Starting phenix.real_space_refine on Sun Aug 24 19:44:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f6x_28891/08_2025/8f6x_28891.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f6x_28891/08_2025/8f6x_28891.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f6x_28891/08_2025/8f6x_28891.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f6x_28891/08_2025/8f6x_28891.map" model { file = "/net/cci-nas-00/data/ceres_data/8f6x_28891/08_2025/8f6x_28891.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f6x_28891/08_2025/8f6x_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.26, per 1000 atoms: 0.22 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: 1.20 Conformation dependent library (CDL) restraints added in 485.1 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.67 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: 2.05 Time building geometry restraints manager: 1.61 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: 8354 17.97 - 35.95: 759 35.95 - 53.92: 119 53.92 - 71.90: 24 71.90 - 89.87: 17 Dihedral angle restraints: 9273 sinusoidal: 3600 harmonic: 5673 Sorted by residual: dihedral pdb=" CB CYS B 384 " pdb=" SG CYS B 384 " pdb=" SG CYS B 390 " pdb=" CB CYS B 390 " ideal model delta sinusoidal sigma weight residual 93.00 170.56 -77.56 1 1.00e+01 1.00e-02 7.53e+01 dihedral pdb=" CB CYS A 28 " pdb=" SG CYS A 28 " pdb=" SG CYS A 407 " pdb=" CB CYS A 407 " ideal model delta sinusoidal sigma weight residual 93.00 159.94 -66.94 1 1.00e+01 1.00e-02 5.84e+01 dihedral pdb=" CB CYS C 28 " pdb=" SG CYS C 28 " pdb=" SG CYS C 407 " pdb=" CB CYS C 407 " ideal model delta sinusoidal sigma weight residual 93.00 156.98 -63.98 1 1.00e+01 1.00e-02 5.39e+01 ... (remaining 9270 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2161 0.075 - 0.150: 225 0.150 - 0.225: 3 0.225 - 0.300: 1 0.300 - 0.375: 1 Chirality restraints: 2391 Sorted by residual: chirality pdb=" C1 NAG B 601 " pdb=" ND2 ASN B 172 " pdb=" C2 NAG B 601 " pdb=" O5 NAG B 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CA ASN C 172 " pdb=" N ASN C 172 " pdb=" C ASN C 172 " pdb=" CB ASN C 172 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" C1 NAG C 601 " pdb=" ND2 ASN C 172 " pdb=" C2 NAG C 601 " pdb=" O5 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 2388 not shown) Planarity restraints: 2655 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 172 " 0.001 2.00e-02 2.50e+03 3.73e-02 1.74e+01 pdb=" CG ASN C 172 " -0.047 2.00e-02 2.50e+03 pdb=" OD1 ASN C 172 " 0.045 2.00e-02 2.50e+03 pdb=" ND2 ASN C 172 " -0.037 2.00e-02 2.50e+03 pdb=" C1 NAG C 601 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 172 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.06e+00 pdb=" CG ASN C 172 " -0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN C 172 " 0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN C 172 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE C 451 " 0.037 5.00e-02 4.00e+02 5.61e-02 5.03e+00 pdb=" N PRO C 452 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO C 452 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 452 " 0.031 5.00e-02 4.00e+02 ... (remaining 2652 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 728 2.72 - 3.27: 14638 3.27 - 3.81: 24025 3.81 - 4.36: 29262 4.36 - 4.90: 52341 Nonbonded interactions: 120994 Sorted by model distance: nonbonded pdb=" OG SER B 37 " pdb=" OG1 THR B 281 " model vdw 2.181 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: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 12.640 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 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 : 13.801 89.874 5541 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.66 % Favored : 94.29 % Rotamer: Outliers : 0.06 % Allowed : 0.42 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.00244 (15210) covalent geometry : angle 0.51248 (20628) SS BOND : bond 0.00282 ( 36) SS BOND : angle 1.10364 ( 72) hydrogen bonds : bond 0.12596 ( 631) hydrogen bonds : angle 5.94111 ( 1692) link_NAG-ASN : bond 0.01046 ( 3) link_NAG-ASN : angle 5.55729 ( 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 : 0.570 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: 0.1424 time to fit residues: 19.4096 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 : 0.602 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: B 455 GLN B 457 ASN C 351 ASN ** C 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.038565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.027560 restraints weight = 89396.663| |-----------------------------------------------------------------------------| r_work (start): 0.2659 rms_B_bonded: 4.67 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 15249 Z= 0.234 Angle : 0.587 6.878 20709 Z= 0.305 Chirality : 0.043 0.251 2391 Planarity : 0.004 0.057 2652 Dihedral : 4.803 59.885 2199 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 : 6.82 % Favored : 93.06 % 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 aren 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 0.004 0.000 ARG E 72 TYR 0.013 0.001 TYR C 385 PHE 0.009 0.001 PHE D 111 TRP 0.007 0.001 TRP B 309 HIS 0.003 0.001 HIS B 368 Details of bonding type rmsd covalent geometry : bond 0.00505 (15210) covalent geometry : angle 0.58009 (20628) SS BOND : bond 0.00314 ( 36) SS BOND : angle 1.11575 ( 72) hydrogen bonds : bond 0.03255 ( 631) hydrogen bonds : angle 5.04177 ( 1692) link_NAG-ASN : bond 0.00530 ( 3) link_NAG-ASN : angle 3.34766 ( 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 : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 250 MET cc_start: 0.8839 (tpp) cc_final: 0.8476 (mmm) REVERT: A 372 MET cc_start: 0.8592 (ppp) cc_final: 0.8302 (ppp) REVERT: B 372 MET cc_start: 0.8452 (ppp) cc_final: 0.8200 (ppp) REVERT: C 372 MET cc_start: 0.8496 (ppp) cc_final: 0.8212 (ppp) REVERT: D 34 MET cc_start: 0.8479 (mmm) cc_final: 0.8187 (mmm) REVERT: D 46 GLU cc_start: 0.8400 (tt0) cc_final: 0.7967 (pt0) REVERT: D 83 MET cc_start: 0.9319 (mtm) cc_final: 0.8563 (mpp) REVERT: D 229 GLU cc_start: 0.9020 (tm-30) cc_final: 0.8803 (tp30) REVERT: E 34 MET cc_start: 0.8880 (mmm) cc_final: 0.8525 (mmm) REVERT: E 46 GLU cc_start: 0.8730 (tt0) cc_final: 0.8425 (tt0) REVERT: E 83 MET cc_start: 0.9302 (mtm) cc_final: 0.8582 (mpp) REVERT: E 113 ILE cc_start: 0.9297 (mm) cc_final: 0.9076 (mt) REVERT: F 46 GLU cc_start: 0.8343 (tt0) cc_final: 0.7845 (pt0) REVERT: F 229 GLU cc_start: 0.8872 (pp20) cc_final: 0.8621 (pp20) outliers start: 2 outliers final: 1 residues processed: 65 average time/residue: 0.1365 time to fit residues: 13.0875 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 : 0.453 ------------------------------------------------------------------------------- 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: 10.0000 chunk 75 optimal weight: 9.9990 chunk 143 optimal weight: 0.0570 chunk 110 optimal weight: 4.9990 chunk 144 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 120 optimal weight: 10.0000 chunk 188 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 79 optimal weight: 0.9980 overall best weight: 2.8102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN A 351 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.038544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.027494 restraints weight = 90944.124| |-----------------------------------------------------------------------------| r_work (start): 0.2659 rms_B_bonded: 4.76 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15249 Z= 0.165 Angle : 0.513 6.332 20709 Z= 0.266 Chirality : 0.042 0.222 2391 Planarity : 0.004 0.056 2652 Dihedral : 4.491 51.218 2199 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.45 % Favored : 94.50 % Rotamer: Outliers : 0.79 % Allowed : 8.33 % Favored : 90.88 % 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 aren not related in a simple way. whole: -0.27 (0.20), residues: 1962 helix: 1.32 (0.29), residues: 384 sheet: -0.16 (0.21), residues: 621 loop : -0.76 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 87 TYR 0.012 0.001 TYR C 385 PHE 0.008 0.001 PHE D 95 TRP 0.005 0.001 TRP D 47 HIS 0.003 0.001 HIS B 368 Details of bonding type rmsd covalent geometry : bond 0.00359 (15210) covalent geometry : angle 0.50884 (20628) SS BOND : bond 0.00264 ( 36) SS BOND : angle 0.86085 ( 72) hydrogen bonds : bond 0.02749 ( 631) hydrogen bonds : angle 4.71362 ( 1692) link_NAG-ASN : bond 0.00365 ( 3) link_NAG-ASN : angle 2.60446 ( 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 75 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 ASP cc_start: 0.9165 (OUTLIER) cc_final: 0.8637 (t0) REVERT: A 372 MET cc_start: 0.8644 (ppp) cc_final: 0.8276 (ppp) REVERT: B 372 MET cc_start: 0.8544 (ppp) cc_final: 0.8191 (ppp) REVERT: C 270 MET cc_start: 0.8615 (ptm) cc_final: 0.8384 (ppp) REVERT: C 280 ASP cc_start: 0.9138 (OUTLIER) cc_final: 0.8803 (t0) REVERT: C 372 MET cc_start: 0.8583 (ppp) cc_final: 0.8196 (ppp) REVERT: D 34 MET cc_start: 0.8544 (mmm) cc_final: 0.8253 (mmm) REVERT: D 46 GLU cc_start: 0.8366 (tt0) cc_final: 0.7971 (pt0) REVERT: D 83 MET cc_start: 0.9315 (mtm) cc_final: 0.8930 (mpp) REVERT: D 229 GLU cc_start: 0.9087 (tm-30) cc_final: 0.8779 (tm-30) REVERT: E 34 MET cc_start: 0.8873 (mmm) cc_final: 0.8595 (mmm) REVERT: E 46 GLU cc_start: 0.8625 (tt0) cc_final: 0.8310 (tt0) REVERT: E 83 MET cc_start: 0.9301 (mtm) cc_final: 0.8574 (mpp) REVERT: F 46 GLU cc_start: 0.8316 (tt0) cc_final: 0.7947 (pt0) REVERT: F 83 MET cc_start: 0.8956 (mpp) cc_final: 0.8679 (mpp) REVERT: F 229 GLU cc_start: 0.8983 (pp20) cc_final: 0.8731 (pp20) outliers start: 13 outliers final: 6 residues processed: 72 average time/residue: 0.1291 time to fit residues: 14.0190 Evaluate side-chains 61 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.582 ------------------------------------------------------------------------------- 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 250 MET 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 194 ILE 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: 8.9990 chunk 189 optimal weight: 0.9990 chunk 170 optimal weight: 5.9990 chunk 11 optimal weight: 20.0000 chunk 169 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 190 optimal weight: 7.9990 chunk 175 optimal weight: 9.9990 chunk 145 optimal weight: 20.0000 chunk 10 optimal weight: 4.9990 chunk 126 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 GLN ** C 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.037007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.026163 restraints weight = 92647.696| |-----------------------------------------------------------------------------| r_work (start): 0.2605 rms_B_bonded: 4.69 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 15249 Z= 0.313 Angle : 0.602 7.402 20709 Z= 0.313 Chirality : 0.043 0.197 2391 Planarity : 0.004 0.053 2652 Dihedral : 4.512 50.943 2199 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.17 % Favored : 93.78 % Rotamer: Outliers : 0.60 % Allowed : 10.51 % Favored : 88.89 % 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 aren not related in a simple way. whole: -0.61 (0.19), residues: 1962 helix: 0.66 (0.27), residues: 408 sheet: -0.30 (0.20), residues: 639 loop : -0.89 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 79 TYR 0.010 0.001 TYR F 104 PHE 0.010 0.001 PHE D 95 TRP 0.006 0.001 TRP B 309 HIS 0.006 0.001 HIS B 368 Details of bonding type rmsd covalent geometry : bond 0.00669 (15210) covalent geometry : angle 0.59639 (20628) SS BOND : bond 0.00486 ( 36) SS BOND : angle 1.31460 ( 72) hydrogen bonds : bond 0.03155 ( 631) hydrogen bonds : angle 5.03802 ( 1692) link_NAG-ASN : bond 0.00345 ( 3) link_NAG-ASN : angle 2.46799 ( 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 65 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: A 250 MET cc_start: 0.8908 (mmm) cc_final: 0.8482 (mmm) REVERT: A 280 ASP cc_start: 0.9153 (OUTLIER) cc_final: 0.8435 (t0) REVERT: A 372 MET cc_start: 0.8667 (ppp) cc_final: 0.8286 (ppp) REVERT: B 372 MET cc_start: 0.8653 (ppp) cc_final: 0.8283 (ppp) REVERT: C 270 MET cc_start: 0.8794 (ptm) cc_final: 0.8520 (ptm) REVERT: C 280 ASP cc_start: 0.9199 (OUTLIER) cc_final: 0.8525 (t0) REVERT: C 372 MET cc_start: 0.8603 (ppp) cc_final: 0.8197 (ppp) REVERT: D 34 MET cc_start: 0.8617 (mmm) cc_final: 0.8367 (mmm) REVERT: D 46 GLU cc_start: 0.8376 (tt0) cc_final: 0.7999 (pt0) REVERT: D 83 MET cc_start: 0.9257 (mtm) cc_final: 0.8507 (mpp) REVERT: D 229 GLU cc_start: 0.9151 (tm-30) cc_final: 0.8846 (tm-30) REVERT: E 13 LYS cc_start: 0.9584 (tppt) cc_final: 0.9281 (tppt) REVERT: E 34 MET cc_start: 0.8882 (mmm) cc_final: 0.8635 (mmm) REVERT: E 46 GLU cc_start: 0.8634 (tt0) cc_final: 0.8159 (tt0) REVERT: E 83 MET cc_start: 0.9220 (mtm) cc_final: 0.8512 (mpp) REVERT: E 229 GLU cc_start: 0.9110 (pm20) cc_final: 0.8816 (pm20) REVERT: F 46 GLU cc_start: 0.8364 (tt0) cc_final: 0.7958 (pt0) REVERT: F 83 MET cc_start: 0.8961 (mpp) cc_final: 0.8708 (mpp) outliers start: 10 outliers final: 7 residues processed: 63 average time/residue: 0.1211 time to fit residues: 11.8428 Evaluate side-chains 56 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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: 8.9990 chunk 22 optimal weight: 0.9990 chunk 32 optimal weight: 20.0000 chunk 80 optimal weight: 9.9990 chunk 114 optimal weight: 9.9990 chunk 168 optimal weight: 6.9990 chunk 130 optimal weight: 0.0020 chunk 166 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 135 optimal weight: 6.9990 overall best weight: 2.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 GLN B 422 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.037948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.027081 restraints weight = 90932.404| |-----------------------------------------------------------------------------| r_work (start): 0.2652 rms_B_bonded: 4.72 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15249 Z= 0.145 Angle : 0.497 7.040 20709 Z= 0.258 Chirality : 0.043 0.192 2391 Planarity : 0.004 0.053 2652 Dihedral : 4.242 51.013 2199 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.25 % Favored : 94.70 % Rotamer: Outliers : 0.66 % Allowed : 11.17 % Favored : 88.16 % 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 aren not related in a simple way. whole: -0.15 (0.20), residues: 1962 helix: 1.48 (0.29), residues: 384 sheet: -0.24 (0.21), residues: 639 loop : -0.59 (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 0.009 0.001 PHE B 446 TRP 0.004 0.001 TRP E 36 HIS 0.004 0.001 HIS B 368 Details of bonding type rmsd covalent geometry : bond 0.00317 (15210) covalent geometry : angle 0.49265 (20628) SS BOND : bond 0.00269 ( 36) SS BOND : angle 0.91581 ( 72) hydrogen bonds : bond 0.02572 ( 631) hydrogen bonds : angle 4.64238 ( 1692) link_NAG-ASN : bond 0.00309 ( 3) link_NAG-ASN : angle 2.14166 ( 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 69 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.463 Fit side-chains revert: symmetry clash REVERT: A 280 ASP cc_start: 0.9140 (OUTLIER) cc_final: 0.8601 (t0) REVERT: A 372 MET cc_start: 0.8745 (ppp) cc_final: 0.8278 (ppp) REVERT: B 372 MET cc_start: 0.8691 (ppp) cc_final: 0.8298 (ppp) REVERT: C 280 ASP cc_start: 0.9140 (OUTLIER) cc_final: 0.8782 (t0) REVERT: C 372 MET cc_start: 0.8650 (ppp) cc_final: 0.8092 (ppp) REVERT: D 34 MET cc_start: 0.8554 (mmm) cc_final: 0.8311 (mmm) REVERT: D 46 GLU cc_start: 0.8328 (tt0) cc_final: 0.7957 (pt0) REVERT: D 83 MET cc_start: 0.9256 (mtm) cc_final: 0.8528 (mpp) REVERT: D 229 GLU cc_start: 0.9172 (tm-30) cc_final: 0.8860 (tm-30) REVERT: E 13 LYS cc_start: 0.9598 (tppt) cc_final: 0.9257 (tppt) REVERT: E 34 MET cc_start: 0.8861 (mmm) cc_final: 0.8552 (mmm) REVERT: E 46 GLU cc_start: 0.8580 (tt0) cc_final: 0.8147 (tt0) REVERT: E 83 MET cc_start: 0.9239 (mtm) cc_final: 0.8610 (mpp) REVERT: E 229 GLU cc_start: 0.9131 (pm20) cc_final: 0.8800 (pm20) REVERT: F 46 GLU cc_start: 0.8301 (tt0) cc_final: 0.7953 (pt0) REVERT: F 83 MET cc_start: 0.9084 (mpp) cc_final: 0.8845 (mpp) REVERT: F 116 GLN cc_start: 0.9133 (tp40) cc_final: 0.8642 (tp40) outliers start: 11 outliers final: 6 residues processed: 67 average time/residue: 0.1023 time to fit residues: 10.7836 Evaluate side-chains 60 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.540 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 5 optimal weight: 7.9990 chunk 178 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 134 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 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: 0.0270 overall best weight: 4.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3090 r_free = 0.3090 target = 0.037280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.026467 restraints weight = 91955.650| |-----------------------------------------------------------------------------| r_work (start): 0.2655 rms_B_bonded: 4.70 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.2465 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 : 0.553 7.549 20709 Z= 0.287 Chirality : 0.042 0.182 2391 Planarity : 0.004 0.053 2652 Dihedral : 4.303 51.135 2199 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.22 % Favored : 93.73 % Rotamer: Outliers : 0.85 % Allowed : 12.38 % Favored : 86.78 % 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 aren not related in a simple way. whole: -0.22 (0.20), residues: 1962 helix: 1.23 (0.28), residues: 387 sheet: -0.26 (0.20), residues: 639 loop : -0.56 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 72 TYR 0.009 0.001 TYR C 385 PHE 0.010 0.001 PHE B 446 TRP 0.005 0.001 TRP F 47 HIS 0.005 0.001 HIS B 368 Details of bonding type rmsd covalent geometry : bond 0.00502 (15210) covalent geometry : angle 0.54281 (20628) SS BOND : bond 0.00311 ( 36) SS BOND : angle 1.72885 ( 72) hydrogen bonds : bond 0.02936 ( 631) hydrogen bonds : angle 4.81764 ( 1692) link_NAG-ASN : bond 0.00252 ( 3) link_NAG-ASN : angle 1.97446 ( 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: 14 poor density : 51 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: A 280 ASP cc_start: 0.9153 (OUTLIER) cc_final: 0.8499 (t0) REVERT: A 372 MET cc_start: 0.8759 (ppp) cc_final: 0.8290 (ppp) REVERT: B 372 MET cc_start: 0.8754 (ppp) cc_final: 0.8375 (ppp) REVERT: B 446 PHE cc_start: 0.7344 (OUTLIER) cc_final: 0.6382 (t80) REVERT: C 270 MET cc_start: 0.8686 (ptm) cc_final: 0.8290 (ppp) REVERT: C 280 ASP cc_start: 0.9176 (OUTLIER) cc_final: 0.8597 (t0) REVERT: C 372 MET cc_start: 0.8677 (ppp) cc_final: 0.8126 (ppp) REVERT: C 446 PHE cc_start: 0.7673 (OUTLIER) cc_final: 0.6846 (t80) REVERT: D 34 MET cc_start: 0.8632 (mmm) cc_final: 0.8423 (mmm) REVERT: D 46 GLU cc_start: 0.8330 (tt0) cc_final: 0.7964 (pt0) REVERT: D 83 MET cc_start: 0.9214 (mtm) cc_final: 0.8533 (mpp) REVERT: D 229 GLU cc_start: 0.9230 (tm-30) cc_final: 0.8925 (tm-30) REVERT: E 13 LYS cc_start: 0.9631 (tppt) cc_final: 0.9315 (tppt) REVERT: E 34 MET cc_start: 0.8867 (mmm) cc_final: 0.8589 (mmm) REVERT: E 46 GLU cc_start: 0.8551 (tt0) cc_final: 0.8101 (tt0) REVERT: E 83 MET cc_start: 0.9214 (mtm) cc_final: 0.8565 (mpp) REVERT: F 46 GLU cc_start: 0.8301 (tt0) cc_final: 0.7935 (pt0) REVERT: F 83 MET cc_start: 0.9098 (mpp) cc_final: 0.8891 (mpp) outliers start: 14 outliers final: 9 residues processed: 63 average time/residue: 0.1065 time to fit residues: 10.3804 Evaluate side-chains 60 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 B residue 446 PHE 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 143 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 160 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 98 optimal weight: 5.9990 chunk 56 optimal weight: 0.5980 chunk 36 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3095 r_free = 0.3095 target = 0.037544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.026806 restraints weight = 90463.100| |-----------------------------------------------------------------------------| r_work (start): 0.2636 rms_B_bonded: 4.66 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15249 Z= 0.196 Angle : 0.522 7.544 20709 Z= 0.271 Chirality : 0.042 0.180 2391 Planarity : 0.004 0.054 2652 Dihedral : 4.232 51.153 2199 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.07 % Favored : 93.88 % Rotamer: Outliers : 1.09 % Allowed : 12.68 % Favored : 86.23 % 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 aren not related in a simple way. whole: -0.19 (0.20), residues: 1962 helix: 1.27 (0.28), residues: 387 sheet: -0.26 (0.20), residues: 639 loop : -0.54 (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 0.010 0.001 PHE B 446 TRP 0.005 0.001 TRP D 36 HIS 0.005 0.001 HIS B 368 Details of bonding type rmsd covalent geometry : bond 0.00423 (15210) covalent geometry : angle 0.51656 (20628) SS BOND : bond 0.00334 ( 36) SS BOND : angle 1.24570 ( 72) hydrogen bonds : bond 0.02750 ( 631) hydrogen bonds : angle 4.71090 ( 1692) link_NAG-ASN : bond 0.00255 ( 3) link_NAG-ASN : angle 1.86436 ( 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 71 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 53 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 280 ASP cc_start: 0.9159 (OUTLIER) cc_final: 0.8498 (t0) REVERT: A 372 MET cc_start: 0.8789 (ppp) cc_final: 0.8303 (ppp) REVERT: A 446 PHE cc_start: 0.7190 (t80) cc_final: 0.6539 (t80) REVERT: B 372 MET cc_start: 0.8756 (ppp) cc_final: 0.8399 (ppp) REVERT: B 446 PHE cc_start: 0.7456 (OUTLIER) cc_final: 0.6504 (t80) REVERT: C 270 MET cc_start: 0.8709 (ptm) cc_final: 0.8484 (ptm) REVERT: C 280 ASP cc_start: 0.9164 (OUTLIER) cc_final: 0.8603 (t0) REVERT: C 372 MET cc_start: 0.8708 (ppp) cc_final: 0.8160 (ppp) REVERT: C 446 PHE cc_start: 0.7694 (OUTLIER) cc_final: 0.6967 (t80) REVERT: D 34 MET cc_start: 0.8514 (mmm) cc_final: 0.8234 (mmm) REVERT: D 46 GLU cc_start: 0.8363 (tt0) cc_final: 0.7983 (pt0) REVERT: D 83 MET cc_start: 0.9215 (mtm) cc_final: 0.8546 (mpp) REVERT: D 229 GLU cc_start: 0.9251 (tm-30) cc_final: 0.8948 (tm-30) REVERT: E 13 LYS cc_start: 0.9616 (tppt) cc_final: 0.9355 (tppt) REVERT: E 34 MET cc_start: 0.8852 (mmm) cc_final: 0.8565 (mmm) REVERT: E 46 GLU cc_start: 0.8536 (tt0) cc_final: 0.8041 (tt0) REVERT: E 83 MET cc_start: 0.9219 (mtm) cc_final: 0.8580 (mpp) REVERT: F 46 GLU cc_start: 0.8304 (tt0) cc_final: 0.7937 (pt0) REVERT: F 83 MET cc_start: 0.9112 (mpp) cc_final: 0.8905 (mpp) REVERT: F 116 GLN cc_start: 0.9181 (tp40) cc_final: 0.8717 (tp40) outliers start: 18 outliers final: 10 residues processed: 69 average time/residue: 0.1153 time to fit residues: 12.3691 Evaluate side-chains 63 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.495 ------------------------------------------------------------------------------- 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 B residue 446 PHE 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 202 SER 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: 3.9990 chunk 11 optimal weight: 1.9990 chunk 175 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 chunk 114 optimal weight: 7.9990 chunk 148 optimal weight: 10.0000 chunk 101 optimal weight: 0.8980 chunk 194 optimal weight: 0.8980 chunk 100 optimal weight: 6.9990 chunk 171 optimal weight: 10.0000 chunk 118 optimal weight: 0.7980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3170 r_free = 0.3170 target = 0.039647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.028376 restraints weight = 91028.749| |-----------------------------------------------------------------------------| r_work (start): 0.2675 rms_B_bonded: 4.66 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15249 Z= 0.118 Angle : 0.494 7.527 20709 Z= 0.255 Chirality : 0.043 0.191 2391 Planarity : 0.003 0.057 2652 Dihedral : 4.077 51.559 2199 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.56 % Favored : 94.39 % Rotamer: Outliers : 1.15 % Allowed : 13.16 % Favored : 85.69 % 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 aren not related in a simple way. whole: -0.06 (0.20), residues: 1962 helix: 1.52 (0.29), residues: 384 sheet: -0.27 (0.20), residues: 642 loop : -0.44 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 87 TYR 0.009 0.001 TYR C 385 PHE 0.008 0.001 PHE D 208 TRP 0.005 0.001 TRP D 47 HIS 0.004 0.001 HIS B 368 Details of bonding type rmsd covalent geometry : bond 0.00266 (15210) covalent geometry : angle 0.48966 (20628) SS BOND : bond 0.00242 ( 36) SS BOND : angle 1.08492 ( 72) hydrogen bonds : bond 0.02485 ( 631) hydrogen bonds : angle 4.48652 ( 1692) link_NAG-ASN : bond 0.00287 ( 3) link_NAG-ASN : angle 1.61727 ( 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 73 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 54 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 280 ASP cc_start: 0.9148 (OUTLIER) cc_final: 0.8627 (t0) REVERT: A 372 MET cc_start: 0.8831 (ppp) cc_final: 0.8351 (ppp) REVERT: A 446 PHE cc_start: 0.7071 (t80) cc_final: 0.6512 (t80) REVERT: B 372 MET cc_start: 0.8730 (ppp) cc_final: 0.8378 (ppp) REVERT: B 446 PHE cc_start: 0.7453 (OUTLIER) cc_final: 0.6564 (t80) REVERT: C 280 ASP cc_start: 0.9110 (OUTLIER) cc_final: 0.8805 (t0) REVERT: C 372 MET cc_start: 0.8731 (ppp) cc_final: 0.8163 (ppp) REVERT: C 446 PHE cc_start: 0.7723 (OUTLIER) cc_final: 0.6998 (t80) REVERT: D 34 MET cc_start: 0.8477 (mmm) cc_final: 0.8184 (mmm) REVERT: D 46 GLU cc_start: 0.8335 (tt0) cc_final: 0.7957 (pt0) REVERT: D 83 MET cc_start: 0.9245 (mtm) cc_final: 0.8560 (mpp) REVERT: D 229 GLU cc_start: 0.9256 (tm-30) cc_final: 0.8943 (tm-30) REVERT: E 13 LYS cc_start: 0.9664 (tppt) cc_final: 0.9409 (tppt) REVERT: E 34 MET cc_start: 0.8852 (mmm) cc_final: 0.8550 (mmm) REVERT: E 46 GLU cc_start: 0.8506 (tt0) cc_final: 0.8044 (tt0) REVERT: E 83 MET cc_start: 0.9231 (mtm) cc_final: 0.8590 (mpp) REVERT: F 46 GLU cc_start: 0.8265 (tt0) cc_final: 0.7933 (pt0) REVERT: F 83 MET cc_start: 0.9127 (mpp) cc_final: 0.8908 (mpp) REVERT: F 116 GLN cc_start: 0.9187 (tp40) cc_final: 0.8696 (tp40) REVERT: F 188 THR cc_start: 0.8834 (OUTLIER) cc_final: 0.8591 (p) outliers start: 19 outliers final: 12 residues processed: 71 average time/residue: 0.1213 time to fit residues: 12.9530 Evaluate side-chains 71 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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 285 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 446 PHE 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 147 VAL Chi-restraints excluded: chain D residue 202 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 107 optimal weight: 4.9990 chunk 92 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 179 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 146 optimal weight: 9.9990 chunk 149 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.037701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.026940 restraints weight = 91097.440| |-----------------------------------------------------------------------------| r_work (start): 0.2687 rms_B_bonded: 4.69 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15249 Z= 0.193 Angle : 0.524 8.030 20709 Z= 0.270 Chirality : 0.042 0.177 2391 Planarity : 0.004 0.057 2652 Dihedral : 4.124 51.459 2199 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.91 % Favored : 94.04 % Rotamer: Outliers : 1.15 % Allowed : 13.29 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.20), residues: 1962 helix: 1.41 (0.29), residues: 384 sheet: -0.17 (0.21), residues: 636 loop : -0.46 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 239 TYR 0.008 0.001 TYR C 385 PHE 0.008 0.001 PHE B 446 TRP 0.005 0.001 TRP F 47 HIS 0.005 0.001 HIS B 368 Details of bonding type rmsd covalent geometry : bond 0.00420 (15210) covalent geometry : angle 0.52008 (20628) SS BOND : bond 0.00307 ( 36) SS BOND : angle 1.11269 ( 72) hydrogen bonds : bond 0.02672 ( 631) hydrogen bonds : angle 4.59758 ( 1692) link_NAG-ASN : bond 0.00232 ( 3) link_NAG-ASN : angle 1.65262 ( 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 71 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 52 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 280 ASP cc_start: 0.9180 (OUTLIER) cc_final: 0.8539 (t0) REVERT: A 372 MET cc_start: 0.8800 (ppp) cc_final: 0.8320 (ppp) REVERT: A 446 PHE cc_start: 0.7064 (t80) cc_final: 0.6574 (t80) REVERT: B 372 MET cc_start: 0.8727 (ppp) cc_final: 0.8372 (ppp) REVERT: B 446 PHE cc_start: 0.7518 (OUTLIER) cc_final: 0.6621 (t80) REVERT: C 270 MET cc_start: 0.8713 (ptm) cc_final: 0.8383 (ppp) REVERT: C 280 ASP cc_start: 0.9163 (OUTLIER) cc_final: 0.8653 (t0) REVERT: C 372 MET cc_start: 0.8729 (ppp) cc_final: 0.8206 (ppp) REVERT: C 446 PHE cc_start: 0.7677 (OUTLIER) cc_final: 0.6977 (t80) REVERT: D 34 MET cc_start: 0.8557 (mmm) cc_final: 0.8268 (mmm) REVERT: D 46 GLU cc_start: 0.8357 (tt0) cc_final: 0.7973 (pt0) REVERT: D 83 MET cc_start: 0.9234 (mtm) cc_final: 0.8554 (mpp) REVERT: D 229 GLU cc_start: 0.9277 (tm-30) cc_final: 0.8978 (tm-30) REVERT: E 13 LYS cc_start: 0.9666 (tppt) cc_final: 0.9417 (tppt) REVERT: E 34 MET cc_start: 0.8868 (mmm) cc_final: 0.8589 (mmm) REVERT: E 46 GLU cc_start: 0.8544 (tt0) cc_final: 0.8063 (tt0) REVERT: E 83 MET cc_start: 0.9248 (mtm) cc_final: 0.8603 (mpp) REVERT: F 34 MET cc_start: 0.9060 (mmp) cc_final: 0.8851 (mmp) REVERT: F 46 GLU cc_start: 0.8286 (tt0) cc_final: 0.7939 (pt0) REVERT: F 83 MET cc_start: 0.9120 (mpp) cc_final: 0.8909 (mpp) REVERT: F 116 GLN cc_start: 0.9198 (tp40) cc_final: 0.8736 (tp40) REVERT: F 188 THR cc_start: 0.8832 (OUTLIER) cc_final: 0.8585 (p) outliers start: 19 outliers final: 11 residues processed: 69 average time/residue: 0.1112 time to fit residues: 11.8478 Evaluate side-chains 68 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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 285 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 446 PHE Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 446 PHE Chi-restraints excluded: chain D residue 79 LEU 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 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: 9.9990 chunk 67 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 149 optimal weight: 9.9990 chunk 142 optimal weight: 7.9990 chunk 85 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 105 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 133 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 GLN ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 462 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** F 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.036784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.026071 restraints weight = 92287.429| |-----------------------------------------------------------------------------| r_work (start): 0.2601 rms_B_bonded: 4.65 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 15249 Z= 0.343 Angle : 0.648 13.071 20709 Z= 0.334 Chirality : 0.043 0.179 2391 Planarity : 0.004 0.057 2652 Dihedral : 4.453 51.163 2199 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.37 % Favored : 93.58 % Rotamer: Outliers : 1.09 % Allowed : 13.47 % Favored : 85.45 % 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 aren not related in a simple way. whole: -0.56 (0.19), residues: 1962 helix: 0.45 (0.27), residues: 408 sheet: -0.27 (0.20), residues: 645 loop : -0.72 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 79 TYR 0.011 0.001 TYR D 195 PHE 0.009 0.001 PHE A 256 TRP 0.006 0.001 TRP A 309 HIS 0.008 0.001 HIS B 368 Details of bonding type rmsd covalent geometry : bond 0.00734 (15210) covalent geometry : angle 0.63395 (20628) SS BOND : bond 0.00437 ( 36) SS BOND : angle 2.25868 ( 72) hydrogen bonds : bond 0.03246 ( 631) hydrogen bonds : angle 5.03110 ( 1692) link_NAG-ASN : bond 0.00312 ( 3) link_NAG-ASN : angle 1.84737 ( 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 65 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 47 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 280 ASP cc_start: 0.9168 (OUTLIER) cc_final: 0.8438 (t0) REVERT: A 372 MET cc_start: 0.8748 (ppp) cc_final: 0.8339 (ppp) REVERT: A 446 PHE cc_start: 0.7071 (OUTLIER) cc_final: 0.6554 (t80) REVERT: B 372 MET cc_start: 0.8718 (ppp) cc_final: 0.8380 (ppp) REVERT: B 446 PHE cc_start: 0.7660 (OUTLIER) cc_final: 0.6788 (t80) REVERT: C 270 MET cc_start: 0.8800 (ptm) cc_final: 0.8427 (ppp) REVERT: C 280 ASP cc_start: 0.9190 (OUTLIER) cc_final: 0.8599 (t70) REVERT: C 372 MET cc_start: 0.8728 (ppp) cc_final: 0.8259 (ppp) REVERT: C 446 PHE cc_start: 0.7695 (OUTLIER) cc_final: 0.7048 (t80) REVERT: D 34 MET cc_start: 0.8583 (mmm) cc_final: 0.8309 (mmm) REVERT: D 46 GLU cc_start: 0.8391 (tt0) cc_final: 0.8028 (pt0) REVERT: D 83 MET cc_start: 0.9217 (mtm) cc_final: 0.8571 (mpp) REVERT: D 229 GLU cc_start: 0.9299 (tm-30) cc_final: 0.9021 (tm-30) REVERT: E 13 LYS cc_start: 0.9655 (tppt) cc_final: 0.9430 (tppt) REVERT: E 34 MET cc_start: 0.8829 (mmm) cc_final: 0.8576 (mmm) REVERT: E 46 GLU cc_start: 0.8496 (tt0) cc_final: 0.8002 (tt0) REVERT: E 83 MET cc_start: 0.9234 (mtm) cc_final: 0.8576 (mpp) REVERT: F 46 GLU cc_start: 0.8352 (tt0) cc_final: 0.7950 (pt0) REVERT: F 188 THR cc_start: 0.8855 (OUTLIER) cc_final: 0.8597 (p) outliers start: 18 outliers final: 11 residues processed: 62 average time/residue: 0.1079 time to fit residues: 10.2470 Evaluate side-chains 64 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 47 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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 B residue 446 PHE Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 446 PHE Chi-restraints excluded: chain D residue 79 LEU 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 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 121 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 176 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 7 optimal weight: 30.0000 chunk 150 optimal weight: 0.1980 chunk 97 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 188 optimal weight: 4.9990 chunk 104 optimal weight: 9.9990 chunk 66 optimal weight: 0.8980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN B 307 GLN ** B 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.038483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.027754 restraints weight = 90431.435| |-----------------------------------------------------------------------------| r_work (start): 0.2673 rms_B_bonded: 4.70 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 15249 Z= 0.101 Angle : 0.526 9.639 20709 Z= 0.269 Chirality : 0.043 0.179 2391 Planarity : 0.004 0.061 2652 Dihedral : 4.144 51.461 2199 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.30 % Favored : 94.65 % Rotamer: Outliers : 0.91 % Allowed : 13.71 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.20), residues: 1962 helix: 1.37 (0.29), residues: 384 sheet: -0.30 (0.20), residues: 645 loop : -0.47 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 87 TYR 0.008 0.001 TYR C 385 PHE 0.009 0.001 PHE D 208 TRP 0.008 0.001 TRP D 47 HIS 0.005 0.001 HIS B 368 Details of bonding type rmsd covalent geometry : bond 0.00228 (15210) covalent geometry : angle 0.51586 (20628) SS BOND : bond 0.00293 ( 36) SS BOND : angle 1.71266 ( 72) hydrogen bonds : bond 0.02595 ( 631) hydrogen bonds : angle 4.50275 ( 1692) link_NAG-ASN : bond 0.00262 ( 3) link_NAG-ASN : angle 1.59121 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1915.98 seconds wall clock time: 34 minutes 11.07 seconds (2051.07 seconds total)