Starting phenix.real_space_refine on Thu Jun 19 12:45:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f6x_28891/06_2025/8f6x_28891.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f6x_28891/06_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_28891/06_2025/8f6x_28891.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f6x_28891/06_2025/8f6x_28891.map" model { file = "/net/cci-nas-00/data/ceres_data/8f6x_28891/06_2025/8f6x_28891.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f6x_28891/06_2025/8f6x_28891.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9396 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 99 5.16 5 C 9336 2.51 5 N 2547 2.21 5 O 2970 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14952 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3248 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 15, 'TRANS': 413} Chain: "B" Number of atoms: 3248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3248 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 15, 'TRANS': 413} Chain: "C" Number of atoms: 3248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3248 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 15, 'TRANS': 413} Chain: "D" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1722 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "E" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1722 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "F" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1722 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.84, per 1000 atoms: 0.59 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: 3.97 Conformation dependent library (CDL) restraints added in 2.1 seconds 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3624 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 33 sheets defined 21.4% alpha, 32.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.61 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: 6.06 Time building geometry restraints manager: 4.47 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.010 Extract box with map and model: 0.660 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 38.520 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.070 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:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.960 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.19), residues: 1962 helix: 0.38 (0.28), residues: 408 sheet: -0.42 (0.20), residues: 621 loop : -1.12 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 47 HIS 0.001 0.000 HIS B 368 PHE 0.011 0.001 PHE D 111 TYR 0.017 0.001 TYR C 385 ARG 0.004 0.000 ARG D 87 Details of bonding type rmsd link_NAG-ASN : bond 0.01046 ( 3) link_NAG-ASN : angle 5.55729 ( 9) hydrogen bonds : bond 0.12596 ( 631) hydrogen bonds : angle 5.94111 ( 1692) SS BOND : bond 0.00282 ( 36) SS BOND : angle 1.10364 ( 72) covalent geometry : bond 0.00244 (15210) covalent geometry : angle 0.51248 (20628) *********************** 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 : 1.679 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: 0.3547 time to fit residues: 48.3336 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 : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 10.0000 chunk 147 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 chunk 78 optimal weight: 3.9990 chunk 152 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 113 optimal weight: 9.9990 chunk 177 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 ASN B 455 GLN ** B 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 ASN ** C 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 GLN D 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 = 0.3089 r_free = 0.3089 target = 0.037580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.026639 restraints weight = 90775.835| |-----------------------------------------------------------------------------| r_work (start): 0.2625 rms_B_bonded: 4.67 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 15249 Z= 0.327 Angle : 0.655 7.663 20709 Z= 0.339 Chirality : 0.044 0.243 2391 Planarity : 0.004 0.056 2652 Dihedral : 4.964 59.148 2199 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.07 % Favored : 93.88 % Rotamer: Outliers : 0.30 % Allowed : 7.55 % Favored : 92.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.19), residues: 1962 helix: 0.56 (0.28), residues: 408 sheet: -0.38 (0.20), residues: 639 loop : -0.98 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 309 HIS 0.004 0.001 HIS B 368 PHE 0.010 0.002 PHE A 256 TYR 0.013 0.001 TYR C 385 ARG 0.004 0.001 ARG E 207 Details of bonding type rmsd link_NAG-ASN : bond 0.00466 ( 3) link_NAG-ASN : angle 3.25099 ( 9) hydrogen bonds : bond 0.03451 ( 631) hydrogen bonds : angle 5.20826 ( 1692) SS BOND : bond 0.00369 ( 36) SS BOND : angle 1.30100 ( 72) covalent geometry : bond 0.00701 (15210) covalent geometry : angle 0.64864 (20628) *********************** 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 67 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 1.695 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 MET cc_start: 0.8896 (tpp) cc_final: 0.8633 (tpp) REVERT: A 372 MET cc_start: 0.8523 (ppp) cc_final: 0.8239 (ppp) REVERT: C 270 MET cc_start: 0.8789 (ptm) cc_final: 0.8567 (ptm) REVERT: C 372 MET cc_start: 0.8467 (ppp) cc_final: 0.8205 (ppp) REVERT: D 34 MET cc_start: 0.8545 (mmm) cc_final: 0.8277 (mmm) REVERT: D 46 GLU cc_start: 0.8437 (tt0) cc_final: 0.8020 (pt0) REVERT: D 83 MET cc_start: 0.9297 (mtm) cc_final: 0.8547 (mpp) REVERT: D 229 GLU cc_start: 0.9055 (tm-30) cc_final: 0.8714 (tp30) REVERT: E 34 MET cc_start: 0.8941 (mmm) cc_final: 0.8625 (mmm) REVERT: E 46 GLU cc_start: 0.8684 (tt0) cc_final: 0.8360 (tt0) REVERT: E 83 MET cc_start: 0.9277 (mtm) cc_final: 0.8578 (mpp) REVERT: E 229 GLU cc_start: 0.9121 (pm20) cc_final: 0.8899 (pm20) REVERT: F 46 GLU cc_start: 0.8333 (tt0) cc_final: 0.7833 (pt0) REVERT: F 229 GLU cc_start: 0.9003 (pp20) cc_final: 0.8701 (pp20) outliers start: 5 outliers final: 2 residues processed: 66 average time/residue: 0.3174 time to fit residues: 31.1034 Evaluate side-chains 52 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 VAL 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 58 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 85 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 104 optimal weight: 5.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 457 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.038726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.027716 restraints weight = 89919.451| |-----------------------------------------------------------------------------| r_work (start): 0.2668 rms_B_bonded: 4.74 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1788 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= 0.121 Angle : 0.503 6.289 20709 Z= 0.261 Chirality : 0.043 0.225 2391 Planarity : 0.004 0.061 2652 Dihedral : 4.483 50.905 2199 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.30 % Favored : 94.65 % Rotamer: Outliers : 0.66 % Allowed : 8.88 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.20), residues: 1962 helix: 1.43 (0.29), residues: 381 sheet: -0.24 (0.20), residues: 630 loop : -0.70 (0.21), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 47 HIS 0.003 0.000 HIS B 368 PHE 0.007 0.001 PHE D 95 TYR 0.013 0.001 TYR C 385 ARG 0.003 0.000 ARG D 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00445 ( 3) link_NAG-ASN : angle 2.58422 ( 9) hydrogen bonds : bond 0.02638 ( 631) hydrogen bonds : angle 4.68754 ( 1692) SS BOND : bond 0.00245 ( 36) SS BOND : angle 0.89702 ( 72) covalent geometry : bond 0.00267 (15210) covalent geometry : angle 0.49829 (20628) *********************** 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: 11 poor density : 64 time to evaluate : 1.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 ASP cc_start: 0.9136 (OUTLIER) cc_final: 0.8622 (t0) REVERT: A 372 MET cc_start: 0.8615 (ppp) cc_final: 0.8246 (ppp) REVERT: B 372 MET cc_start: 0.8809 (ppp) cc_final: 0.8484 (ppp) REVERT: B 464 PHE cc_start: 0.6436 (m-80) cc_final: 0.6219 (m-80) REVERT: C 280 ASP cc_start: 0.9150 (OUTLIER) cc_final: 0.8779 (t0) REVERT: C 372 MET cc_start: 0.8526 (ppp) cc_final: 0.8165 (ppp) REVERT: D 34 MET cc_start: 0.8520 (mmm) cc_final: 0.8235 (mmm) REVERT: D 46 GLU cc_start: 0.8389 (tt0) cc_final: 0.8013 (pt0) REVERT: D 83 MET cc_start: 0.9317 (mtm) cc_final: 0.8934 (mpp) REVERT: D 229 GLU cc_start: 0.9101 (tm-30) cc_final: 0.8788 (tm-30) REVERT: E 34 MET cc_start: 0.8889 (mmm) cc_final: 0.8587 (mmm) REVERT: E 46 GLU cc_start: 0.8630 (tt0) cc_final: 0.8283 (tt0) REVERT: E 83 MET cc_start: 0.9321 (mtm) cc_final: 0.8617 (mpp) REVERT: E 113 ILE cc_start: 0.9363 (mm) cc_final: 0.9067 (mt) REVERT: E 229 GLU cc_start: 0.9122 (pm20) cc_final: 0.8811 (pm20) REVERT: F 46 GLU cc_start: 0.8363 (tt0) cc_final: 0.7957 (pt0) REVERT: F 83 MET cc_start: 0.8963 (mpp) cc_final: 0.8701 (mpp) REVERT: F 229 GLU cc_start: 0.9013 (pp20) cc_final: 0.8766 (pp20) outliers start: 11 outliers final: 5 residues processed: 71 average time/residue: 0.2913 time to fit residues: 31.4377 Evaluate side-chains 65 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain B residue 250 MET Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 280 ASP 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 168 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 157 optimal weight: 20.0000 chunk 180 optimal weight: 8.9990 chunk 190 optimal weight: 0.0060 chunk 51 optimal weight: 10.0000 chunk 151 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 26 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 overall best weight: 6.2004 ------------------------------------------------------------------------------- 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** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.036926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.026096 restraints weight = 92429.634| |-----------------------------------------------------------------------------| r_work (start): 0.2602 rms_B_bonded: 4.67 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 15249 Z= 0.332 Angle : 0.611 7.463 20709 Z= 0.317 Chirality : 0.043 0.202 2391 Planarity : 0.004 0.058 2652 Dihedral : 4.517 50.727 2199 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.01 % Favored : 93.93 % Rotamer: Outliers : 0.66 % Allowed : 10.69 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.19), residues: 1962 helix: 0.68 (0.28), residues: 408 sheet: -0.31 (0.20), residues: 645 loop : -0.90 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 309 HIS 0.006 0.001 HIS B 368 PHE 0.010 0.001 PHE D 95 TYR 0.010 0.001 TYR D 195 ARG 0.003 0.000 ARG E 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00396 ( 3) link_NAG-ASN : angle 2.51101 ( 9) hydrogen bonds : bond 0.03156 ( 631) hydrogen bonds : angle 5.05444 ( 1692) SS BOND : bond 0.00348 ( 36) SS BOND : angle 1.28212 ( 72) covalent geometry : bond 0.00708 (15210) covalent geometry : angle 0.60530 (20628) *********************** 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 67 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 1.830 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 250 MET cc_start: 0.8912 (mmm) cc_final: 0.8471 (mmm) REVERT: A 280 ASP cc_start: 0.9124 (OUTLIER) cc_final: 0.8439 (t0) REVERT: A 372 MET cc_start: 0.8665 (ppp) cc_final: 0.8323 (ppp) REVERT: B 372 MET cc_start: 0.8830 (ppp) cc_final: 0.8592 (ppp) REVERT: C 280 ASP cc_start: 0.9195 (OUTLIER) cc_final: 0.8483 (t0) REVERT: C 372 MET cc_start: 0.8612 (ppp) cc_final: 0.8205 (ppp) REVERT: D 34 MET cc_start: 0.8604 (mmm) cc_final: 0.8362 (mmm) REVERT: D 46 GLU cc_start: 0.8392 (tt0) cc_final: 0.8017 (pt0) REVERT: D 83 MET cc_start: 0.9230 (mtm) cc_final: 0.8525 (mpp) REVERT: D 229 GLU cc_start: 0.9157 (tm-30) cc_final: 0.8844 (tm-30) REVERT: E 13 LYS cc_start: 0.9600 (tppt) cc_final: 0.9293 (tppt) REVERT: E 34 MET cc_start: 0.8875 (mmm) cc_final: 0.8583 (mmm) REVERT: E 46 GLU cc_start: 0.8631 (tt0) cc_final: 0.8136 (tt0) REVERT: E 83 MET cc_start: 0.9231 (mtm) cc_final: 0.8523 (mpp) REVERT: F 46 GLU cc_start: 0.8393 (tt0) cc_final: 0.7987 (pt0) REVERT: F 83 MET cc_start: 0.8945 (mpp) cc_final: 0.8710 (mpp) REVERT: F 229 GLU cc_start: 0.9152 (pp20) cc_final: 0.8949 (pp20) outliers start: 11 outliers final: 7 residues processed: 65 average time/residue: 0.3033 time to fit residues: 30.4637 Evaluate side-chains 58 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 1.815 ------------------------------------------------------------------------------- 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 153 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 177 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 112 optimal weight: 0.9990 chunk 190 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 161 optimal weight: 10.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.038093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.027216 restraints weight = 91404.122| |-----------------------------------------------------------------------------| r_work (start): 0.2657 rms_B_bonded: 4.75 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15249 Z= 0.123 Angle : 0.491 7.282 20709 Z= 0.254 Chirality : 0.043 0.194 2391 Planarity : 0.004 0.057 2652 Dihedral : 4.213 50.970 2199 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.99 % Favored : 94.95 % Rotamer: Outliers : 0.66 % Allowed : 11.35 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.20), residues: 1962 helix: 1.52 (0.29), residues: 384 sheet: -0.24 (0.21), residues: 639 loop : -0.58 (0.21), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 47 HIS 0.004 0.001 HIS B 368 PHE 0.009 0.001 PHE D 208 TYR 0.010 0.001 TYR C 385 ARG 0.002 0.000 ARG D 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00307 ( 3) link_NAG-ASN : angle 2.14806 ( 9) hydrogen bonds : bond 0.02508 ( 631) hydrogen bonds : angle 4.60075 ( 1692) SS BOND : bond 0.00248 ( 36) SS BOND : angle 0.84617 ( 72) covalent geometry : bond 0.00271 (15210) covalent geometry : angle 0.48708 (20628) *********************** 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 72 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 250 MET cc_start: 0.8908 (mmm) cc_final: 0.8369 (mmm) REVERT: A 280 ASP cc_start: 0.9125 (OUTLIER) cc_final: 0.8621 (t0) REVERT: A 372 MET cc_start: 0.8736 (ppp) cc_final: 0.8277 (ppp) REVERT: C 280 ASP cc_start: 0.9140 (OUTLIER) cc_final: 0.8753 (t0) REVERT: C 372 MET cc_start: 0.8672 (ppp) cc_final: 0.8095 (ppp) REVERT: D 34 MET cc_start: 0.8539 (mmm) cc_final: 0.8311 (mmm) REVERT: D 46 GLU cc_start: 0.8356 (tt0) cc_final: 0.8013 (pt0) REVERT: D 83 MET cc_start: 0.9224 (mtm) cc_final: 0.8515 (mpp) REVERT: D 229 GLU cc_start: 0.9172 (tm-30) cc_final: 0.8850 (tm-30) REVERT: E 13 LYS cc_start: 0.9597 (tppt) cc_final: 0.9326 (tppt) REVERT: E 34 MET cc_start: 0.8848 (mmm) cc_final: 0.8543 (mmm) REVERT: E 46 GLU cc_start: 0.8571 (tt0) cc_final: 0.8144 (tt0) REVERT: E 83 MET cc_start: 0.9263 (mtm) cc_final: 0.8622 (mpp) REVERT: F 46 GLU cc_start: 0.8299 (tt0) cc_final: 0.7931 (pt0) REVERT: F 83 MET cc_start: 0.9082 (mpp) cc_final: 0.8849 (mpp) REVERT: F 116 GLN cc_start: 0.9133 (tp40) cc_final: 0.8653 (tp40) REVERT: F 229 GLU cc_start: 0.9124 (pp20) cc_final: 0.8888 (pp20) outliers start: 11 outliers final: 6 residues processed: 70 average time/residue: 0.2767 time to fit residues: 29.8433 Evaluate side-chains 62 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 1.685 ------------------------------------------------------------------------------- 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 127 optimal weight: 20.0000 chunk 25 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 157 optimal weight: 8.9990 chunk 185 optimal weight: 20.0000 chunk 59 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 147 optimal weight: 6.9990 chunk 194 optimal weight: 8.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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 = 0.3098 r_free = 0.3098 target = 0.037461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.026655 restraints weight = 91324.433| |-----------------------------------------------------------------------------| r_work (start): 0.2664 rms_B_bonded: 4.69 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15249 Z= 0.202 Angle : 0.533 8.253 20709 Z= 0.276 Chirality : 0.042 0.184 2391 Planarity : 0.004 0.055 2652 Dihedral : 4.216 51.118 2199 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.96 % Favored : 93.99 % Rotamer: Outliers : 0.85 % Allowed : 12.44 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.20), residues: 1962 helix: 1.32 (0.29), residues: 387 sheet: -0.23 (0.20), residues: 639 loop : -0.55 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 47 HIS 0.005 0.001 HIS B 368 PHE 0.011 0.001 PHE B 464 TYR 0.008 0.001 TYR C 385 ARG 0.003 0.000 ARG E 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00258 ( 3) link_NAG-ASN : angle 2.00703 ( 9) hydrogen bonds : bond 0.02829 ( 631) hydrogen bonds : angle 4.72355 ( 1692) SS BOND : bond 0.00318 ( 36) SS BOND : angle 1.68167 ( 72) covalent geometry : bond 0.00436 (15210) covalent geometry : angle 0.52316 (20628) *********************** 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 69 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 1.772 Fit side-chains revert: symmetry clash REVERT: A 280 ASP cc_start: 0.9178 (OUTLIER) cc_final: 0.8487 (t0) REVERT: A 372 MET cc_start: 0.8748 (ppp) cc_final: 0.8306 (ppp) REVERT: C 280 ASP cc_start: 0.9192 (OUTLIER) cc_final: 0.8557 (t0) REVERT: C 372 MET cc_start: 0.8705 (ppp) cc_final: 0.8152 (ppp) REVERT: D 34 MET cc_start: 0.8620 (mmm) cc_final: 0.8410 (mmm) REVERT: D 46 GLU cc_start: 0.8347 (tt0) cc_final: 0.7962 (pt0) REVERT: D 83 MET cc_start: 0.9237 (mtm) cc_final: 0.8537 (mpp) REVERT: D 229 GLU cc_start: 0.9219 (tm-30) cc_final: 0.8906 (tm-30) REVERT: E 13 LYS cc_start: 0.9632 (tppt) cc_final: 0.9309 (tppt) REVERT: E 34 MET cc_start: 0.8870 (mmm) cc_final: 0.8579 (mmm) REVERT: E 46 GLU cc_start: 0.8588 (tt0) cc_final: 0.8110 (tt0) REVERT: E 83 MET cc_start: 0.9250 (mtm) cc_final: 0.8576 (mpp) REVERT: F 46 GLU cc_start: 0.8316 (tt0) cc_final: 0.7944 (pt0) REVERT: F 83 MET cc_start: 0.9103 (mpp) cc_final: 0.8892 (mpp) REVERT: F 116 GLN cc_start: 0.9190 (tp40) cc_final: 0.8716 (tp40) REVERT: F 229 GLU cc_start: 0.9155 (pp20) cc_final: 0.8914 (pp20) outliers start: 14 outliers final: 10 residues processed: 67 average time/residue: 0.2858 time to fit residues: 29.4031 Evaluate side-chains 63 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 1.754 ------------------------------------------------------------------------------- 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 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 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 183 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 177 optimal weight: 10.0000 chunk 137 optimal weight: 0.8980 chunk 154 optimal weight: 0.9990 chunk 49 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 127 optimal weight: 0.9990 chunk 156 optimal weight: 5.9990 chunk 131 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 = 0.3109 r_free = 0.3109 target = 0.037921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.027188 restraints weight = 90494.300| |-----------------------------------------------------------------------------| r_work (start): 0.2654 rms_B_bonded: 4.69 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15249 Z= 0.153 Angle : 0.501 7.718 20709 Z= 0.259 Chirality : 0.042 0.181 2391 Planarity : 0.004 0.056 2652 Dihedral : 4.132 51.250 2199 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.61 % Favored : 94.34 % Rotamer: Outliers : 0.91 % Allowed : 13.22 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.20), residues: 1962 helix: 1.42 (0.29), residues: 387 sheet: -0.22 (0.20), residues: 639 loop : -0.53 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 47 HIS 0.005 0.001 HIS B 368 PHE 0.007 0.001 PHE B 446 TYR 0.008 0.001 TYR C 385 ARG 0.002 0.000 ARG E 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00269 ( 3) link_NAG-ASN : angle 1.86749 ( 9) hydrogen bonds : bond 0.02609 ( 631) hydrogen bonds : angle 4.59104 ( 1692) SS BOND : bond 0.00284 ( 36) SS BOND : angle 1.17407 ( 72) covalent geometry : bond 0.00333 (15210) covalent geometry : angle 0.49564 (20628) *********************** 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 72 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 1.714 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 280 ASP cc_start: 0.9156 (OUTLIER) cc_final: 0.8550 (t0) REVERT: A 372 MET cc_start: 0.8776 (ppp) cc_final: 0.8312 (ppp) REVERT: A 446 PHE cc_start: 0.7174 (t80) cc_final: 0.6568 (t80) REVERT: B 372 MET cc_start: 0.8823 (ppp) cc_final: 0.8464 (ppp) REVERT: C 280 ASP cc_start: 0.9134 (OUTLIER) cc_final: 0.8595 (t0) REVERT: C 372 MET cc_start: 0.8719 (ppp) cc_final: 0.8165 (ppp) REVERT: C 446 PHE cc_start: 0.7699 (OUTLIER) cc_final: 0.6931 (t80) REVERT: D 34 MET cc_start: 0.8478 (mmm) cc_final: 0.8199 (mmm) REVERT: D 46 GLU cc_start: 0.8364 (tt0) cc_final: 0.7983 (pt0) REVERT: D 83 MET cc_start: 0.9223 (mtm) cc_final: 0.8537 (mpp) REVERT: D 229 GLU cc_start: 0.9231 (tm-30) cc_final: 0.8914 (tm-30) REVERT: E 13 LYS cc_start: 0.9612 (tppt) cc_final: 0.9339 (tppt) REVERT: E 34 MET cc_start: 0.8873 (mmm) cc_final: 0.8583 (mmm) REVERT: E 46 GLU cc_start: 0.8552 (tt0) cc_final: 0.8085 (tt0) REVERT: E 83 MET cc_start: 0.9233 (mtm) cc_final: 0.8574 (mpp) REVERT: F 46 GLU cc_start: 0.8292 (tt0) cc_final: 0.7949 (pt0) REVERT: F 83 MET cc_start: 0.9118 (mpp) cc_final: 0.8899 (mpp) REVERT: F 116 GLN cc_start: 0.9173 (tp40) cc_final: 0.8716 (tp40) REVERT: F 229 GLU cc_start: 0.9196 (pp20) cc_final: 0.8963 (pp20) outliers start: 15 outliers final: 8 residues processed: 70 average time/residue: 0.3205 time to fit residues: 34.5812 Evaluate side-chains 65 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 1.896 ------------------------------------------------------------------------------- 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 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 244 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 135 optimal weight: 2.9990 chunk 162 optimal weight: 20.0000 chunk 99 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 106 optimal weight: 0.2980 chunk 166 optimal weight: 9.9990 chunk 165 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- 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** ** E 150 GLN ** 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 = 0.3132 r_free = 0.3132 target = 0.038464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.027768 restraints weight = 89213.557| |-----------------------------------------------------------------------------| r_work (start): 0.2679 rms_B_bonded: 4.65 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15249 Z= 0.108 Angle : 0.485 7.480 20709 Z= 0.251 Chirality : 0.043 0.180 2391 Planarity : 0.003 0.057 2652 Dihedral : 4.024 51.649 2199 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.20 % Favored : 94.75 % Rotamer: Outliers : 1.15 % Allowed : 12.86 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.20), residues: 1962 helix: 1.57 (0.29), residues: 384 sheet: -0.24 (0.20), residues: 645 loop : -0.55 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 47 HIS 0.004 0.001 HIS B 368 PHE 0.009 0.001 PHE D 208 TYR 0.009 0.001 TYR C 385 ARG 0.002 0.000 ARG D 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00297 ( 3) link_NAG-ASN : angle 1.71740 ( 9) hydrogen bonds : bond 0.02436 ( 631) hydrogen bonds : angle 4.43279 ( 1692) SS BOND : bond 0.00270 ( 36) SS BOND : angle 1.06151 ( 72) covalent geometry : bond 0.00242 (15210) covalent geometry : angle 0.48055 (20628) *********************** 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 78 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 59 time to evaluate : 1.823 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 280 ASP cc_start: 0.9155 (OUTLIER) cc_final: 0.8641 (t0) REVERT: A 372 MET cc_start: 0.8794 (ppp) cc_final: 0.8326 (ppp) REVERT: A 446 PHE cc_start: 0.7042 (t80) cc_final: 0.6476 (t80) REVERT: B 372 MET cc_start: 0.8803 (ppp) cc_final: 0.8388 (ppp) REVERT: C 280 ASP cc_start: 0.9136 (OUTLIER) cc_final: 0.8804 (t0) REVERT: C 372 MET cc_start: 0.8733 (ppp) cc_final: 0.8176 (ppp) REVERT: C 446 PHE cc_start: 0.7699 (OUTLIER) cc_final: 0.6969 (t80) REVERT: D 34 MET cc_start: 0.8486 (mmm) cc_final: 0.8195 (mmm) REVERT: D 46 GLU cc_start: 0.8361 (tt0) cc_final: 0.7976 (pt0) REVERT: D 83 MET cc_start: 0.9257 (mtm) cc_final: 0.8555 (mpp) REVERT: D 229 GLU cc_start: 0.9245 (tm-30) cc_final: 0.8923 (tm-30) REVERT: E 13 LYS cc_start: 0.9662 (tppt) cc_final: 0.9399 (tppt) REVERT: E 34 MET cc_start: 0.8858 (mmm) cc_final: 0.8555 (mmm) REVERT: E 46 GLU cc_start: 0.8525 (tt0) cc_final: 0.8096 (tt0) REVERT: E 83 MET cc_start: 0.9276 (mtm) cc_final: 0.8614 (mpp) REVERT: F 46 GLU cc_start: 0.8269 (tt0) cc_final: 0.7947 (pt0) REVERT: F 83 MET cc_start: 0.9140 (mpp) cc_final: 0.8915 (mpp) REVERT: F 116 GLN cc_start: 0.9186 (tp40) cc_final: 0.8711 (tp40) REVERT: F 188 THR cc_start: 0.8835 (OUTLIER) cc_final: 0.8596 (p) REVERT: F 229 GLU cc_start: 0.9166 (pp20) cc_final: 0.8907 (pp20) outliers start: 19 outliers final: 12 residues processed: 76 average time/residue: 0.2959 time to fit residues: 34.2857 Evaluate side-chains 70 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 1.620 ------------------------------------------------------------------------------- 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 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 151 THR 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 128 optimal weight: 2.9990 chunk 106 optimal weight: 0.0370 chunk 45 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 53 optimal weight: 20.0000 chunk 31 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 180 optimal weight: 20.0000 chunk 6 optimal weight: 6.9990 overall best weight: 3.4066 ------------------------------------------------------------------------------- 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 = 0.3105 r_free = 0.3105 target = 0.037763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.026984 restraints weight = 90297.405| |-----------------------------------------------------------------------------| r_work (start): 0.2643 rms_B_bonded: 4.67 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15249 Z= 0.193 Angle : 0.521 8.062 20709 Z= 0.269 Chirality : 0.042 0.179 2391 Planarity : 0.004 0.058 2652 Dihedral : 4.118 51.511 2199 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.56 % Favored : 94.39 % Rotamer: Outliers : 1.09 % Allowed : 13.04 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.20), residues: 1962 helix: 1.45 (0.29), residues: 387 sheet: -0.30 (0.20), residues: 651 loop : -0.45 (0.22), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 47 HIS 0.005 0.001 HIS B 368 PHE 0.008 0.001 PHE B 446 TYR 0.008 0.001 TYR C 385 ARG 0.003 0.000 ARG E 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00236 ( 3) link_NAG-ASN : angle 1.71064 ( 9) hydrogen bonds : bond 0.02655 ( 631) hydrogen bonds : angle 4.57468 ( 1692) SS BOND : bond 0.00338 ( 36) SS BOND : angle 1.24202 ( 72) covalent geometry : bond 0.00419 (15210) covalent geometry : angle 0.51547 (20628) *********************** 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 73 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 1.803 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 280 ASP cc_start: 0.9164 (OUTLIER) cc_final: 0.8535 (t0) REVERT: A 372 MET cc_start: 0.8776 (ppp) cc_final: 0.8306 (ppp) REVERT: A 446 PHE cc_start: 0.7041 (t80) cc_final: 0.6501 (t80) REVERT: B 372 MET cc_start: 0.8829 (ppp) cc_final: 0.8449 (ppp) REVERT: C 280 ASP cc_start: 0.9143 (OUTLIER) cc_final: 0.8586 (t0) REVERT: C 372 MET cc_start: 0.8704 (ppp) cc_final: 0.8155 (ppp) REVERT: C 446 PHE cc_start: 0.7661 (OUTLIER) cc_final: 0.6962 (t80) REVERT: D 34 MET cc_start: 0.8543 (mmm) cc_final: 0.8265 (mmm) REVERT: D 46 GLU cc_start: 0.8385 (tt0) cc_final: 0.7986 (pt0) REVERT: D 83 MET cc_start: 0.9227 (mtm) cc_final: 0.8548 (mpp) REVERT: D 229 GLU cc_start: 0.9253 (tm-30) cc_final: 0.8940 (tm-30) REVERT: E 13 LYS cc_start: 0.9644 (tppt) cc_final: 0.9397 (tppt) REVERT: E 34 MET cc_start: 0.8879 (mmm) cc_final: 0.8603 (mmm) REVERT: E 46 GLU cc_start: 0.8540 (tt0) cc_final: 0.8098 (tt0) REVERT: E 83 MET cc_start: 0.9251 (mtm) cc_final: 0.8608 (mpp) REVERT: F 34 MET cc_start: 0.9029 (mmp) cc_final: 0.8827 (mmp) REVERT: F 46 GLU cc_start: 0.8284 (tt0) cc_final: 0.7952 (pt0) REVERT: F 83 MET cc_start: 0.9125 (mpp) cc_final: 0.8911 (mpp) REVERT: F 116 GLN cc_start: 0.9192 (tp40) cc_final: 0.8733 (tp40) REVERT: F 188 THR cc_start: 0.8825 (OUTLIER) cc_final: 0.8542 (p) REVERT: F 229 GLU cc_start: 0.9209 (pp20) cc_final: 0.8978 (pp20) outliers start: 18 outliers final: 13 residues processed: 71 average time/residue: 0.2821 time to fit residues: 31.1778 Evaluate side-chains 70 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 1.727 ------------------------------------------------------------------------------- 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 C residue 280 ASP Chi-restraints excluded: chain C residue 446 PHE Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 151 THR 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 41 optimal weight: 0.0970 chunk 14 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 54 optimal weight: 10.0000 chunk 175 optimal weight: 10.0000 chunk 79 optimal weight: 0.0170 chunk 178 optimal weight: 3.9990 chunk 151 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 overall best weight: 2.0222 ------------------------------------------------------------------------------- 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** C 57 ASN ** 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 = 0.3128 r_free = 0.3128 target = 0.038351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.027552 restraints weight = 90137.695| |-----------------------------------------------------------------------------| r_work (start): 0.2669 rms_B_bonded: 4.69 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15249 Z= 0.130 Angle : 0.519 12.309 20709 Z= 0.268 Chirality : 0.043 0.177 2391 Planarity : 0.003 0.059 2652 Dihedral : 4.060 51.622 2199 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.35 % Favored : 94.60 % Rotamer: Outliers : 1.09 % Allowed : 13.16 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.20), residues: 1962 helix: 1.48 (0.29), residues: 387 sheet: -0.22 (0.20), residues: 645 loop : -0.47 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 47 HIS 0.004 0.001 HIS B 368 PHE 0.008 0.001 PHE D 208 TYR 0.010 0.001 TYR C 385 ARG 0.002 0.000 ARG E 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00261 ( 3) link_NAG-ASN : angle 1.60985 ( 9) hydrogen bonds : bond 0.02612 ( 631) hydrogen bonds : angle 4.46224 ( 1692) SS BOND : bond 0.00306 ( 36) SS BOND : angle 2.09434 ( 72) covalent geometry : bond 0.00290 (15210) covalent geometry : angle 0.50432 (20628) ********************** 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 72 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 1.713 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 280 ASP cc_start: 0.9185 (OUTLIER) cc_final: 0.8612 (t0) REVERT: A 372 MET cc_start: 0.8775 (ppp) cc_final: 0.8303 (ppp) REVERT: A 446 PHE cc_start: 0.7028 (OUTLIER) cc_final: 0.6487 (t80) REVERT: B 372 MET cc_start: 0.8829 (ppp) cc_final: 0.8437 (ppp) REVERT: C 280 ASP cc_start: 0.9158 (OUTLIER) cc_final: 0.8629 (t0) REVERT: C 372 MET cc_start: 0.8694 (ppp) cc_final: 0.8166 (ppp) REVERT: C 446 PHE cc_start: 0.7681 (OUTLIER) cc_final: 0.6980 (t80) REVERT: D 34 MET cc_start: 0.8493 (mmm) cc_final: 0.8192 (mmm) REVERT: D 46 GLU cc_start: 0.8363 (tt0) cc_final: 0.7963 (pt0) REVERT: D 83 MET cc_start: 0.9280 (mtm) cc_final: 0.8579 (mpp) REVERT: D 229 GLU cc_start: 0.9272 (tm-30) cc_final: 0.8959 (tm-30) REVERT: E 13 LYS cc_start: 0.9652 (tppt) cc_final: 0.9391 (tppt) REVERT: E 34 MET cc_start: 0.8870 (mmm) cc_final: 0.8571 (mmm) REVERT: E 46 GLU cc_start: 0.8540 (tt0) cc_final: 0.8085 (tt0) REVERT: E 83 MET cc_start: 0.9295 (mtm) cc_final: 0.8626 (mpp) REVERT: F 34 MET cc_start: 0.9076 (mmp) cc_final: 0.8809 (mmp) REVERT: F 46 GLU cc_start: 0.8301 (tt0) cc_final: 0.7956 (pt0) REVERT: F 83 MET cc_start: 0.9158 (mpp) cc_final: 0.8933 (mpp) REVERT: F 116 GLN cc_start: 0.9219 (tp40) cc_final: 0.8753 (tp40) REVERT: F 188 THR cc_start: 0.8852 (OUTLIER) cc_final: 0.8619 (p) REVERT: F 229 GLU cc_start: 0.9178 (pp20) cc_final: 0.8937 (pp20) outliers start: 18 outliers final: 12 residues processed: 68 average time/residue: 0.2913 time to fit residues: 30.7721 Evaluate side-chains 69 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 1.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 446 PHE Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 446 PHE Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain F residue 188 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 90 optimal weight: 8.9990 chunk 193 optimal weight: 20.0000 chunk 147 optimal weight: 10.0000 chunk 82 optimal weight: 20.0000 chunk 81 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- 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** ** C 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.037381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.026591 restraints weight = 91504.567| |-----------------------------------------------------------------------------| r_work (start): 0.2624 rms_B_bonded: 4.68 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15249 Z= 0.245 Angle : 0.571 10.540 20709 Z= 0.295 Chirality : 0.043 0.176 2391 Planarity : 0.004 0.060 2652 Dihedral : 4.219 51.316 2199 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.81 % Favored : 94.14 % Rotamer: Outliers : 1.03 % Allowed : 13.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.20), residues: 1962 helix: 1.24 (0.28), residues: 387 sheet: -0.16 (0.20), residues: 636 loop : -0.51 (0.21), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 47 HIS 0.006 0.001 HIS B 368 PHE 0.009 0.001 PHE B 446 TYR 0.009 0.001 TYR C 385 ARG 0.002 0.000 ARG E 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00237 ( 3) link_NAG-ASN : angle 1.69059 ( 9) hydrogen bonds : bond 0.02924 ( 631) hydrogen bonds : angle 4.73692 ( 1692) SS BOND : bond 0.00355 ( 36) SS BOND : angle 2.02997 ( 72) covalent geometry : bond 0.00529 (15210) covalent geometry : angle 0.55819 (20628) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4804.40 seconds wall clock time: 84 minutes 28.57 seconds (5068.57 seconds total)