5673 Sorted by residual: dihedral pdb=" CB CYS B 384 " pdb=" SG CYS B 384 " pdb=" SG CYS B 390 " pdb=" CB CYS B 390 " ideal model delta sinusoidal sigma weight residual 93.00 170.56 -77.56 1 1.00e+01 1.00e-02 7.53e+01 dihedral pdb=" CB CYS A 28 " pdb=" SG CYS A 28 " pdb=" SG CYS A 407 " pdb=" CB CYS A 407 " ideal model delta sinusoidal sigma weight residual 93.00 159.94 -66.94 1 1.00e+01 1.00e-02 5.84e+01 dihedral pdb=" CB CYS C 28 " pdb=" SG CYS C 28 " pdb=" SG CYS C 407 " pdb=" CB CYS C 407 " ideal model delta sinusoidal sigma weight residual 93.00 156.98 -63.98 1 1.00e+01 1.00e-02 5.39e+01 ... (remaining 9270 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2161 0.075 - 0.150: 225 0.150 - 0.225: 3 0.225 - 0.300: 1 0.300 - 0.375: 1 Chirality restraints: 2391 Sorted by residual: chirality pdb=" C1 NAG B 601 " pdb=" ND2 ASN B 172 " pdb=" C2 NAG B 601 " pdb=" O5 NAG B 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CA ASN C 172 " pdb=" N ASN C 172 " pdb=" C ASN C 172 " pdb=" CB ASN C 172 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" C1 NAG C 601 " pdb=" ND2 ASN C 172 " pdb=" C2 NAG C 601 " pdb=" O5 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 2388 not shown) Planarity restraints: 2655 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 172 " 0.001 2.00e-02 2.50e+03 3.73e-02 1.74e+01 pdb=" CG ASN C 172 " -0.047 2.00e-02 2.50e+03 pdb=" OD1 ASN C 172 " 0.045 2.00e-02 2.50e+03 pdb=" ND2 ASN C 172 " -0.037 2.00e-02 2.50e+03 pdb=" C1 NAG C 601 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 172 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.06e+00 pdb=" CG ASN C 172 " -0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN C 172 " 0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN C 172 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE C 451 " 0.037 5.00e-02 4.00e+02 5.61e-02 5.03e+00 pdb=" N PRO C 452 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO C 452 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 452 " 0.031 5.00e-02 4.00e+02 ... (remaining 2652 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 728 2.72 - 3.27: 14638 3.27 - 3.81: 24025 3.81 - 4.36: 29262 4.36 - 4.90: 52341 Nonbonded interactions: 120994 Sorted by model distance: nonbonded pdb=" OG SER B 37 " pdb=" OG1 THR B 281 " model vdw 2.181 2.440 nonbonded pdb=" OG SER A 37 " pdb=" OG1 THR A 281 " model vdw 2.193 2.440 nonbonded pdb=" OG SER C 37 " pdb=" OG1 THR C 281 " model vdw 2.198 2.440 nonbonded pdb=" OH TYR F 182 " pdb=" OE1 GLN F 235 " model vdw 2.235 2.440 nonbonded pdb=" OG SER C 237 " pdb=" OE1 GLN C 240 " model vdw 2.242 2.440 ... (remaining 120989 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 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.010 Extract box with map and model: 6.280 Check model and map are aligned: 0.230 Set scattering table: 0.130 Process input model: 40.440 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 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 : 0.002 0.064 15210 Z= 0.161 Angle : 0.512 7.601 20628 Z= 0.269 Chirality : 0.044 0.375 2391 Planarity : 0.004 0.056 2652 Dihedral : 13.801 89.874 5541 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.66 % Favored : 94.29 % Rotamer: Outliers : 0.06 % Allowed : 0.42 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.19), residues: 1962 helix: 0.38 (0.28), residues: 408 sheet: -0.42 (0.20), residues: 621 loop : -1.12 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 47 HIS 0.001 0.000 HIS B 368 PHE 0.011 0.001 PHE D 111 TYR 0.017 0.001 TYR C 385 ARG 0.004 0.000 ARG D 87 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 1.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 97 average time/residue: 0.3677 time to fit residues: 49.7157 Evaluate side-chains 58 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 1.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 10.0000 chunk 147 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 152 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 177 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 307 GLN ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 GLN ** B 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 ASN ** C 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 GLN D 199 ASN ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 GLN F 116 GLN F 150 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 15210 Z= 0.472 Angle : 0.638 7.430 20628 Z= 0.332 Chirality : 0.044 0.265 2391 Planarity : 0.004 0.055 2652 Dihedral : 4.957 59.542 2199 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.57 % Favored : 93.37 % Rotamer: Outliers : 0.12 % Allowed : 7.49 % Favored : 92.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.19), residues: 1962 helix: 0.54 (0.28), residues: 408 sheet: -0.32 (0.20), residues: 639 loop : -1.02 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 309 HIS 0.004 0.001 HIS B 368 PHE 0.010 0.001 PHE A 256 TYR 0.012 0.002 TYR C 385 ARG 0.004 0.000 ARG C 79 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 63 average time/residue: 0.2762 time to fit residues: 25.6272 Evaluate side-chains 50 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 49 time to evaluate : 1.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 244 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 147 optimal weight: 8.9990 chunk 120 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 177 optimal weight: 6.9990 chunk 191 optimal weight: 2.9990 chunk 157 optimal weight: 10.0000 chunk 175 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN B 457 ASN ** C 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 GLN ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 183 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15210 Z= 0.270 Angle : 0.521 7.503 20628 Z= 0.270 Chirality : 0.042 0.224 2391 Planarity : 0.004 0.057 2652 Dihedral : 4.588 51.143 2199 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.17 % Favored : 93.78 % Rotamer: Outliers : 0.66 % Allowed : 9.24 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.19), residues: 1962 helix: 0.81 (0.28), residues: 408 sheet: -0.20 (0.21), residues: 627 loop : -0.98 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 181 HIS 0.004 0.001 HIS B 368 PHE 0.007 0.001 PHE D 95 TYR 0.013 0.001 TYR C 385 ARG 0.005 0.000 ARG E 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 54 time to evaluate : 1.722 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 63 average time/residue: 0.3021 time to fit residues: 29.4625 Evaluate side-chains 47 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 43 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 244 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 175 optimal weight: 10.0000 chunk 133 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 119 optimal weight: 0.8980 chunk 178 optimal weight: 6.9990 chunk 188 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 chunk 168 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 ASN C 368 HIS ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 15210 Z= 0.381 Angle : 0.567 8.894 20628 Z= 0.293 Chirality : 0.042 0.203 2391 Planarity : 0.004 0.060 2652 Dihedral : 4.485 50.943 2199 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.17 % Favored : 93.78 % Rotamer: Outliers : 0.85 % Allowed : 10.87 % Favored : 88.29 % 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: -0.56 (0.19), residues: 1962 helix: 0.75 (0.27), residues: 408 sheet: -0.32 (0.20), residues: 645 loop : -0.85 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 309 HIS 0.005 0.001 HIS B 368 PHE 0.009 0.001 PHE D 95 TYR 0.009 0.001 TYR C 385 ARG 0.003 0.000 ARG C 79 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 50 time to evaluate : 1.784 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 11 residues processed: 62 average time/residue: 0.2811 time to fit residues: 27.2813 Evaluate side-chains 56 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 45 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 140 CYS Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain F residue 238 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 156 optimal weight: 6.9990 chunk 106 optimal weight: 0.3980 chunk 2 optimal weight: 1.9990 chunk 140 optimal weight: 7.9990 chunk 77 optimal weight: 8.9990 chunk 160 optimal weight: 8.9990 chunk 130 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 chunk 169 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15210 Z= 0.263 Angle : 0.518 8.186 20628 Z= 0.266 Chirality : 0.042 0.195 2391 Planarity : 0.004 0.056 2652 Dihedral : 4.318 50.988 2199 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.27 % Favored : 93.68 % Rotamer: Outliers : 1.09 % Allowed : 11.78 % Favored : 87.14 % 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: -0.20 (0.20), residues: 1962 helix: 1.29 (0.28), residues: 384 sheet: -0.27 (0.21), residues: 633 loop : -0.55 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 47 HIS 0.005 0.001 HIS B 368 PHE 0.006 0.001 PHE D 95 TYR 0.009 0.001 TYR C 385 ARG 0.002 0.000 ARG D 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 51 time to evaluate : 1.718 Fit side-chains revert: symmetry clash REVERT: D 34 MET cc_start: 0.7053 (mmm) cc_final: 0.6781 (mmp) outliers start: 18 outliers final: 15 residues processed: 68 average time/residue: 0.2805 time to fit residues: 30.1172 Evaluate side-chains 60 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 45 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 140 CYS Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain F residue 238 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 63 optimal weight: 10.0000 chunk 169 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 110 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 188 optimal weight: 9.9990 chunk 156 optimal weight: 9.9990 chunk 87 optimal weight: 9.9990 chunk 15 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15210 Z= 0.283 Angle : 0.518 8.518 20628 Z= 0.266 Chirality : 0.042 0.187 2391 Planarity : 0.004 0.055 2652 Dihedral : 4.267 51.100 2199 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.47 % Favored : 93.48 % Rotamer: Outliers : 1.39 % Allowed : 12.02 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.20), residues: 1962 helix: 1.31 (0.28), residues: 384 sheet: -0.24 (0.21), residues: 633 loop : -0.53 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 47 HIS 0.005 0.001 HIS B 368 PHE 0.006 0.001 PHE A 456 TYR 0.008 0.001 TYR C 385 ARG 0.002 0.000 ARG C 79 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 48 time to evaluate : 1.703 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 18 residues processed: 70 average time/residue: 0.2799 time to fit residues: 30.6260 Evaluate side-chains 60 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 42 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 140 CYS Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain F residue 238 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 181 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 chunk 158 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 187 optimal weight: 10.0000 chunk 117 optimal weight: 5.9990 chunk 114 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 15210 Z= 0.300 Angle : 0.532 9.623 20628 Z= 0.272 Chirality : 0.042 0.184 2391 Planarity : 0.004 0.058 2652 Dihedral : 4.274 51.157 2199 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.57 % Favored : 93.37 % Rotamer: Outliers : 1.27 % Allowed : 12.92 % Favored : 85.81 % 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: -0.12 (0.20), residues: 1962 helix: 1.32 (0.28), residues: 381 sheet: -0.17 (0.21), residues: 624 loop : -0.51 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 47 HIS 0.006 0.001 HIS B 368 PHE 0.008 0.001 PHE C 451 TYR 0.007 0.001 TYR C 385 ARG 0.002 0.000 ARG F 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 48 time to evaluate : 1.888 Fit side-chains revert: symmetry clash REVERT: D 34 MET cc_start: 0.7031 (mmm) cc_final: 0.6715 (mmp) outliers start: 21 outliers final: 18 residues processed: 68 average time/residue: 0.2652 time to fit residues: 28.5859 Evaluate side-chains 59 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 41 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 140 CYS Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain F residue 238 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 116 optimal weight: 20.0000 chunk 75 optimal weight: 8.9990 chunk 112 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 119 optimal weight: 10.0000 chunk 128 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 17 optimal weight: 0.5980 chunk 147 optimal weight: 10.0000 chunk 170 optimal weight: 5.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15210 Z= 0.349 Angle : 0.559 8.386 20628 Z= 0.286 Chirality : 0.042 0.182 2391 Planarity : 0.004 0.059 2652 Dihedral : 4.350 51.233 2199 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.68 % Favored : 93.27 % Rotamer: Outliers : 1.21 % Allowed : 13.29 % Favored : 85.51 % 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: -0.20 (0.20), residues: 1962 helix: 1.22 (0.28), residues: 381 sheet: -0.21 (0.21), residues: 624 loop : -0.55 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 47 HIS 0.007 0.001 HIS B 368 PHE 0.008 0.001 PHE F 95 TYR 0.009 0.001 TYR C 385 ARG 0.002 0.000 ARG C 79 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 47 time to evaluate : 1.727 Fit side-chains revert: symmetry clash REVERT: D 34 MET cc_start: 0.7139 (mmm) cc_final: 0.6849 (mmp) outliers start: 20 outliers final: 19 residues processed: 66 average time/residue: 0.2891 time to fit residues: 30.0040 Evaluate side-chains 62 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 43 time to evaluate : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 140 CYS Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain F residue 238 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 180 optimal weight: 9.9990 chunk 164 optimal weight: 6.9990 chunk 175 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 53 optimal weight: 0.0040 chunk 158 optimal weight: 5.9990 chunk 165 optimal weight: 0.9990 chunk 174 optimal weight: 7.9990 chunk 115 optimal weight: 1.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN B 457 ASN C 455 GLN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15210 Z= 0.175 Angle : 0.500 7.945 20628 Z= 0.254 Chirality : 0.042 0.181 2391 Planarity : 0.004 0.058 2652 Dihedral : 4.144 51.398 2199 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.07 % Favored : 93.88 % Rotamer: Outliers : 1.15 % Allowed : 13.35 % Favored : 85.51 % 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: -0.04 (0.20), residues: 1962 helix: 1.54 (0.29), residues: 384 sheet: -0.14 (0.21), residues: 627 loop : -0.52 (0.21), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 47 HIS 0.006 0.001 HIS B 368 PHE 0.041 0.001 PHE A 446 TYR 0.010 0.001 TYR C 385 ARG 0.002 0.000 ARG F 72 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 50 time to evaluate : 1.821 Fit side-chains revert: symmetry clash REVERT: D 34 MET cc_start: 0.7072 (mmm) cc_final: 0.6800 (mmp) outliers start: 19 outliers final: 18 residues processed: 67 average time/residue: 0.2827 time to fit residues: 29.4597 Evaluate side-chains 64 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 46 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 140 CYS Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain F residue 238 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 185 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 chunk 87 optimal weight: 9.9990 chunk 128 optimal weight: 10.0000 chunk 194 optimal weight: 10.0000 chunk 178 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15210 Z= 0.303 Angle : 0.544 8.555 20628 Z= 0.278 Chirality : 0.042 0.185 2391 Planarity : 0.004 0.059 2652 Dihedral : 4.220 51.449 2199 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.42 % Favored : 93.53 % Rotamer: Outliers : 1.33 % Allowed : 13.16 % Favored : 85.51 % 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: -0.07 (0.20), residues: 1962 helix: 1.37 (0.28), residues: 381 sheet: -0.13 (0.21), residues: 624 loop : -0.50 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 47 HIS 0.007 0.001 HIS B 368 PHE 0.010 0.001 PHE A 446 TYR 0.010 0.001 TYR C 385 ARG 0.002 0.000 ARG C 79 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 47 time to evaluate : 1.769 Fit side-chains revert: symmetry clash REVERT: D 34 MET cc_start: 0.7110 (mmm) cc_final: 0.6831 (mmp) outliers start: 22 outliers final: 19 residues processed: 66 average time/residue: 0.2827 time to fit residues: 29.4779 Evaluate side-chains 66 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 47 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 140 CYS Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain F residue 238 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 142 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 154 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 0.0270 chunk 136 optimal weight: 0.9990 overall best weight: 1.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.038787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.028038 restraints weight = 91130.226| |-----------------------------------------------------------------------------| r_work (start): 0.2685 rms_B_bonded: 4.74 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15210 Z= 0.146 Angle : 0.510 9.292 20628 Z= 0.255 Chirality : 0.042 0.180 2391 Planarity : 0.003 0.060 2652 Dihedral : 4.061 51.734 2199 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.86 % Favored : 94.09 % Rotamer: Outliers : 1.09 % Allowed : 13.35 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.20), residues: 1962 helix: 1.64 (0.29), residues: 384 sheet: -0.12 (0.21), residues: 627 loop : -0.49 (0.21), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 47 HIS 0.005 0.001 HIS B 368 PHE 0.023 0.001 PHE A 446 TYR 0.011 0.001 TYR C 385 ARG 0.003 0.000 ARG F 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2185.32 seconds wall clock time: 44 minutes 13.03 seconds (2653.03 seconds total)