Starting phenix.real_space_refine on Sun Aug 4 11:30:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvf_41640/08_2024/8tvf_41640.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvf_41640/08_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_41640/08_2024/8tvf_41640.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvf_41640/08_2024/8tvf_41640.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvf_41640/08_2024/8tvf_41640.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvf_41640/08_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-5409/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: 6.84, per 1000 atoms: 0.65 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: 4.28 Conformation dependent library (CDL) restraints added in 2.0 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: 1.42 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: 3.78 Time building geometry restraints manager: 4.69 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 3.120 nonbonded pdb=" OD1 ASP A 61 " pdb=" NE ARG A 64 " model vdw 2.371 3.120 nonbonded pdb=" OD1 ASP B 61 " pdb=" NE ARG B 64 " model vdw 2.372 3.120 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 Time spend for trying shortcut: 0.00 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: 2.280 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: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 32.670 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 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:11.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.550 ------------------------------------------------------------------------------- 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 : 1.192 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 116 average time/residue: 1.8631 time to fit residues: 227.5811 Evaluate side-chains 62 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 1.087 ------------------------------------------------------------------------------- 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: 0.5980 chunk 97 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 101 optimal weight: 0.0070 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 ASN B 320 ASN B 454 GLN A 260 ASN C 260 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1669 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= 0.199 Angle : 0.594 7.085 13647 Z= 0.319 Chirality : 0.045 0.136 1725 Planarity : 0.004 0.045 1728 Dihedral : 10.064 72.077 1623 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.09 % Favored : 98.68 % Rotamer: Outliers : 1.21 % Allowed : 5.76 % Favored : 93.04 % 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: 0.80 (0.22), residues: 1284 helix: 1.27 (0.24), residues: 483 sheet: 0.30 (0.30), residues: 267 loop : 0.11 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 303 HIS 0.002 0.001 HIS C 130 PHE 0.014 0.002 PHE A 230 TYR 0.019 0.002 TYR C 249 ARG 0.008 0.001 ARG C 131 *********************** 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 : 1.209 Fit side-chains outliers start: 13 outliers final: 4 residues processed: 71 average time/residue: 1.4986 time to fit residues: 114.0954 Evaluate side-chains 58 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 1.175 ------------------------------------------------------------------------------- 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: 2.9990 chunk 97 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 116 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 A 177 ASN C 177 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10023 Z= 0.329 Angle : 0.595 5.701 13647 Z= 0.317 Chirality : 0.047 0.154 1725 Planarity : 0.004 0.042 1728 Dihedral : 6.856 59.350 1623 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.40 % Favored : 98.36 % Rotamer: Outliers : 0.93 % Allowed : 6.31 % 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: 0.89 (0.23), residues: 1284 helix: 1.45 (0.24), residues: 483 sheet: 0.33 (0.29), residues: 297 loop : 0.05 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 303 HIS 0.004 0.001 HIS A 130 PHE 0.014 0.002 PHE A 230 TYR 0.020 0.002 TYR A 41 ARG 0.007 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 69 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 59 time to evaluate : 1.091 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 60 average time/residue: 1.4522 time to fit residues: 93.7833 Evaluate side-chains 54 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 1.090 ------------------------------------------------------------------------------- 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: 3.9990 chunk 88 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 61 optimal weight: 0.0970 chunk 111 optimal weight: 0.1980 chunk 33 optimal weight: 3.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 C 157 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10023 Z= 0.148 Angle : 0.482 5.331 13647 Z= 0.258 Chirality : 0.044 0.177 1725 Planarity : 0.003 0.032 1728 Dihedral : 5.587 46.429 1623 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.23 % Allowed : 0.55 % Favored : 99.22 % Rotamer: Outliers : 1.95 % Allowed : 6.22 % Favored : 91.83 % 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: 1.69 (0.24), residues: 483 sheet: 0.41 (0.30), residues: 297 loop : 0.03 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 303 HIS 0.002 0.001 HIS B 130 PHE 0.011 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 86 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 65 time to evaluate : 1.199 Fit side-chains REVERT: B 455 LEU cc_start: 0.7414 (tp) cc_final: 0.7181 (mt) outliers start: 21 outliers final: 3 residues processed: 76 average time/residue: 1.4354 time to fit residues: 117.9062 Evaluate side-chains 54 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 51 time to evaluate : 1.229 ------------------------------------------------------------------------------- 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 367 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 0.9980 chunk 70 optimal weight: 0.0470 chunk 1 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- 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: 0.7973 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10023 Z= 0.183 Angle : 0.486 5.422 13647 Z= 0.260 Chirality : 0.044 0.162 1725 Planarity : 0.003 0.034 1728 Dihedral : 5.065 34.470 1623 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.48 % Favored : 98.29 % Rotamer: Outliers : 1.11 % Allowed : 8.26 % Favored : 90.62 % 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: 0.41 (0.30), residues: 297 loop : 0.02 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 303 HIS 0.002 0.001 HIS A 130 PHE 0.009 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 72 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 60 time to evaluate : 1.192 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 63 average time/residue: 1.3697 time to fit residues: 93.7874 Evaluate side-chains 58 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 1.186 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 24 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 162 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2731 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= 0.207 Angle : 0.487 5.681 13647 Z= 0.262 Chirality : 0.044 0.196 1725 Planarity : 0.003 0.033 1728 Dihedral : 4.784 22.477 1623 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.64 % Favored : 98.13 % Rotamer: Outliers : 1.39 % Allowed : 7.99 % Favored : 90.62 % 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: 1.12 (0.23), residues: 1284 helix: 1.84 (0.24), residues: 477 sheet: 0.38 (0.30), residues: 297 loop : 0.03 (0.27), 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 0.009 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 66 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 51 time to evaluate : 1.222 Fit side-chains outliers start: 15 outliers final: 8 residues processed: 58 average time/residue: 1.2251 time to fit residues: 77.7440 Evaluate side-chains 57 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 1.167 ------------------------------------------------------------------------------- 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 68 GLN 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: 0.7980 chunk 71 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 75 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7981 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10023 Z= 0.189 Angle : 0.477 5.064 13647 Z= 0.257 Chirality : 0.044 0.172 1725 Planarity : 0.003 0.033 1728 Dihedral : 4.571 22.868 1623 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.48 % Favored : 98.29 % Rotamer: Outliers : 1.11 % Allowed : 8.54 % Favored : 90.34 % 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: 1.86 (0.24), residues: 477 sheet: 0.46 (0.31), residues: 282 loop : -0.03 (0.26), residues: 525 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 A 277 TYR 0.014 0.001 TYR A 249 ARG 0.004 0.000 ARG B 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 63 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 51 time to evaluate : 1.200 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 55 average time/residue: 1.2904 time to fit residues: 77.4622 Evaluate side-chains 55 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 49 time to evaluate : 1.282 ------------------------------------------------------------------------------- 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 367 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 84 optimal weight: 0.0040 chunk 61 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 0.4980 chunk 119 optimal weight: 4.9990 overall best weight: 1.2998 ------------------------------------------------------------------------------- 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: 0.8013 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 : 0.004 0.048 10023 Z= 0.277 Angle : 0.518 5.801 13647 Z= 0.278 Chirality : 0.045 0.159 1725 Planarity : 0.003 0.032 1728 Dihedral : 4.563 20.938 1623 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 2.16 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: 1.72 (0.24), residues: 483 sheet: 0.27 (0.30), residues: 297 loop : 0.00 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 303 HIS 0.002 0.001 HIS A 130 PHE 0.011 0.002 PHE C 234 TYR 0.014 0.002 TYR A 249 ARG 0.002 0.000 ARG B 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 63 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 52 time to evaluate : 1.171 Fit side-chains REVERT: B 241 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.7979 (mtt) outliers start: 11 outliers final: 6 residues processed: 57 average time/residue: 1.1812 time to fit residues: 73.8433 Evaluate side-chains 56 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 49 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 367 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 0.4980 chunk 115 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 104 optimal weight: 0.4980 chunk 109 optimal weight: 0.4980 chunk 76 optimal weight: 3.9990 chunk 122 optimal weight: 0.0070 overall best weight: 0.5000 ------------------------------------------------------------------------------- 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: 0.7970 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10023 Z= 0.150 Angle : 0.468 6.307 13647 Z= 0.252 Chirality : 0.043 0.159 1725 Planarity : 0.003 0.032 1728 Dihedral : 4.415 20.086 1623 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.17 % Favored : 98.60 % Rotamer: Outliers : 0.93 % Allowed : 9.38 % Favored : 89.69 % 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: 1.09 (0.24), residues: 1284 helix: 1.81 (0.24), residues: 483 sheet: 0.42 (0.31), residues: 282 loop : -0.04 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP C 303 HIS 0.002 0.001 HIS B 130 PHE 0.009 0.001 PHE B 277 TYR 0.013 0.001 TYR A 249 ARG 0.004 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 65 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 55 time to evaluate : 0.987 Fit side-chains REVERT: B 241 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.7986 (mtt) outliers start: 10 outliers final: 4 residues processed: 59 average time/residue: 1.2506 time to fit residues: 80.9028 Evaluate side-chains 54 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 49 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.0020 chunk 85 optimal weight: 7.9990 chunk 128 optimal weight: 9.9990 chunk 118 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 overall best weight: 0.6988 ------------------------------------------------------------------------------- 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: 0.7980 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10023 Z= 0.184 Angle : 0.502 8.081 13647 Z= 0.269 Chirality : 0.044 0.190 1725 Planarity : 0.003 0.032 1728 Dihedral : 4.376 19.685 1623 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.56 % Favored : 98.21 % Rotamer: Outliers : 0.65 % Allowed : 9.56 % Favored : 89.79 % 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: 1.08 (0.23), residues: 1284 helix: 1.78 (0.24), residues: 483 sheet: 0.43 (0.31), residues: 282 loop : -0.03 (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 0.009 0.001 PHE B 277 TYR 0.013 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 57 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 50 time to evaluate : 1.185 Fit side-chains revert: symmetry clash REVERT: B 241 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.7998 (mtt) outliers start: 7 outliers final: 5 residues processed: 54 average time/residue: 1.1663 time to fit residues: 69.6244 Evaluate side-chains 54 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 48 time to evaluate : 1.148 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 15 optimal weight: 0.0970 chunk 28 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.3012 r_free = 0.3012 target = 0.078326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.059648 restraints weight = 17754.118| |-----------------------------------------------------------------------------| r_work (start): 0.2648 rms_B_bonded: 2.73 r_work: 0.2496 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10023 Z= 0.165 Angle : 0.498 11.113 13647 Z= 0.265 Chirality : 0.043 0.151 1725 Planarity : 0.003 0.032 1728 Dihedral : 4.330 19.012 1623 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.32 % Favored : 98.44 % Rotamer: Outliers : 0.56 % Allowed : 9.84 % Favored : 89.60 % 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: 1.16 (0.24), residues: 1284 helix: 1.85 (0.24), residues: 483 sheet: 0.44 (0.31), residues: 282 loop : 0.03 (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 0.009 0.001 PHE B 277 TYR 0.013 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: 2700.65 seconds wall clock time: 48 minutes 31.19 seconds (2911.19 seconds total)