Starting phenix.real_space_refine on Sat Jul 20 08:36:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvf_41640/07_2024/8tvf_41640.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvf_41640/07_2024/8tvf_41640.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvf_41640/07_2024/8tvf_41640.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvf_41640/07_2024/8tvf_41640.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvf_41640/07_2024/8tvf_41640.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvf_41640/07_2024/8tvf_41640.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 6258 2.51 5 N 1647 2.21 5 O 2502 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 204": "OE1" <-> "OE2" Residue "B ARG 220": "NH1" <-> "NH2" Residue "B GLU 274": "OE1" <-> "OE2" Residue "A GLU 204": "OE1" <-> "OE2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A GLU 274": "OE1" <-> "OE2" Residue "C GLU 204": "OE1" <-> "OE2" Residue "C ARG 220": "NH1" <-> "NH2" Residue "C GLU 274": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 10461 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 3246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3246 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 15, 'TRANS': 416} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "A" Number of atoms: 3246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3246 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 15, 'TRANS': 416} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 3246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3246 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 15, 'TRANS': 416} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "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: "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 Chain: "B" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 188 Classifications: {'water': 188} Link IDs: {None: 187} Chain: "A" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 188 Classifications: {'water': 188} Link IDs: {None: 187} Chain: "C" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 188 Classifications: {'water': 188} Link IDs: {None: 187} Time building chain proxies: 6.64, per 1000 atoms: 0.63 Number of scatterers: 10461 At special positions: 0 Unit cell: (105.042, 98.0392, 101.04, 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 54 16.00 O 2502 8.00 N 1647 7.00 C 6258 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 187 " distance=2.18 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 358 " distance=2.02 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 387 " distance=2.08 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 412 " distance=2.03 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 187 " distance=2.18 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 358 " distance=2.02 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 387 " distance=2.08 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 412 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 187 " distance=2.18 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 358 " distance=2.02 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 387 " distance=2.08 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 412 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG A 601 " - " ASN A 65 " " NAG B 601 " - " ASN B 65 " " NAG C 601 " - " ASN C 65 " " NAG D 1 " - " ASN B 459 " " NAG E 1 " - " ASN A 459 " " NAG F 1 " - " ASN C 459 " Time building additional restraints: 4.37 Conformation dependent library (CDL) restraints added in 1.9 seconds 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2418 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 15 sheets defined 41.0% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'B' and resid 24 through 30 removed outlier: 3.844A pdb=" N LYS B 30 " --> pdb=" O ASP B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 94 Proline residue: B 84 - end of helix Processing helix chain 'B' and resid 112 through 116 Processing helix chain 'B' and resid 120 through 132 Processing helix chain 'B' and resid 132 through 141 Processing helix chain 'B' and resid 142 through 148 Processing helix chain 'B' and resid 168 through 178 removed outlier: 3.521A pdb=" N GLY B 172 " --> pdb=" O ASP B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 185 removed outlier: 5.718A pdb=" N ASN B 183 " --> pdb=" O PRO B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 209 Processing helix chain 'B' and resid 209 through 215 Processing helix chain 'B' and resid 223 through 227 Processing helix chain 'B' and resid 233 through 241 removed outlier: 3.524A pdb=" N LEU B 237 " --> pdb=" O ASN B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 247 Processing helix chain 'B' and resid 248 through 254 Processing helix chain 'B' and resid 323 through 326 Processing helix chain 'B' and resid 344 through 352 Processing helix chain 'B' and resid 354 through 358 Processing helix chain 'B' and resid 447 through 461 Processing helix chain 'A' and resid 24 through 30 removed outlier: 3.844A pdb=" N LYS A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 94 Proline residue: A 84 - end of helix Processing helix chain 'A' and resid 112 through 116 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'A' and resid 132 through 141 Processing helix chain 'A' and resid 142 through 148 Processing helix chain 'A' and resid 168 through 178 removed outlier: 3.521A pdb=" N GLY A 172 " --> pdb=" O ASP A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 185 removed outlier: 5.719A pdb=" N ASN A 183 " --> pdb=" O PRO A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 209 Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 223 through 227 Processing helix chain 'A' and resid 233 through 241 removed outlier: 3.523A pdb=" N LEU A 237 " --> pdb=" O ASN A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 248 through 254 Processing helix chain 'A' and resid 323 through 326 Processing helix chain 'A' and resid 344 through 352 Processing helix chain 'A' and resid 354 through 358 Processing helix chain 'A' and resid 447 through 461 Processing helix chain 'C' and resid 24 through 30 removed outlier: 3.845A pdb=" N LYS C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 94 Proline residue: C 84 - end of helix Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'C' and resid 120 through 132 Processing helix chain 'C' and resid 132 through 141 Processing helix chain 'C' and resid 142 through 148 Processing helix chain 'C' and resid 168 through 178 removed outlier: 3.521A pdb=" N GLY C 172 " --> pdb=" O ASP C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 185 removed outlier: 5.719A pdb=" N ASN C 183 " --> pdb=" O PRO C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 209 Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'C' and resid 223 through 227 Processing helix chain 'C' and resid 233 through 241 removed outlier: 3.524A pdb=" N LEU C 237 " --> pdb=" O ASN C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 247 Processing helix chain 'C' and resid 248 through 254 Processing helix chain 'C' and resid 323 through 326 Processing helix chain 'C' and resid 344 through 352 Processing helix chain 'C' and resid 354 through 358 Processing helix chain 'C' and resid 447 through 461 Processing sheet with id=AA1, first strand: chain 'B' and resid 327 through 328 removed outlier: 7.811A pdb=" N VAL B 333 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASN B 40 " --> pdb=" O VAL B 333 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N CYS B 335 " --> pdb=" O ASN B 40 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LYS B 42 " --> pdb=" O CYS B 335 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N ILE B 33 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N LEU B 291 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N LYS B 35 " --> pdb=" O GLN B 289 " (cutoff:3.500A) removed outlier: 10.187A pdb=" N GLN B 289 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 11.016A pdb=" N LEU B 37 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 10.071A pdb=" N VAL B 287 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 11.050A pdb=" N TYR B 39 " --> pdb=" O ASN B 285 " (cutoff:3.500A) removed outlier: 9.655A pdb=" N ASN B 285 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N TYR B 41 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N PHE B 310 " --> pdb=" O ILE B 321 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE B 321 " --> pdb=" O PHE B 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 153 through 157 removed outlier: 7.841A pdb=" N THR B 163 " --> pdb=" O THR B 49 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU B 51 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N TYR B 270 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N VAL B 264 " --> pdb=" O TYR B 270 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA B 272 " --> pdb=" O ILE B 262 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.789A pdb=" N MET B 110 " --> pdb=" O SER C 423 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 118 through 119 Processing sheet with id=AA5, first strand: chain 'B' and resid 296 through 298 Processing sheet with id=AA6, first strand: chain 'B' and resid 405 through 407 Processing sheet with id=AA7, first strand: chain 'B' and resid 394 through 395 Processing sheet with id=AA8, first strand: chain 'A' and resid 327 through 328 removed outlier: 7.811A pdb=" N VAL A 333 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASN A 40 " --> pdb=" O VAL A 333 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N CYS A 335 " --> pdb=" O ASN A 40 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LYS A 42 " --> pdb=" O CYS A 335 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N ILE A 33 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N LEU A 291 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N LYS A 35 " --> pdb=" O GLN A 289 " (cutoff:3.500A) removed outlier: 10.188A pdb=" N GLN A 289 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 11.016A pdb=" N LEU A 37 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 10.071A pdb=" N VAL A 287 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 11.050A pdb=" N TYR A 39 " --> pdb=" O ASN A 285 " (cutoff:3.500A) removed outlier: 9.655A pdb=" N ASN A 285 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N TYR A 41 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N PHE A 310 " --> pdb=" O ILE A 321 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE A 321 " --> pdb=" O PHE A 310 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 153 through 157 removed outlier: 7.841A pdb=" N THR A 163 " --> pdb=" O THR A 49 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU A 51 " --> pdb=" O THR A 163 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N TYR A 270 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N VAL A 264 " --> pdb=" O TYR A 270 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA A 272 " --> pdb=" O ILE A 262 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 296 through 298 Processing sheet with id=AB2, first strand: chain 'A' and resid 405 through 407 Processing sheet with id=AB3, first strand: chain 'A' and resid 394 through 395 Processing sheet with id=AB4, first strand: chain 'C' and resid 327 through 328 removed outlier: 7.811A pdb=" N VAL C 333 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASN C 40 " --> pdb=" O VAL C 333 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N CYS C 335 " --> pdb=" O ASN C 40 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LYS C 42 " --> pdb=" O CYS C 335 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N ILE C 33 " --> pdb=" O LEU C 291 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N LEU C 291 " --> pdb=" O ILE C 33 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N LYS C 35 " --> pdb=" O GLN C 289 " (cutoff:3.500A) removed outlier: 10.187A pdb=" N GLN C 289 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 11.016A pdb=" N LEU C 37 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 10.071A pdb=" N VAL C 287 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 11.050A pdb=" N TYR C 39 " --> pdb=" O ASN C 285 " (cutoff:3.500A) removed outlier: 9.655A pdb=" N ASN C 285 " --> pdb=" O TYR C 39 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N TYR C 41 " --> pdb=" O VAL C 283 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N PHE C 310 " --> pdb=" O ILE C 321 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE C 321 " --> pdb=" O PHE C 310 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 153 through 157 removed outlier: 7.841A pdb=" N THR C 163 " --> pdb=" O THR C 49 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU C 51 " --> pdb=" O THR C 163 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N TYR C 270 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N VAL C 264 " --> pdb=" O TYR C 270 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA C 272 " --> pdb=" O ILE C 262 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 296 through 298 496 hydrogen bonds defined for protein. 1317 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: 3.83 Time building geometry restraints manager: 4.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1954 1.32 - 1.45: 2325 1.45 - 1.58: 5663 1.58 - 1.72: 3 1.72 - 1.85: 78 Bond restraints: 10023 Sorted by residual: bond pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sigma weight residual 1.417 1.500 -0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" C5 BMA E 3 " pdb=" O5 BMA E 3 " ideal model delta sigma weight residual 1.417 1.500 -0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" C5 BMA F 3 " pdb=" O5 BMA F 3 " ideal model delta sigma weight residual 1.417 1.500 -0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" NE ARG C 370 " pdb=" CZ ARG C 370 " ideal model delta sigma weight residual 1.326 1.371 -0.045 1.10e-02 8.26e+03 1.70e+01 bond pdb=" NE ARG B 370 " pdb=" CZ ARG B 370 " ideal model delta sigma weight residual 1.326 1.371 -0.045 1.10e-02 8.26e+03 1.69e+01 ... (remaining 10018 not shown) Histogram of bond angle deviations from ideal: 100.64 - 107.23: 281 107.23 - 113.83: 5670 113.83 - 120.43: 3972 120.43 - 127.02: 3696 127.02 - 133.62: 28 Bond angle restraints: 13647 Sorted by residual: angle pdb=" C GLY C 441 " pdb=" N PRO C 442 " pdb=" CA PRO C 442 " ideal model delta sigma weight residual 119.66 125.54 -5.88 7.20e-01 1.93e+00 6.68e+01 angle pdb=" C GLY B 441 " pdb=" N PRO B 442 " pdb=" CA PRO B 442 " ideal model delta sigma weight residual 119.66 125.52 -5.86 7.20e-01 1.93e+00 6.62e+01 angle pdb=" C GLY A 441 " pdb=" N PRO A 442 " pdb=" CA PRO A 442 " ideal model delta sigma weight residual 119.66 125.51 -5.85 7.20e-01 1.93e+00 6.60e+01 angle pdb=" C SER A 46 " pdb=" N PRO A 47 " pdb=" CA PRO A 47 " ideal model delta sigma weight residual 120.31 127.85 -7.54 9.80e-01 1.04e+00 5.92e+01 angle pdb=" C SER C 46 " pdb=" N PRO C 47 " pdb=" CA PRO C 47 " ideal model delta sigma weight residual 120.31 127.84 -7.53 9.80e-01 1.04e+00 5.90e+01 ... (remaining 13642 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.32: 6084 21.32 - 42.64: 129 42.64 - 63.95: 48 63.95 - 85.27: 18 85.27 - 106.59: 18 Dihedral angle restraints: 6297 sinusoidal: 2538 harmonic: 3759 Sorted by residual: dihedral pdb=" CB CYS A 66 " pdb=" SG CYS A 66 " pdb=" SG CYS A 187 " pdb=" CB CYS A 187 " ideal model delta sinusoidal sigma weight residual -86.00 -40.01 -45.99 1 1.00e+01 1.00e-02 2.93e+01 dihedral pdb=" CB CYS C 66 " pdb=" SG CYS C 66 " pdb=" SG CYS C 187 " pdb=" CB CYS C 187 " ideal model delta sinusoidal sigma weight residual -86.00 -40.01 -45.99 1 1.00e+01 1.00e-02 2.93e+01 dihedral pdb=" CB CYS B 66 " pdb=" SG CYS B 66 " pdb=" SG CYS B 187 " pdb=" CB CYS B 187 " ideal model delta sinusoidal sigma weight residual -86.00 -40.03 -45.97 1 1.00e+01 1.00e-02 2.93e+01 ... (remaining 6294 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1239 0.090 - 0.179: 395 0.179 - 0.269: 61 0.269 - 0.358: 24 0.358 - 0.448: 6 Chirality restraints: 1725 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-02 2.50e+03 4.00e+01 chirality pdb=" C1 BMA E 3 " pdb=" O4 NAG E 2 " pdb=" C2 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-02 2.50e+03 3.94e+01 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-02 2.50e+03 3.92e+01 ... (remaining 1722 not shown) Planarity restraints: 1734 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 459 " 0.022 2.00e-02 2.50e+03 2.36e-02 6.93e+00 pdb=" CG ASN A 459 " -0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN A 459 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN A 459 " -0.037 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 459 " 0.022 2.00e-02 2.50e+03 2.35e-02 6.90e+00 pdb=" CG ASN B 459 " -0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN B 459 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN B 459 " -0.037 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 459 " 0.022 2.00e-02 2.50e+03 2.35e-02 6.88e+00 pdb=" CG ASN C 459 " -0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN C 459 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN C 459 " -0.037 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " 0.029 2.00e-02 2.50e+03 ... (remaining 1731 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 3548 2.88 - 3.38: 9629 3.38 - 3.89: 18208 3.89 - 4.39: 21164 4.39 - 4.90: 34074 Nonbonded interactions: 86623 Sorted by model distance: nonbonded pdb=" OD1 ASP C 61 " pdb=" NE ARG C 64 " model vdw 2.371 2.520 nonbonded pdb=" OD1 ASP A 61 " pdb=" NE ARG A 64 " model vdw 2.371 2.520 nonbonded pdb=" OD1 ASP B 61 " pdb=" NE ARG B 64 " model vdw 2.372 2.520 nonbonded pdb=" N VAL B 368 " pdb=" O VAL B 368 " model vdw 2.498 2.496 nonbonded pdb=" N VAL A 368 " pdb=" O VAL A 368 " model vdw 2.498 2.496 ... (remaining 86618 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 32.130 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 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 : 0.014 0.083 10023 Z= 0.927 Angle : 1.357 10.340 13647 Z= 0.927 Chirality : 0.092 0.448 1725 Planarity : 0.005 0.020 1728 Dihedral : 12.896 106.589 3834 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 0.75 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.40 % Favored : 98.36 % Rotamer: Outliers : 0.28 % Allowed : 0.84 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.03 (0.21), residues: 1284 helix: 0.06 (0.22), residues: 447 sheet: 0.29 (0.30), residues: 261 loop : 0.05 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.005 TRP C 303 HIS 0.004 0.001 HIS A 253 PHE 0.011 0.004 PHE C 71 TYR 0.030 0.006 TYR B 41 ARG 0.004 0.001 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 114 time to evaluate : 1.090 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 116 average time/residue: 1.9440 time to fit residues: 237.4403 Evaluate side-chains 62 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 320 ASN B 454 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10023 Z= 0.220 Angle : 0.595 6.908 13647 Z= 0.318 Chirality : 0.046 0.138 1725 Planarity : 0.004 0.041 1728 Dihedral : 9.916 70.433 1623 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.23 % Allowed : 0.86 % Favored : 98.91 % Rotamer: Outliers : 1.21 % Allowed : 5.57 % Favored : 93.22 % 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: 0.77 (0.22), residues: 1284 helix: 1.30 (0.24), residues: 483 sheet: 0.23 (0.30), residues: 267 loop : 0.06 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 303 HIS 0.002 0.001 HIS C 130 PHE 0.014 0.002 PHE A 230 TYR 0.021 0.002 TYR C 249 ARG 0.009 0.001 ARG A 64 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 68 time to evaluate : 1.242 Fit side-chains outliers start: 13 outliers final: 4 residues processed: 71 average time/residue: 1.5306 time to fit residues: 116.7256 Evaluate side-chains 61 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 57 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 367 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 79 optimal weight: 0.0170 chunk 32 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 116 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.5624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 GLN B 177 ASN B 454 GLN A 177 ASN C 177 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10023 Z= 0.350 Angle : 0.586 5.471 13647 Z= 0.311 Chirality : 0.047 0.152 1725 Planarity : 0.004 0.034 1728 Dihedral : 7.119 59.970 1623 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.56 % Favored : 98.21 % Rotamer: Outliers : 1.02 % Allowed : 6.22 % Favored : 92.76 % 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: 0.90 (0.23), residues: 1284 helix: 1.47 (0.24), residues: 483 sheet: 0.37 (0.29), residues: 297 loop : 0.02 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 303 HIS 0.005 0.001 HIS A 130 PHE 0.012 0.002 PHE B 234 TYR 0.018 0.002 TYR A 41 ARG 0.008 0.001 ARG A 64 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 59 time to evaluate : 1.258 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 60 average time/residue: 1.5121 time to fit residues: 97.6667 Evaluate side-chains 55 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 367 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 4.9990 chunk 88 optimal weight: 0.2980 chunk 60 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 61 optimal weight: 0.4980 chunk 111 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 454 GLN A 157 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10023 Z= 0.203 Angle : 0.496 5.335 13647 Z= 0.265 Chirality : 0.044 0.182 1725 Planarity : 0.003 0.033 1728 Dihedral : 5.636 47.591 1623 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.23 % Allowed : 0.86 % Favored : 98.91 % Rotamer: Outliers : 1.49 % Allowed : 6.87 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.23), residues: 1284 helix: 1.63 (0.23), residues: 483 sheet: 0.41 (0.30), residues: 297 loop : -0.01 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 303 HIS 0.002 0.001 HIS C 130 PHE 0.010 0.001 PHE C 277 TYR 0.016 0.001 TYR A 249 ARG 0.004 0.000 ARG A 64 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 55 time to evaluate : 1.243 Fit side-chains REVERT: B 455 LEU cc_start: 0.7460 (tp) cc_final: 0.7257 (mt) outliers start: 16 outliers final: 4 residues processed: 63 average time/residue: 1.2804 time to fit residues: 87.7865 Evaluate side-chains 54 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 2.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 367 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 1.9990 chunk 70 optimal weight: 0.0670 chunk 1 optimal weight: 0.7980 chunk 92 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 overall best weight: 0.8922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 454 GLN C 157 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10023 Z= 0.213 Angle : 0.487 5.313 13647 Z= 0.263 Chirality : 0.044 0.150 1725 Planarity : 0.003 0.033 1728 Dihedral : 5.069 34.121 1623 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.64 % Favored : 98.13 % Rotamer: Outliers : 1.30 % Allowed : 7.34 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.23), residues: 1284 helix: 1.78 (0.24), residues: 477 sheet: 0.38 (0.30), residues: 297 loop : -0.05 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 303 HIS 0.003 0.001 HIS A 130 PHE 0.008 0.001 PHE A 277 TYR 0.015 0.001 TYR A 249 ARG 0.004 0.000 ARG C 131 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 56 time to evaluate : 1.192 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 62 average time/residue: 1.3631 time to fit residues: 91.5224 Evaluate side-chains 58 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 51 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain C residue 239 LYS Chi-restraints excluded: chain C residue 367 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 7.9990 chunk 112 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 73 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 124 optimal weight: 0.0270 chunk 103 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10023 Z= 0.161 Angle : 0.473 5.879 13647 Z= 0.255 Chirality : 0.044 0.193 1725 Planarity : 0.003 0.033 1728 Dihedral : 4.729 21.390 1623 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.40 % Favored : 98.36 % Rotamer: Outliers : 1.67 % Allowed : 7.34 % Favored : 90.99 % 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: 1.09 (0.23), residues: 1284 helix: 1.81 (0.24), residues: 477 sheet: 0.51 (0.31), residues: 282 loop : -0.09 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 303 HIS 0.002 0.001 HIS A 130 PHE 0.008 0.001 PHE A 277 TYR 0.014 0.001 TYR A 249 ARG 0.003 0.000 ARG C 131 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 53 time to evaluate : 1.241 Fit side-chains outliers start: 18 outliers final: 8 residues processed: 64 average time/residue: 1.3492 time to fit residues: 93.6099 Evaluate side-chains 59 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 51 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain C residue 239 LYS Chi-restraints excluded: chain C residue 367 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 0.3980 chunk 71 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 124 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10023 Z= 0.178 Angle : 0.474 5.552 13647 Z= 0.254 Chirality : 0.044 0.157 1725 Planarity : 0.003 0.033 1728 Dihedral : 4.524 21.320 1623 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.71 % Favored : 98.05 % Rotamer: Outliers : 1.21 % Allowed : 7.89 % Favored : 90.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.23), residues: 1284 helix: 1.85 (0.24), residues: 477 sheet: 0.52 (0.31), residues: 282 loop : -0.07 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 303 HIS 0.002 0.001 HIS A 130 PHE 0.008 0.001 PHE B 277 TYR 0.014 0.001 TYR A 249 ARG 0.003 0.000 ARG C 131 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 53 time to evaluate : 1.261 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 59 average time/residue: 1.2706 time to fit residues: 81.7369 Evaluate side-chains 56 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 49 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 239 LYS Chi-restraints excluded: chain C residue 367 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 61 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10023 Z= 0.242 Angle : 0.501 5.942 13647 Z= 0.268 Chirality : 0.044 0.149 1725 Planarity : 0.003 0.032 1728 Dihedral : 4.456 19.853 1623 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.79 % Favored : 97.98 % Rotamer: Outliers : 1.30 % Allowed : 8.26 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.23), residues: 1284 helix: 1.76 (0.24), residues: 483 sheet: 0.46 (0.31), residues: 282 loop : -0.08 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP C 303 HIS 0.002 0.001 HIS A 130 PHE 0.009 0.001 PHE C 234 TYR 0.014 0.001 TYR A 249 ARG 0.002 0.000 ARG C 131 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 52 time to evaluate : 1.265 Fit side-chains REVERT: B 241 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8065 (mtt) outliers start: 14 outliers final: 10 residues processed: 59 average time/residue: 1.2736 time to fit residues: 82.0279 Evaluate side-chains 61 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 50 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 241 MET Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 239 LYS Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain C residue 367 TYR Chi-restraints excluded: chain C residue 455 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10023 Z= 0.251 Angle : 0.501 6.883 13647 Z= 0.269 Chirality : 0.044 0.151 1725 Planarity : 0.003 0.033 1728 Dihedral : 4.425 19.798 1623 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.79 % Favored : 97.98 % Rotamer: Outliers : 1.02 % Allowed : 8.82 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.23), residues: 1284 helix: 1.73 (0.24), residues: 483 sheet: 0.44 (0.31), residues: 282 loop : -0.12 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 303 HIS 0.002 0.001 HIS A 130 PHE 0.008 0.001 PHE B 234 TYR 0.014 0.001 TYR A 249 ARG 0.003 0.000 ARG C 131 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 53 time to evaluate : 1.205 Fit side-chains REVERT: B 241 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8013 (mtt) outliers start: 11 outliers final: 8 residues processed: 59 average time/residue: 1.2613 time to fit residues: 81.1106 Evaluate side-chains 58 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 49 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 241 MET Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 239 LYS Chi-restraints excluded: chain C residue 367 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 128 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10023 Z= 0.250 Angle : 0.521 10.922 13647 Z= 0.278 Chirality : 0.045 0.150 1725 Planarity : 0.003 0.033 1728 Dihedral : 4.408 19.221 1623 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.79 % Favored : 97.98 % Rotamer: Outliers : 0.84 % Allowed : 9.10 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.23), residues: 1284 helix: 1.71 (0.24), residues: 483 sheet: 0.41 (0.31), residues: 282 loop : -0.09 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 303 HIS 0.002 0.001 HIS A 130 PHE 0.008 0.001 PHE B 277 TYR 0.014 0.001 TYR A 249 ARG 0.003 0.000 ARG C 131 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 50 time to evaluate : 1.233 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 8 residues processed: 56 average time/residue: 1.2381 time to fit residues: 76.1212 Evaluate side-chains 55 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 47 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 239 LYS Chi-restraints excluded: chain C residue 367 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 15 optimal weight: 0.0970 chunk 28 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.077897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.058988 restraints weight = 17840.541| |-----------------------------------------------------------------------------| r_work (start): 0.2613 rms_B_bonded: 2.73 r_work: 0.2461 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2311 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10023 Z= 0.216 Angle : 0.497 6.820 13647 Z= 0.267 Chirality : 0.044 0.155 1725 Planarity : 0.003 0.032 1728 Dihedral : 4.356 18.519 1623 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.87 % Favored : 97.90 % Rotamer: Outliers : 1.02 % Allowed : 9.01 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.23), residues: 1284 helix: 1.74 (0.24), residues: 483 sheet: 0.39 (0.30), residues: 282 loop : -0.08 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 303 HIS 0.003 0.001 HIS A 130 PHE 0.008 0.001 PHE B 277 TYR 0.014 0.001 TYR A 249 ARG 0.003 0.000 ARG C 131 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2852.98 seconds wall clock time: 51 minutes 37.49 seconds (3097.49 seconds total)