Starting phenix.real_space_refine on Sat Jul 4 17:47:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8f6x_28891/07_2026/8f6x_28891.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f6x_28891/07_2026/8f6x_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8f6x_28891/07_2026/8f6x_28891.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8f6x_28891/07_2026/8f6x_28891.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8f6x_28891/07_2026/8f6x_28891.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f6x_28891/07_2026/8f6x_28891.map" model { file = "/net/cci-nas-00/data/ceres_data/8f6x_28891/07_2026/8f6x_28891.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f6x_28891/07_2026/8f6x_28891.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } 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. Time to flip 18 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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 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 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 chiralities: 1 Time building chain proxies: 3.60, per 1000 atoms: 0.24 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 - 3.00 Amino acid : True - 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: 1.15 Conformation dependent library (CDL) restraints added in 773.2 milliseconds 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: 0.42 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: 2.92 Time building geometry restraints manager: 1.63 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: 0.00 - 1.52: 20229 1.52 - 3.04: 332 3.04 - 4.56: 57 4.56 - 6.08: 4 6.08 - 7.60: 6 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: 8299 17.97 - 35.95: 755 35.95 - 53.92: 118 53.92 - 71.90: 21 71.90 - 89.87: 17 Dihedral angle restraints: 9210 sinusoidal: 3537 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 9207 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 3.040 nonbonded pdb=" OG SER A 37 " pdb=" OG1 THR A 281 " model vdw 2.193 3.040 nonbonded pdb=" OG SER C 37 " pdb=" OG1 THR C 281 " model vdw 2.198 3.040 nonbonded pdb=" OH TYR F 182 " pdb=" OE1 GLN F 235 " model vdw 2.235 3.040 nonbonded pdb=" OG SER C 237 " pdb=" OE1 GLN C 240 " model vdw 2.242 3.040 ... (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 Time spend for trying shortcut: 0.01 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.580 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 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 15249 Z= 0.114 Angle : 0.528 13.173 20709 Z= 0.273 Chirality : 0.044 0.375 2391 Planarity : 0.004 0.056 2652 Dihedral : 13.777 89.874 5478 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.004 0.000 ARG D 87 TYR 0.017 0.001 TYR C 385 PHE 0.011 0.001 PHE D 111 TRP 0.009 0.001 TRP D 47 HIS 0.001 0.000 HIS B 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (15210) covalent geometry : angle 0.51248 / 0.27 (20628) SS BOND : bond 0.00282 / 0.16 ( 36) SS BOND : angle 1.10364 / 0.75 ( 72) hydrogen bonds : bond 0.12596 / 8.17 ( 631) hydrogen bonds : angle 5.94111 / 4.25 ( 1692) link_NAG-ASN : bond 0.01046 / 0.50 ( 3) link_NAG-ASN : angle 5.55729 / 3.01 ( 9) *********************** 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 to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 0.596 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: 0.1554 time to fit residues: 21.4317 Evaluate side-chains 58 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 8.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 455 GLN B 457 ASN C 351 ASN ** C 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN D 82 GLN D 150 GLN D 183 GLN D 199 ASN ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 GLN E 183 GLN F 150 GLN F 183 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.038584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.027591 restraints weight = 89311.875| |-----------------------------------------------------------------------------| r_work (start): 0.2661 rms_B_bonded: 4.67 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 15249 Z= 0.233 Angle : 0.584 6.872 20709 Z= 0.303 Chirality : 0.043 0.242 2391 Planarity : 0.004 0.056 2652 Dihedral : 4.095 19.503 2136 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.86 % Favored : 94.09 % Rotamer: Outliers : 0.12 % Allowed : 6.70 % Favored : 93.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.19), residues: 1962 helix: 0.75 (0.28), residues: 411 sheet: -0.27 (0.20), residues: 621 loop : -1.08 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 72 TYR 0.013 0.001 TYR C 385 PHE 0.009 0.001 PHE D 111 TRP 0.006 0.001 TRP B 309 HIS 0.002 0.001 HIS B 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.23 (15210) covalent geometry : angle 0.57694 / 0.30 (20628) SS BOND : bond 0.00308 / 0.20 ( 36) SS BOND : angle 1.10236 / 0.76 ( 72) hydrogen bonds : bond 0.03274 / 2.24 ( 631) hydrogen bonds : angle 5.04515 / 3.59 ( 1692) link_NAG-ASN : bond 0.00512 / 0.25 ( 3) link_NAG-ASN : angle 3.30577 / 1.70 ( 9) *********************** 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 66 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 250 MET cc_start: 0.8839 (tpp) cc_final: 0.8459 (mmm) REVERT: A 372 MET cc_start: 0.8588 (ppp) cc_final: 0.8283 (ppp) REVERT: B 372 MET cc_start: 0.8440 (ppp) cc_final: 0.8182 (ppp) REVERT: C 372 MET cc_start: 0.8494 (ppp) cc_final: 0.8208 (ppp) REVERT: D 34 MET cc_start: 0.8485 (mmm) cc_final: 0.8171 (mmm) REVERT: D 46 GLU cc_start: 0.8383 (tt0) cc_final: 0.7969 (pt0) REVERT: D 83 MET cc_start: 0.9322 (mtm) cc_final: 0.8565 (mpp) REVERT: D 229 GLU cc_start: 0.9016 (tm-30) cc_final: 0.8666 (tp30) REVERT: E 34 MET cc_start: 0.8876 (mmm) cc_final: 0.8524 (mmm) REVERT: E 46 GLU cc_start: 0.8738 (tt0) cc_final: 0.8433 (tt0) REVERT: E 83 MET cc_start: 0.9301 (mtm) cc_final: 0.8580 (mpp) REVERT: E 113 ILE cc_start: 0.9292 (mm) cc_final: 0.9073 (mt) REVERT: F 46 GLU cc_start: 0.8350 (tt0) cc_final: 0.7854 (pt0) REVERT: F 229 GLU cc_start: 0.8869 (pp20) cc_final: 0.8610 (pp20) outliers start: 2 outliers final: 1 residues processed: 65 average time/residue: 0.1505 time to fit residues: 14.3646 Evaluate side-chains 54 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.636 ------------------------------------------------------------------------------- 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 138 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 chunk 143 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 144 optimal weight: 8.9990 chunk 63 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 188 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 79 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 351 ASN ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.037826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.026842 restraints weight = 91579.333| |-----------------------------------------------------------------------------| r_work (start): 0.2632 rms_B_bonded: 4.73 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 15249 Z= 0.232 Angle : 0.551 7.004 20709 Z= 0.287 Chirality : 0.043 0.204 2391 Planarity : 0.004 0.052 2652 Dihedral : 4.064 18.717 2136 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.91 % Favored : 94.04 % Rotamer: Outliers : 0.72 % Allowed : 8.70 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.19), residues: 1962 helix: 0.75 (0.28), residues: 408 sheet: -0.29 (0.20), residues: 639 loop : -0.92 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 72 TYR 0.011 0.001 TYR C 385 PHE 0.009 0.001 PHE D 95 TRP 0.005 0.001 TRP B 309 HIS 0.005 0.001 HIS B 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.23 (15210) covalent geometry : angle 0.54637 / 0.29 (20628) SS BOND : bond 0.00304 / 0.19 ( 36) SS BOND : angle 0.98942 / 0.70 ( 72) hydrogen bonds : bond 0.02974 / 2.03 ( 631) hydrogen bonds : angle 4.85809 / 3.45 ( 1692) link_NAG-ASN : bond 0.00278 / 0.14 ( 3) link_NAG-ASN : angle 2.62091 / 1.28 ( 9) *********************** 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 72 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 ASP cc_start: 0.9172 (OUTLIER) cc_final: 0.8519 (t0) REVERT: A 372 MET cc_start: 0.8614 (ppp) cc_final: 0.8258 (ppp) REVERT: B 372 MET cc_start: 0.8566 (ppp) cc_final: 0.8210 (ppp) REVERT: C 270 MET cc_start: 0.8685 (ptm) cc_final: 0.8389 (ppp) REVERT: C 280 ASP cc_start: 0.9164 (OUTLIER) cc_final: 0.8765 (t0) REVERT: C 372 MET cc_start: 0.8560 (ppp) cc_final: 0.8172 (ppp) REVERT: D 34 MET cc_start: 0.8570 (mmm) cc_final: 0.8291 (mmm) REVERT: D 46 GLU cc_start: 0.8377 (tt0) cc_final: 0.8059 (pt0) REVERT: D 83 MET cc_start: 0.9284 (mtm) cc_final: 0.8480 (mpp) REVERT: D 229 GLU cc_start: 0.9115 (tm-30) cc_final: 0.8809 (tm-30) REVERT: E 34 MET cc_start: 0.8885 (mmm) cc_final: 0.8624 (mmm) REVERT: E 46 GLU cc_start: 0.8651 (tt0) cc_final: 0.8275 (tt0) REVERT: E 83 MET cc_start: 0.9287 (mtm) cc_final: 0.8593 (mpp) REVERT: F 13 LYS cc_start: 0.9560 (tppt) cc_final: 0.9358 (tppt) REVERT: F 46 GLU cc_start: 0.8320 (tt0) cc_final: 0.7924 (pt0) REVERT: F 83 MET cc_start: 0.8939 (mpp) cc_final: 0.8665 (mpp) REVERT: F 229 GLU cc_start: 0.9052 (pp20) cc_final: 0.8836 (pp20) outliers start: 12 outliers final: 4 residues processed: 69 average time/residue: 0.1379 time to fit residues: 14.6049 Evaluate side-chains 60 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 280 ASP 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 150 optimal weight: 10.0000 chunk 189 optimal weight: 0.9990 chunk 170 optimal weight: 7.9990 chunk 11 optimal weight: 20.0000 chunk 169 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 190 optimal weight: 9.9990 chunk 175 optimal weight: 4.9990 chunk 145 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 126 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 ASN ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN ** D 160 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.036983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.026163 restraints weight = 92795.881| |-----------------------------------------------------------------------------| r_work (start): 0.2604 rms_B_bonded: 4.69 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 15249 Z= 0.293 Angle : 0.586 7.437 20709 Z= 0.304 Chirality : 0.043 0.185 2391 Planarity : 0.004 0.067 2652 Dihedral : 4.177 18.557 2136 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.27 % Favored : 93.68 % Rotamer: Outliers : 0.66 % Allowed : 10.57 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.19), residues: 1962 helix: 0.69 (0.28), residues: 408 sheet: -0.33 (0.20), residues: 639 loop : -0.90 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 72 TYR 0.009 0.001 TYR D 195 PHE 0.010 0.001 PHE D 95 TRP 0.005 0.001 TRP B 309 HIS 0.006 0.001 HIS B 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00627 / 0.29 (15210) covalent geometry : angle 0.58063 / 0.30 (20628) SS BOND : bond 0.00403 / 0.27 ( 36) SS BOND : angle 1.23171 / 0.93 ( 72) hydrogen bonds : bond 0.03076 / 2.12 ( 631) hydrogen bonds : angle 5.01326 / 3.56 ( 1692) link_NAG-ASN : bond 0.00383 / 0.19 ( 3) link_NAG-ASN : angle 2.42997 / 1.18 ( 9) *********************** 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 to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.709 Fit side-chains revert: symmetry clash REVERT: A 280 ASP cc_start: 0.9144 (OUTLIER) cc_final: 0.8481 (t0) REVERT: A 372 MET cc_start: 0.8695 (ppp) cc_final: 0.8341 (ppp) REVERT: B 372 MET cc_start: 0.8674 (ppp) cc_final: 0.8296 (ppp) REVERT: C 270 MET cc_start: 0.8718 (ptm) cc_final: 0.8501 (ptm) REVERT: C 280 ASP cc_start: 0.9201 (OUTLIER) cc_final: 0.8532 (t0) REVERT: C 372 MET cc_start: 0.8637 (ppp) cc_final: 0.8218 (ppp) REVERT: D 34 MET cc_start: 0.8595 (mmm) cc_final: 0.8357 (mmm) REVERT: D 46 GLU cc_start: 0.8371 (tt0) cc_final: 0.7992 (pt0) REVERT: D 83 MET cc_start: 0.9240 (mtm) cc_final: 0.8507 (mpp) REVERT: D 229 GLU cc_start: 0.9159 (tm-30) cc_final: 0.8862 (tm-30) REVERT: E 13 LYS cc_start: 0.9596 (tppt) cc_final: 0.9293 (tppt) REVERT: E 34 MET cc_start: 0.8874 (mmm) cc_final: 0.8579 (mmm) REVERT: E 46 GLU cc_start: 0.8585 (tt0) cc_final: 0.8100 (tt0) REVERT: E 83 MET cc_start: 0.9216 (mtm) cc_final: 0.8526 (mpp) REVERT: F 46 GLU cc_start: 0.8368 (tt0) cc_final: 0.7964 (pt0) REVERT: F 83 MET cc_start: 0.8971 (mpp) cc_final: 0.8719 (mpp) outliers start: 11 outliers final: 7 residues processed: 63 average time/residue: 0.1298 time to fit residues: 12.5804 Evaluate side-chains 52 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 244 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 83 optimal weight: 20.0000 chunk 89 optimal weight: 9.9990 chunk 22 optimal weight: 0.9980 chunk 32 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 chunk 114 optimal weight: 0.0050 chunk 168 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 166 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 135 optimal weight: 5.9990 overall best weight: 1.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 ASN B 422 ASN ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.038268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.027395 restraints weight = 90946.641| |-----------------------------------------------------------------------------| r_work (start): 0.2663 rms_B_bonded: 4.74 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15249 Z= 0.105 Angle : 0.487 7.302 20709 Z= 0.252 Chirality : 0.043 0.196 2391 Planarity : 0.004 0.056 2652 Dihedral : 3.903 18.410 2136 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.10 % Favored : 94.85 % Rotamer: Outliers : 0.60 % Allowed : 11.41 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.20), residues: 1962 helix: 1.58 (0.29), residues: 381 sheet: -0.25 (0.20), residues: 642 loop : -0.54 (0.21), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 87 TYR 0.010 0.001 TYR C 385 PHE 0.011 0.001 PHE B 464 TRP 0.005 0.001 TRP E 181 HIS 0.004 0.001 HIS B 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 (15210) covalent geometry : angle 0.48333 / 0.25 (20628) SS BOND : bond 0.00247 / 0.15 ( 36) SS BOND : angle 0.83054 / 0.58 ( 72) hydrogen bonds : bond 0.02453 / 1.68 ( 631) hydrogen bonds : angle 4.54705 / 3.24 ( 1692) link_NAG-ASN : bond 0.00317 / 0.16 ( 3) link_NAG-ASN : angle 2.03805 / 0.98 ( 9) *********************** 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 67 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 280 ASP cc_start: 0.9154 (OUTLIER) cc_final: 0.8629 (t0) REVERT: A 372 MET cc_start: 0.8755 (ppp) cc_final: 0.8298 (ppp) REVERT: B 372 MET cc_start: 0.8724 (ppp) cc_final: 0.8322 (ppp) REVERT: C 280 ASP cc_start: 0.9109 (OUTLIER) cc_final: 0.8777 (t0) REVERT: C 372 MET cc_start: 0.8707 (ppp) cc_final: 0.8130 (ppp) REVERT: D 34 MET cc_start: 0.8522 (mmm) cc_final: 0.8302 (mmm) REVERT: D 46 GLU cc_start: 0.8319 (tt0) cc_final: 0.7936 (pt0) REVERT: D 83 MET cc_start: 0.9262 (mtm) cc_final: 0.8529 (mpp) REVERT: D 229 GLU cc_start: 0.9181 (tm-30) cc_final: 0.8866 (tm-30) REVERT: E 13 LYS cc_start: 0.9618 (tppt) cc_final: 0.9328 (tppt) REVERT: E 34 MET cc_start: 0.8871 (mmm) cc_final: 0.8559 (mmm) REVERT: E 46 GLU cc_start: 0.8542 (tt0) cc_final: 0.8120 (tt0) REVERT: E 83 MET cc_start: 0.9259 (mtm) cc_final: 0.8644 (mpp) REVERT: F 46 GLU cc_start: 0.8284 (tt0) cc_final: 0.7951 (pt0) REVERT: F 83 MET cc_start: 0.9095 (mpp) cc_final: 0.8857 (mpp) REVERT: F 116 GLN cc_start: 0.9099 (tp40) cc_final: 0.8587 (tp40) outliers start: 10 outliers final: 5 residues processed: 65 average time/residue: 0.1340 time to fit residues: 13.3529 Evaluate side-chains 57 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 244 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 5 optimal weight: 6.9990 chunk 178 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 134 optimal weight: 6.9990 chunk 41 optimal weight: 0.6980 chunk 42 optimal weight: 10.0000 chunk 126 optimal weight: 9.9990 chunk 49 optimal weight: 20.0000 chunk 138 optimal weight: 8.9990 chunk 173 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 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 = 0.3111 r_free = 0.3111 target = 0.037862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.026934 restraints weight = 91664.883| |-----------------------------------------------------------------------------| r_work (start): 0.2645 rms_B_bonded: 4.74 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15249 Z= 0.160 Angle : 0.514 7.693 20709 Z= 0.267 Chirality : 0.042 0.183 2391 Planarity : 0.004 0.054 2652 Dihedral : 3.856 18.007 2136 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.81 % Favored : 94.14 % Rotamer: Outliers : 0.66 % Allowed : 12.50 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.20), residues: 1962 helix: 1.44 (0.29), residues: 384 sheet: -0.20 (0.20), residues: 639 loop : -0.46 (0.21), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 72 TYR 0.010 0.001 TYR C 385 PHE 0.007 0.001 PHE F 95 TRP 0.005 0.001 TRP F 47 HIS 0.004 0.001 HIS B 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (15210) covalent geometry : angle 0.50429 / 0.26 (20628) SS BOND : bond 0.00300 / 0.17 ( 36) SS BOND : angle 1.65788 / 1.02 ( 72) hydrogen bonds : bond 0.02698 / 1.83 ( 631) hydrogen bonds : angle 4.60746 / 3.29 ( 1692) link_NAG-ASN : bond 0.00237 / 0.12 ( 3) link_NAG-ASN : angle 1.87839 / 0.90 ( 9) *********************** 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 65 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 280 ASP cc_start: 0.9137 (OUTLIER) cc_final: 0.8630 (t0) REVERT: A 372 MET cc_start: 0.8761 (ppp) cc_final: 0.8307 (ppp) REVERT: B 372 MET cc_start: 0.8754 (ppp) cc_final: 0.8355 (ppp) REVERT: C 280 ASP cc_start: 0.9124 (OUTLIER) cc_final: 0.8791 (t0) REVERT: C 372 MET cc_start: 0.8711 (ppp) cc_final: 0.8138 (ppp) REVERT: D 46 GLU cc_start: 0.8332 (tt0) cc_final: 0.7953 (pt0) REVERT: D 83 MET cc_start: 0.9266 (mtm) cc_final: 0.8541 (mpp) REVERT: D 229 GLU cc_start: 0.9209 (tm-30) cc_final: 0.8898 (tm-30) REVERT: E 13 LYS cc_start: 0.9633 (tppt) cc_final: 0.9318 (tppt) REVERT: E 34 MET cc_start: 0.8869 (mmm) cc_final: 0.8589 (mmm) REVERT: E 46 GLU cc_start: 0.8553 (tt0) cc_final: 0.8120 (tt0) REVERT: E 83 MET cc_start: 0.9227 (mtm) cc_final: 0.8570 (mpp) REVERT: F 46 GLU cc_start: 0.8265 (tt0) cc_final: 0.7936 (pt0) REVERT: F 83 MET cc_start: 0.9112 (mpp) cc_final: 0.8895 (mpp) REVERT: F 116 GLN cc_start: 0.9152 (tp40) cc_final: 0.8637 (tp40) outliers start: 11 outliers final: 8 residues processed: 63 average time/residue: 0.1217 time to fit residues: 11.7125 Evaluate side-chains 58 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 244 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 143 optimal weight: 5.9990 chunk 60 optimal weight: 8.9990 chunk 160 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 98 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 36 optimal weight: 0.0040 chunk 77 optimal weight: 10.0000 chunk 33 optimal weight: 0.0870 chunk 30 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 overall best weight: 2.0174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 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 = 0.3122 r_free = 0.3122 target = 0.038291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.027554 restraints weight = 89492.044| |-----------------------------------------------------------------------------| r_work (start): 0.2709 rms_B_bonded: 4.67 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15249 Z= 0.128 Angle : 0.488 7.044 20709 Z= 0.252 Chirality : 0.042 0.175 2391 Planarity : 0.003 0.056 2652 Dihedral : 3.792 18.274 2136 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.40 % Favored : 94.55 % Rotamer: Outliers : 1.03 % Allowed : 12.56 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.20), residues: 1962 helix: 1.49 (0.29), residues: 384 sheet: -0.23 (0.21), residues: 642 loop : -0.45 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 72 TYR 0.009 0.001 TYR C 385 PHE 0.007 0.001 PHE D 208 TRP 0.005 0.001 TRP D 36 HIS 0.004 0.001 HIS B 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (15210) covalent geometry : angle 0.48243 / 0.25 (20628) SS BOND : bond 0.00272 / 0.15 ( 36) SS BOND : angle 1.14367 / 0.72 ( 72) hydrogen bonds : bond 0.02518 / 1.72 ( 631) hydrogen bonds : angle 4.48390 / 3.20 ( 1692) link_NAG-ASN : bond 0.00261 / 0.13 ( 3) link_NAG-ASN : angle 1.75761 / 0.84 ( 9) *********************** 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 to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 250 MET cc_start: 0.8852 (mmm) cc_final: 0.8290 (mmm) REVERT: A 280 ASP cc_start: 0.9159 (OUTLIER) cc_final: 0.8613 (t0) REVERT: A 372 MET cc_start: 0.8768 (ppp) cc_final: 0.8304 (ppp) REVERT: A 446 PHE cc_start: 0.7006 (OUTLIER) cc_final: 0.6490 (t80) REVERT: B 372 MET cc_start: 0.8775 (ppp) cc_final: 0.8399 (ppp) REVERT: C 280 ASP cc_start: 0.9139 (OUTLIER) cc_final: 0.8795 (t0) REVERT: C 372 MET cc_start: 0.8724 (ppp) cc_final: 0.8160 (ppp) REVERT: D 46 GLU cc_start: 0.8351 (tt0) cc_final: 0.7955 (pt0) REVERT: D 83 MET cc_start: 0.9290 (mtm) cc_final: 0.8577 (mpp) REVERT: D 229 GLU cc_start: 0.9224 (tm-30) cc_final: 0.8907 (tm-30) REVERT: E 13 LYS cc_start: 0.9632 (tppt) cc_final: 0.9369 (tppt) REVERT: E 34 MET cc_start: 0.8882 (mmm) cc_final: 0.8583 (mmm) REVERT: E 46 GLU cc_start: 0.8557 (tt0) cc_final: 0.8099 (tt0) REVERT: E 83 MET cc_start: 0.9255 (mtm) cc_final: 0.8599 (mpp) REVERT: F 46 GLU cc_start: 0.8278 (tt0) cc_final: 0.7943 (pt0) REVERT: F 83 MET cc_start: 0.9151 (mpp) cc_final: 0.8935 (mpp) REVERT: F 116 GLN cc_start: 0.9188 (tp40) cc_final: 0.8670 (tp40) outliers start: 17 outliers final: 9 residues processed: 66 average time/residue: 0.1265 time to fit residues: 13.0694 Evaluate side-chains 61 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 446 PHE Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 244 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 16 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 175 optimal weight: 10.0000 chunk 137 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 148 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 171 optimal weight: 8.9990 chunk 118 optimal weight: 8.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 ASN ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.037708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.026967 restraints weight = 91013.109| |-----------------------------------------------------------------------------| r_work (start): 0.2645 rms_B_bonded: 4.66 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15249 Z= 0.201 Angle : 0.524 7.344 20709 Z= 0.271 Chirality : 0.042 0.200 2391 Planarity : 0.004 0.057 2652 Dihedral : 3.871 18.068 2136 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.66 % Favored : 94.29 % Rotamer: Outliers : 1.21 % Allowed : 12.92 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.20), residues: 1962 helix: 1.40 (0.29), residues: 384 sheet: -0.19 (0.21), residues: 639 loop : -0.46 (0.21), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 72 TYR 0.008 0.001 TYR C 385 PHE 0.008 0.001 PHE F 95 TRP 0.005 0.001 TRP F 47 HIS 0.005 0.001 HIS B 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.20 (15210) covalent geometry : angle 0.51887 / 0.27 (20628) SS BOND : bond 0.00362 / 0.22 ( 36) SS BOND : angle 1.20948 / 0.86 ( 72) hydrogen bonds : bond 0.02714 / 1.86 ( 631) hydrogen bonds : angle 4.62078 / 3.29 ( 1692) link_NAG-ASN : bond 0.00223 / 0.11 ( 3) link_NAG-ASN : angle 1.72689 / 0.82 ( 9) *********************** 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 70 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 50 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 250 MET cc_start: 0.8946 (mmm) cc_final: 0.8405 (mmm) REVERT: A 280 ASP cc_start: 0.9187 (OUTLIER) cc_final: 0.8498 (t0) REVERT: A 372 MET cc_start: 0.8766 (ppp) cc_final: 0.8306 (ppp) REVERT: A 446 PHE cc_start: 0.7098 (OUTLIER) cc_final: 0.6568 (t80) REVERT: B 372 MET cc_start: 0.8697 (ppp) cc_final: 0.8354 (ppp) REVERT: C 280 ASP cc_start: 0.9179 (OUTLIER) cc_final: 0.8619 (t0) REVERT: C 372 MET cc_start: 0.8713 (ppp) cc_final: 0.8167 (ppp) REVERT: C 446 PHE cc_start: 0.7697 (OUTLIER) cc_final: 0.6992 (t80) REVERT: D 46 GLU cc_start: 0.8364 (tt0) cc_final: 0.7981 (pt0) REVERT: D 83 MET cc_start: 0.9270 (mtm) cc_final: 0.8564 (mpp) REVERT: D 229 GLU cc_start: 0.9244 (tm-30) cc_final: 0.8937 (tm-30) REVERT: E 13 LYS cc_start: 0.9644 (tppt) cc_final: 0.9400 (tppt) REVERT: E 34 MET cc_start: 0.8879 (mmm) cc_final: 0.8594 (mmm) REVERT: E 46 GLU cc_start: 0.8568 (tt0) cc_final: 0.8073 (tt0) REVERT: E 83 MET cc_start: 0.9268 (mtm) cc_final: 0.8601 (mpp) REVERT: F 46 GLU cc_start: 0.8308 (tt0) cc_final: 0.7938 (pt0) REVERT: F 83 MET cc_start: 0.9158 (mpp) cc_final: 0.8949 (mpp) REVERT: F 116 GLN cc_start: 0.9217 (tp40) cc_final: 0.8734 (tp40) REVERT: F 188 THR cc_start: 0.8774 (OUTLIER) cc_final: 0.8470 (p) outliers start: 20 outliers final: 13 residues processed: 67 average time/residue: 0.1342 time to fit residues: 13.6076 Evaluate side-chains 67 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 446 PHE Chi-restraints excluded: chain B residue 31 ILE 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 280 ASP Chi-restraints excluded: chain C residue 446 PHE 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 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 188 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 107 optimal weight: 0.7980 chunk 92 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 179 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 146 optimal weight: 6.9990 chunk 149 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 chunk 110 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 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 = 0.3108 r_free = 0.3108 target = 0.037826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.027023 restraints weight = 90915.634| |-----------------------------------------------------------------------------| r_work (start): 0.2688 rms_B_bonded: 4.70 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15249 Z= 0.170 Angle : 0.513 8.129 20709 Z= 0.265 Chirality : 0.042 0.170 2391 Planarity : 0.004 0.057 2652 Dihedral : 3.858 18.178 2136 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.76 % Favored : 94.19 % Rotamer: Outliers : 0.97 % Allowed : 13.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.20), residues: 1962 helix: 1.43 (0.29), residues: 384 sheet: -0.24 (0.21), residues: 642 loop : -0.43 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 72 TYR 0.008 0.001 TYR C 385 PHE 0.007 0.001 PHE D 208 TRP 0.005 0.001 TRP F 47 HIS 0.005 0.001 HIS B 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (15210) covalent geometry : angle 0.50817 / 0.26 (20628) SS BOND : bond 0.00299 / 0.18 ( 36) SS BOND : angle 1.11082 / 0.78 ( 72) hydrogen bonds : bond 0.02618 / 1.80 ( 631) hydrogen bonds : angle 4.54930 / 3.24 ( 1692) link_NAG-ASN : bond 0.00217 / 0.11 ( 3) link_NAG-ASN : angle 1.62833 / 0.76 ( 9) *********************** 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 66 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 50 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 250 MET cc_start: 0.8928 (mmm) cc_final: 0.8371 (mmm) REVERT: A 280 ASP cc_start: 0.9176 (OUTLIER) cc_final: 0.8602 (t0) REVERT: A 372 MET cc_start: 0.8790 (ppp) cc_final: 0.8321 (ppp) REVERT: A 446 PHE cc_start: 0.7020 (OUTLIER) cc_final: 0.6498 (t80) REVERT: B 372 MET cc_start: 0.8703 (ppp) cc_final: 0.8369 (ppp) REVERT: C 250 MET cc_start: 0.8772 (tpp) cc_final: 0.8531 (mmt) REVERT: C 280 ASP cc_start: 0.9173 (OUTLIER) cc_final: 0.8650 (t0) REVERT: C 372 MET cc_start: 0.8738 (ppp) cc_final: 0.8183 (ppp) REVERT: C 446 PHE cc_start: 0.7641 (OUTLIER) cc_final: 0.6944 (t80) REVERT: D 46 GLU cc_start: 0.8365 (tt0) cc_final: 0.7985 (pt0) REVERT: D 83 MET cc_start: 0.9294 (mtm) cc_final: 0.8578 (mpp) REVERT: D 229 GLU cc_start: 0.9245 (tm-30) cc_final: 0.8938 (tm-30) REVERT: E 13 LYS cc_start: 0.9653 (tppt) cc_final: 0.9401 (tppt) REVERT: E 34 MET cc_start: 0.8877 (mmm) cc_final: 0.8592 (mmm) REVERT: E 46 GLU cc_start: 0.8525 (tt0) cc_final: 0.8038 (tt0) REVERT: E 83 MET cc_start: 0.9271 (mtm) cc_final: 0.8607 (mpp) REVERT: F 34 MET cc_start: 0.9057 (mmp) cc_final: 0.8821 (mmp) REVERT: F 46 GLU cc_start: 0.8301 (tt0) cc_final: 0.7937 (pt0) REVERT: F 83 MET cc_start: 0.9165 (mpp) cc_final: 0.8951 (mpp) REVERT: F 116 GLN cc_start: 0.9204 (tp40) cc_final: 0.8713 (tp40) REVERT: F 188 THR cc_start: 0.8794 (OUTLIER) cc_final: 0.8536 (p) outliers start: 16 outliers final: 10 residues processed: 63 average time/residue: 0.1249 time to fit residues: 12.1166 Evaluate side-chains 65 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 446 PHE Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 446 PHE 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 E residue 22 CYS Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain F residue 188 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 154 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 56 optimal weight: 0.2980 chunk 149 optimal weight: 10.0000 chunk 142 optimal weight: 7.9990 chunk 85 optimal weight: 9.9990 chunk 51 optimal weight: 0.3980 chunk 105 optimal weight: 0.4980 chunk 12 optimal weight: 10.0000 chunk 133 optimal weight: 3.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 57 ASN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.038428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.027715 restraints weight = 89740.064| |-----------------------------------------------------------------------------| r_work (start): 0.2678 rms_B_bonded: 4.68 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15249 Z= 0.121 Angle : 0.513 11.640 20709 Z= 0.263 Chirality : 0.042 0.172 2391 Planarity : 0.003 0.060 2652 Dihedral : 3.759 17.742 2136 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.40 % Favored : 94.55 % Rotamer: Outliers : 1.03 % Allowed : 13.47 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.20), residues: 1962 helix: 1.47 (0.29), residues: 384 sheet: -0.28 (0.21), residues: 651 loop : -0.40 (0.22), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 87 TYR 0.008 0.001 TYR C 385 PHE 0.008 0.001 PHE D 208 TRP 0.005 0.001 TRP F 47 HIS 0.005 0.001 HIS B 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (15210) covalent geometry : angle 0.49978 / 0.26 (20628) SS BOND : bond 0.00311 / 0.17 ( 36) SS BOND : angle 1.91928 / 0.99 ( 72) hydrogen bonds : bond 0.02619 / 1.79 ( 631) hydrogen bonds : angle 4.44011 / 3.16 ( 1692) link_NAG-ASN : bond 0.00252 / 0.13 ( 3) link_NAG-ASN : angle 1.55863 / 0.75 ( 9) ********************** 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 73 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 280 ASP cc_start: 0.9175 (OUTLIER) cc_final: 0.8613 (t0) REVERT: A 372 MET cc_start: 0.8811 (ppp) cc_final: 0.8340 (ppp) REVERT: A 446 PHE cc_start: 0.7027 (OUTLIER) cc_final: 0.6525 (t80) REVERT: B 372 MET cc_start: 0.8719 (ppp) cc_final: 0.8363 (ppp) REVERT: C 222 MET cc_start: 0.8861 (ttp) cc_final: 0.8648 (ptm) REVERT: C 280 ASP cc_start: 0.9143 (OUTLIER) cc_final: 0.8806 (t0) REVERT: C 372 MET cc_start: 0.8743 (ppp) cc_final: 0.8175 (ppp) REVERT: C 446 PHE cc_start: 0.7573 (OUTLIER) cc_final: 0.6910 (t80) REVERT: D 34 MET cc_start: 0.8807 (mmp) cc_final: 0.8606 (mmp) REVERT: D 46 GLU cc_start: 0.8342 (tt0) cc_final: 0.7923 (pt0) REVERT: D 83 MET cc_start: 0.9317 (mtm) cc_final: 0.8602 (mpp) REVERT: D 229 GLU cc_start: 0.9259 (tm-30) cc_final: 0.8947 (tm-30) REVERT: E 13 LYS cc_start: 0.9655 (tppt) cc_final: 0.9409 (tppt) REVERT: E 34 MET cc_start: 0.8873 (mmm) cc_final: 0.8577 (mmm) REVERT: E 46 GLU cc_start: 0.8531 (tt0) cc_final: 0.8074 (tt0) REVERT: E 83 MET cc_start: 0.9284 (mtm) cc_final: 0.8648 (mpp) REVERT: F 34 MET cc_start: 0.9068 (mmp) cc_final: 0.8796 (mmp) REVERT: F 46 GLU cc_start: 0.8285 (tt0) cc_final: 0.7941 (pt0) REVERT: F 83 MET cc_start: 0.9184 (mpp) cc_final: 0.8963 (mpp) REVERT: F 116 GLN cc_start: 0.9213 (tp40) cc_final: 0.8713 (tp40) REVERT: F 188 THR cc_start: 0.8807 (OUTLIER) cc_final: 0.8556 (p) outliers start: 17 outliers final: 10 residues processed: 70 average time/residue: 0.1266 time to fit residues: 13.5563 Evaluate side-chains 66 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 446 PHE Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 446 PHE Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain F residue 188 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 121 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 chunk 176 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 7 optimal weight: 30.0000 chunk 150 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 188 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 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 = 0.3177 r_free = 0.3177 target = 0.039853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.028572 restraints weight = 91938.196| |-----------------------------------------------------------------------------| r_work (start): 0.2674 rms_B_bonded: 4.69 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15249 Z= 0.129 Angle : 0.519 9.810 20709 Z= 0.265 Chirality : 0.042 0.170 2391 Planarity : 0.003 0.058 2652 Dihedral : 3.724 18.870 2136 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.40 % Favored : 94.55 % Rotamer: Outliers : 0.97 % Allowed : 13.71 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.20), residues: 1962 helix: 1.47 (0.29), residues: 384 sheet: -0.19 (0.21), residues: 630 loop : -0.42 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 87 TYR 0.011 0.001 TYR B 44 PHE 0.007 0.001 PHE D 208 TRP 0.005 0.001 TRP F 47 HIS 0.005 0.001 HIS B 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (15210) covalent geometry : angle 0.50836 / 0.26 (20628) SS BOND : bond 0.00273 / 0.16 ( 36) SS BOND : angle 1.75191 / 0.94 ( 72) hydrogen bonds : bond 0.02580 / 1.75 ( 631) hydrogen bonds : angle 4.43940 / 3.16 ( 1692) link_NAG-ASN : bond 0.00252 / 0.13 ( 3) link_NAG-ASN : angle 1.54235 / 0.73 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2403.87 seconds wall clock time: 42 minutes 41.40 seconds (2561.40 seconds total)