Starting phenix.real_space_refine on Fri Feb 16 22:16:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fsz_29422/02_2024/8fsz_29422_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fsz_29422/02_2024/8fsz_29422.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fsz_29422/02_2024/8fsz_29422_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fsz_29422/02_2024/8fsz_29422_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fsz_29422/02_2024/8fsz_29422_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fsz_29422/02_2024/8fsz_29422.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fsz_29422/02_2024/8fsz_29422.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fsz_29422/02_2024/8fsz_29422_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fsz_29422/02_2024/8fsz_29422_updated.pdb" } resolution = 3.79 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= 0.003 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 45 5.16 5 C 10990 2.51 5 N 2710 2.21 5 O 2945 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 31": "NH1" <-> "NH2" Residue "A ARG 120": "NH1" <-> "NH2" Residue "A ASP 202": "OD1" <-> "OD2" Residue "B ARG 31": "NH1" <-> "NH2" Residue "B ARG 120": "NH1" <-> "NH2" Residue "B ASP 202": "OD1" <-> "OD2" Residue "C ARG 31": "NH1" <-> "NH2" Residue "C ARG 120": "NH1" <-> "NH2" Residue "C ASP 202": "OD1" <-> "OD2" Residue "D ARG 31": "NH1" <-> "NH2" Residue "D ARG 120": "NH1" <-> "NH2" Residue "D ASP 202": "OD1" <-> "OD2" Residue "E ARG 31": "NH1" <-> "NH2" Residue "E ARG 120": "NH1" <-> "NH2" Residue "E ASP 202": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16690 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3273 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Chain: "B" Number of atoms: 3273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3273 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Chain: "C" Number of atoms: 3273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3273 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Chain: "D" Number of atoms: 3273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3273 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Chain: "E" Number of atoms: 3273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3273 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 88 Unusual residues: {'NAG': 3, 'Y7H': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 65 Unusual residues: {'NAG': 3, 'Y7H': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 65 Unusual residues: {'NAG': 3, 'Y7H': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 65 Unusual residues: {'NAG': 3, 'Y7H': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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 Time building chain proxies: 9.30, per 1000 atoms: 0.56 Number of scatterers: 16690 At special positions: 0 Unit cell: (100.1, 97.9, 170.5, 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 45 16.00 O 2945 8.00 N 2710 7.00 C 10990 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 149 " 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 NAG-ASN " NAG A 502 " - " ASN A 82 " " NAG A 503 " - " ASN A 148 " " NAG A 504 " - " ASN A 164 " " NAG B 501 " - " ASN B 82 " " NAG B 502 " - " ASN B 148 " " NAG B 503 " - " ASN B 164 " " NAG C 501 " - " ASN C 82 " " NAG C 502 " - " ASN C 148 " " NAG C 503 " - " ASN C 164 " " NAG D 501 " - " ASN D 82 " " NAG D 502 " - " ASN D 148 " " NAG D 503 " - " ASN D 164 " " NAG E 501 " - " ASN E 82 " " NAG E 502 " - " ASN E 148 " " NAG E 503 " - " ASN E 164 " Time building additional restraints: 6.13 Conformation dependent library (CDL) restraints added in 2.9 seconds 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3840 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 20 sheets defined 41.5% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.71 Creating SS restraints... Processing helix chain 'A' and resid 11 through 19 Processing helix chain 'A' and resid 119 through 121 No H-bonds generated for 'chain 'A' and resid 119 through 121' Processing helix chain 'A' and resid 171 through 175 Processing helix chain 'A' and resid 221 through 240 removed outlier: 3.550A pdb=" N SER A 226 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Proline residue: A 230 - end of helix removed outlier: 4.565A pdb=" N VAL A 236 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N VAL A 237 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ASP A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ILE A 239 " --> pdb=" O MET A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 261 removed outlier: 4.307A pdb=" N LEU A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 272 removed outlier: 3.955A pdb=" N ILE A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 309 removed outlier: 4.202A pdb=" N VAL A 288 " --> pdb=" O GLY A 284 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET A 291 " --> pdb=" O PHE A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 330 Processing helix chain 'A' and resid 398 through 424 removed outlier: 3.716A pdb=" N ILE A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG A 410 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N HIS A 411 " --> pdb=" O SER A 407 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET A 419 " --> pdb=" O LYS A 415 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ARG A 420 " --> pdb=" O ARG A 416 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N GLU A 421 " --> pdb=" O ASP A 417 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL A 422 " --> pdb=" O GLU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 463 removed outlier: 4.650A pdb=" N ARG A 435 " --> pdb=" O TYR A 431 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 436 " --> pdb=" O VAL A 432 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLU A 463 " --> pdb=" O TRP A 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 19 Processing helix chain 'B' and resid 119 through 121 No H-bonds generated for 'chain 'B' and resid 119 through 121' Processing helix chain 'B' and resid 171 through 175 Processing helix chain 'B' and resid 221 through 240 removed outlier: 3.550A pdb=" N SER B 226 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) Proline residue: B 230 - end of helix removed outlier: 4.566A pdb=" N VAL B 236 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N VAL B 237 " --> pdb=" O PHE B 233 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ASP B 238 " --> pdb=" O LEU B 234 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ILE B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 261 removed outlier: 4.306A pdb=" N LEU B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 272 removed outlier: 3.955A pdb=" N ILE B 267 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE B 268 " --> pdb=" O VAL B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 309 removed outlier: 4.203A pdb=" N VAL B 288 " --> pdb=" O GLY B 284 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET B 291 " --> pdb=" O PHE B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 330 Processing helix chain 'B' and resid 398 through 424 removed outlier: 3.715A pdb=" N ILE B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG B 410 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N HIS B 411 " --> pdb=" O SER B 407 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET B 419 " --> pdb=" O LYS B 415 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ARG B 420 " --> pdb=" O ARG B 416 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N GLU B 421 " --> pdb=" O ASP B 417 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL B 422 " --> pdb=" O GLU B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 463 removed outlier: 4.650A pdb=" N ARG B 435 " --> pdb=" O TYR B 431 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 436 " --> pdb=" O VAL B 432 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLU B 463 " --> pdb=" O TRP B 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 19 Processing helix chain 'C' and resid 119 through 121 No H-bonds generated for 'chain 'C' and resid 119 through 121' Processing helix chain 'C' and resid 171 through 175 Processing helix chain 'C' and resid 221 through 240 removed outlier: 3.550A pdb=" N SER C 226 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) Proline residue: C 230 - end of helix removed outlier: 4.566A pdb=" N VAL C 236 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N VAL C 237 " --> pdb=" O PHE C 233 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ASP C 238 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ILE C 239 " --> pdb=" O MET C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 261 removed outlier: 4.307A pdb=" N LEU C 260 " --> pdb=" O ILE C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 272 removed outlier: 3.956A pdb=" N ILE C 267 " --> pdb=" O SER C 263 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE C 268 " --> pdb=" O VAL C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 309 removed outlier: 4.203A pdb=" N VAL C 288 " --> pdb=" O GLY C 284 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET C 291 " --> pdb=" O PHE C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 330 Processing helix chain 'C' and resid 398 through 424 removed outlier: 3.716A pdb=" N ILE C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ARG C 410 " --> pdb=" O LEU C 406 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N HIS C 411 " --> pdb=" O SER C 407 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE C 412 " --> pdb=" O SER C 408 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET C 419 " --> pdb=" O LYS C 415 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ARG C 420 " --> pdb=" O ARG C 416 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N GLU C 421 " --> pdb=" O ASP C 417 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL C 422 " --> pdb=" O GLU C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 463 removed outlier: 4.650A pdb=" N ARG C 435 " --> pdb=" O TYR C 431 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU C 436 " --> pdb=" O VAL C 432 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLU C 463 " --> pdb=" O TRP C 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 19 Processing helix chain 'D' and resid 119 through 121 No H-bonds generated for 'chain 'D' and resid 119 through 121' Processing helix chain 'D' and resid 171 through 175 Processing helix chain 'D' and resid 221 through 240 removed outlier: 3.550A pdb=" N SER D 226 " --> pdb=" O PHE D 222 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU D 229 " --> pdb=" O VAL D 225 " (cutoff:3.500A) Proline residue: D 230 - end of helix removed outlier: 4.565A pdb=" N VAL D 236 " --> pdb=" O ILE D 232 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N VAL D 237 " --> pdb=" O PHE D 233 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ASP D 238 " --> pdb=" O LEU D 234 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ILE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 261 removed outlier: 4.306A pdb=" N LEU D 260 " --> pdb=" O ILE D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 272 removed outlier: 3.955A pdb=" N ILE D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE D 268 " --> pdb=" O VAL D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 309 removed outlier: 4.202A pdb=" N VAL D 288 " --> pdb=" O GLY D 284 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET D 291 " --> pdb=" O PHE D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 330 Processing helix chain 'D' and resid 398 through 424 removed outlier: 3.716A pdb=" N ILE D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG D 410 " --> pdb=" O LEU D 406 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N HIS D 411 " --> pdb=" O SER D 407 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE D 412 " --> pdb=" O SER D 408 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET D 419 " --> pdb=" O LYS D 415 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ARG D 420 " --> pdb=" O ARG D 416 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N GLU D 421 " --> pdb=" O ASP D 417 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL D 422 " --> pdb=" O GLU D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 463 removed outlier: 4.650A pdb=" N ARG D 435 " --> pdb=" O TYR D 431 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU D 436 " --> pdb=" O VAL D 432 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLU D 463 " --> pdb=" O TRP D 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 19 Processing helix chain 'E' and resid 119 through 121 No H-bonds generated for 'chain 'E' and resid 119 through 121' Processing helix chain 'E' and resid 171 through 175 Processing helix chain 'E' and resid 221 through 240 removed outlier: 3.550A pdb=" N SER E 226 " --> pdb=" O PHE E 222 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU E 229 " --> pdb=" O VAL E 225 " (cutoff:3.500A) Proline residue: E 230 - end of helix removed outlier: 4.566A pdb=" N VAL E 236 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N VAL E 237 " --> pdb=" O PHE E 233 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ASP E 238 " --> pdb=" O LEU E 234 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ILE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 261 removed outlier: 4.307A pdb=" N LEU E 260 " --> pdb=" O ILE E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 272 removed outlier: 3.955A pdb=" N ILE E 267 " --> pdb=" O SER E 263 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE E 268 " --> pdb=" O VAL E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 309 removed outlier: 4.203A pdb=" N VAL E 288 " --> pdb=" O GLY E 284 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET E 291 " --> pdb=" O PHE E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 330 Processing helix chain 'E' and resid 398 through 424 removed outlier: 3.715A pdb=" N ILE E 409 " --> pdb=" O GLU E 405 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ARG E 410 " --> pdb=" O LEU E 406 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N HIS E 411 " --> pdb=" O SER E 407 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE E 412 " --> pdb=" O SER E 408 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET E 419 " --> pdb=" O LYS E 415 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ARG E 420 " --> pdb=" O ARG E 416 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N GLU E 421 " --> pdb=" O ASP E 417 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL E 422 " --> pdb=" O GLU E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 428 through 463 removed outlier: 4.649A pdb=" N ARG E 435 " --> pdb=" O TYR E 431 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU E 436 " --> pdb=" O VAL E 432 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLU E 463 " --> pdb=" O TRP E 459 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 163 through 167 removed outlier: 6.811A pdb=" N THR A 37 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N THR A 166 " --> pdb=" O THR A 37 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL A 39 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N TYR A 61 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ILE A 48 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N THR A 59 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 50 through 52 removed outlier: 3.909A pdb=" N ASN A 50 " --> pdb=" O THR A 59 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 85 through 89 Processing sheet with id= D, first strand: chain 'A' and resid 98 through 100 removed outlier: 3.682A pdb=" N THR A 154 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N SER A 155 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA A 208 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU A 191 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ARG A 217 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N LEU A 189 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 163 through 167 removed outlier: 6.811A pdb=" N THR B 37 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N THR B 166 " --> pdb=" O THR B 37 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL B 39 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N TYR B 61 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ILE B 48 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N THR B 59 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 50 through 52 removed outlier: 3.909A pdb=" N ASN B 50 " --> pdb=" O THR B 59 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 85 through 89 Processing sheet with id= H, first strand: chain 'B' and resid 98 through 100 removed outlier: 3.682A pdb=" N THR B 154 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N SER B 155 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA B 208 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU B 191 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ARG B 217 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N LEU B 189 " --> pdb=" O ARG B 217 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 163 through 167 removed outlier: 6.810A pdb=" N THR C 37 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N THR C 166 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL C 39 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N TYR C 61 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ILE C 48 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N THR C 59 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 50 through 52 removed outlier: 3.909A pdb=" N ASN C 50 " --> pdb=" O THR C 59 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 85 through 89 Processing sheet with id= L, first strand: chain 'C' and resid 98 through 100 removed outlier: 3.682A pdb=" N THR C 154 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N SER C 155 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA C 208 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU C 191 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ARG C 217 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N LEU C 189 " --> pdb=" O ARG C 217 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 163 through 167 removed outlier: 6.810A pdb=" N THR D 37 " --> pdb=" O ASN D 164 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N THR D 166 " --> pdb=" O THR D 37 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL D 39 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N TYR D 61 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ILE D 48 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N THR D 59 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 50 through 52 removed outlier: 3.909A pdb=" N ASN D 50 " --> pdb=" O THR D 59 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 85 through 89 Processing sheet with id= P, first strand: chain 'D' and resid 98 through 100 removed outlier: 3.682A pdb=" N THR D 154 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N SER D 155 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA D 208 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU D 191 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ARG D 217 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N LEU D 189 " --> pdb=" O ARG D 217 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 163 through 167 removed outlier: 6.811A pdb=" N THR E 37 " --> pdb=" O ASN E 164 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N THR E 166 " --> pdb=" O THR E 37 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL E 39 " --> pdb=" O THR E 166 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N TYR E 61 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ILE E 48 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N THR E 59 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 50 through 52 removed outlier: 3.909A pdb=" N ASN E 50 " --> pdb=" O THR E 59 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 85 through 89 Processing sheet with id= T, first strand: chain 'E' and resid 98 through 100 removed outlier: 3.683A pdb=" N THR E 154 " --> pdb=" O LEU E 99 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N SER E 155 " --> pdb=" O ALA E 208 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA E 208 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU E 191 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ARG E 217 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N LEU E 189 " --> pdb=" O ARG E 217 " (cutoff:3.500A) 690 hydrogen bonds defined for protein. 2010 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: 4.55 Time building geometry restraints manager: 6.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2692 1.32 - 1.44: 4848 1.44 - 1.56: 9550 1.56 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 17160 Sorted by residual: bond pdb=" C10 Y7H A 505 " pdb=" N3 Y7H A 505 " ideal model delta sigma weight residual 1.040 1.475 -0.435 2.00e-02 2.50e+03 4.72e+02 bond pdb=" C10 Y7H A 501 " pdb=" N3 Y7H A 501 " ideal model delta sigma weight residual 1.040 1.474 -0.434 2.00e-02 2.50e+03 4.71e+02 bond pdb=" C10 Y7H B 504 " pdb=" N3 Y7H B 504 " ideal model delta sigma weight residual 1.040 1.474 -0.434 2.00e-02 2.50e+03 4.71e+02 bond pdb=" C10 Y7H C 504 " pdb=" N3 Y7H C 504 " ideal model delta sigma weight residual 1.040 1.474 -0.434 2.00e-02 2.50e+03 4.71e+02 bond pdb=" C10 Y7H D 504 " pdb=" N3 Y7H D 504 " ideal model delta sigma weight residual 1.040 1.474 -0.434 2.00e-02 2.50e+03 4.71e+02 ... (remaining 17155 not shown) Histogram of bond angle deviations from ideal: 100.68 - 107.82: 882 107.82 - 114.95: 10109 114.95 - 122.09: 9458 122.09 - 129.23: 2786 129.23 - 136.36: 225 Bond angle restraints: 23460 Sorted by residual: angle pdb=" C2 Y7H B 504 " pdb=" C8 Y7H B 504 " pdb=" C7 Y7H B 504 " ideal model delta sigma weight residual 110.98 133.72 -22.74 3.00e+00 1.11e-01 5.75e+01 angle pdb=" C2 Y7H A 505 " pdb=" C8 Y7H A 505 " pdb=" C7 Y7H A 505 " ideal model delta sigma weight residual 110.98 133.70 -22.72 3.00e+00 1.11e-01 5.74e+01 angle pdb=" C2 Y7H C 504 " pdb=" C8 Y7H C 504 " pdb=" C7 Y7H C 504 " ideal model delta sigma weight residual 110.98 133.69 -22.71 3.00e+00 1.11e-01 5.73e+01 angle pdb=" C2 Y7H A 501 " pdb=" C8 Y7H A 501 " pdb=" C7 Y7H A 501 " ideal model delta sigma weight residual 110.98 133.69 -22.71 3.00e+00 1.11e-01 5.73e+01 angle pdb=" C2 Y7H D 504 " pdb=" C8 Y7H D 504 " pdb=" C7 Y7H D 504 " ideal model delta sigma weight residual 110.98 133.65 -22.67 3.00e+00 1.11e-01 5.71e+01 ... (remaining 23455 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.35: 10025 32.35 - 64.70: 225 64.70 - 97.04: 35 97.04 - 129.39: 0 129.39 - 161.74: 25 Dihedral angle restraints: 10310 sinusoidal: 4415 harmonic: 5895 Sorted by residual: dihedral pdb=" C12 Y7H B 504 " pdb=" C13 Y7H B 504 " pdb=" C17 Y7H B 504 " pdb=" C16 Y7H B 504 " ideal model delta sinusoidal sigma weight residual 89.09 -72.65 161.74 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" C12 Y7H D 504 " pdb=" C13 Y7H D 504 " pdb=" C17 Y7H D 504 " pdb=" C16 Y7H D 504 " ideal model delta sinusoidal sigma weight residual 89.09 -72.63 161.72 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" C12 Y7H A 501 " pdb=" C13 Y7H A 501 " pdb=" C17 Y7H A 501 " pdb=" C16 Y7H A 501 " ideal model delta sinusoidal sigma weight residual 89.09 -72.63 161.72 1 3.00e+01 1.11e-03 2.08e+01 ... (remaining 10307 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.051: 2745 1.051 - 2.103: 0 2.103 - 3.154: 0 3.154 - 4.206: 0 4.206 - 5.257: 5 Chirality restraints: 2750 Sorted by residual: chirality pdb=" C13 Y7H A 505 " pdb=" C12 Y7H A 505 " pdb=" C14 Y7H A 505 " pdb=" C17 Y7H A 505 " both_signs ideal model delta sigma weight residual False 2.74 -2.51 5.26 2.00e-01 2.50e+01 6.91e+02 chirality pdb=" C13 Y7H A 501 " pdb=" C12 Y7H A 501 " pdb=" C14 Y7H A 501 " pdb=" C17 Y7H A 501 " both_signs ideal model delta sigma weight residual False 2.74 -2.51 5.25 2.00e-01 2.50e+01 6.90e+02 chirality pdb=" C13 Y7H C 504 " pdb=" C12 Y7H C 504 " pdb=" C14 Y7H C 504 " pdb=" C17 Y7H C 504 " both_signs ideal model delta sigma weight residual False 2.74 -2.51 5.25 2.00e-01 2.50e+01 6.90e+02 ... (remaining 2747 not shown) Planarity restraints: 2865 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 106 " 0.028 2.00e-02 2.50e+03 5.75e-02 3.30e+01 pdb=" C VAL D 106 " -0.099 2.00e-02 2.50e+03 pdb=" O VAL D 106 " 0.038 2.00e-02 2.50e+03 pdb=" N GLY D 107 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 106 " 0.028 2.00e-02 2.50e+03 5.73e-02 3.28e+01 pdb=" C VAL C 106 " -0.099 2.00e-02 2.50e+03 pdb=" O VAL C 106 " 0.038 2.00e-02 2.50e+03 pdb=" N GLY C 107 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 106 " 0.028 2.00e-02 2.50e+03 5.73e-02 3.28e+01 pdb=" C VAL B 106 " -0.099 2.00e-02 2.50e+03 pdb=" O VAL B 106 " 0.038 2.00e-02 2.50e+03 pdb=" N GLY B 107 " 0.033 2.00e-02 2.50e+03 ... (remaining 2862 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 6998 2.93 - 3.43: 16262 3.43 - 3.92: 26485 3.92 - 4.41: 28663 4.41 - 4.90: 47538 Nonbonded interactions: 125946 Sorted by model distance: nonbonded pdb=" N TRP B 63 " pdb=" O TRP B 63 " model vdw 2.443 2.496 nonbonded pdb=" N TRP A 63 " pdb=" O TRP A 63 " model vdw 2.443 2.496 nonbonded pdb=" N TRP C 63 " pdb=" O TRP C 63 " model vdw 2.443 2.496 nonbonded pdb=" N TRP E 63 " pdb=" O TRP E 63 " model vdw 2.443 2.496 nonbonded pdb=" N TRP D 63 " pdb=" O TRP D 63 " model vdw 2.444 2.496 ... (remaining 125941 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' and (resid 7 through 465 or resid 502 through 503)) selection = (chain 'B' and (resid 7 through 465 or resid 502 through 503)) selection = (chain 'C' and (resid 7 through 465 or resid 502 through 503)) selection = (chain 'D' and (resid 7 through 465 or resid 502 through 503)) selection = (chain 'E' and (resid 7 through 465 or resid 502 through 503)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 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: 6.510 Check model and map are aligned: 0.230 Set scattering table: 0.130 Process input model: 45.710 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 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 : 0.015 0.435 17160 Z= 0.962 Angle : 1.239 22.740 23460 Z= 0.680 Chirality : 0.232 5.257 2750 Planarity : 0.006 0.057 2850 Dihedral : 16.718 161.738 6455 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % 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: -2.04 (0.18), residues: 1955 helix: -0.14 (0.17), residues: 825 sheet: -0.99 (0.25), residues: 440 loop : -3.08 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP E 331 HIS 0.003 0.001 HIS A 158 PHE 0.029 0.002 PHE D 265 TYR 0.033 0.002 TYR B 262 ARG 0.004 0.001 ARG B 28 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 2.078 Fit side-chains REVERT: B 291 MET cc_start: 0.7720 (mmt) cc_final: 0.7307 (mmt) REVERT: C 291 MET cc_start: 0.7903 (mmt) cc_final: 0.6875 (mmt) REVERT: D 291 MET cc_start: 0.7705 (mmt) cc_final: 0.7369 (mmt) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.3570 time to fit residues: 70.6090 Evaluate side-chains 47 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 1.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 0.8980 chunk 147 optimal weight: 8.9990 chunk 82 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 152 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 177 optimal weight: 0.7980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN A 311 GLN B 66 GLN B 311 GLN C 311 GLN D 66 GLN D 311 GLN E 66 GLN E 311 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 17160 Z= 0.321 Angle : 1.029 21.918 23460 Z= 0.415 Chirality : 0.091 1.862 2750 Planarity : 0.005 0.037 2850 Dihedral : 17.049 170.261 2565 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.14 % Allowed : 9.59 % Favored : 89.27 % 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 (0.19), residues: 1955 helix: 0.67 (0.18), residues: 840 sheet: -0.72 (0.24), residues: 430 loop : -2.63 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 331 HIS 0.005 0.001 HIS A 119 PHE 0.019 0.002 PHE C 265 TYR 0.018 0.002 TYR A 67 ARG 0.004 0.001 ARG B 424 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 46 time to evaluate : 1.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 291 MET cc_start: 0.7424 (mmt) cc_final: 0.7141 (mmt) outliers start: 21 outliers final: 15 residues processed: 65 average time/residue: 0.2467 time to fit residues: 27.7308 Evaluate side-chains 59 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 44 time to evaluate : 1.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 286 TYR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 262 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 147 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 chunk 48 optimal weight: 0.0570 chunk 177 optimal weight: 3.9990 chunk 191 optimal weight: 0.7980 chunk 157 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 142 optimal weight: 7.9990 overall best weight: 2.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17160 Z= 0.272 Angle : 0.994 21.101 23460 Z= 0.394 Chirality : 0.093 1.941 2750 Planarity : 0.004 0.041 2850 Dihedral : 17.050 171.337 2565 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.11 % Allowed : 11.49 % Favored : 86.40 % 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: -0.73 (0.19), residues: 1955 helix: 0.95 (0.18), residues: 840 sheet: -0.44 (0.25), residues: 435 loop : -2.35 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 331 HIS 0.003 0.001 HIS A 119 PHE 0.025 0.001 PHE D 265 TYR 0.015 0.001 TYR A 67 ARG 0.003 0.000 ARG B 420 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 46 time to evaluate : 1.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 LEU cc_start: 0.7180 (OUTLIER) cc_final: 0.6955 (tp) REVERT: B 273 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.7123 (tt) REVERT: C 400 ARG cc_start: 0.3953 (mmp-170) cc_final: 0.3498 (mmt180) outliers start: 39 outliers final: 25 residues processed: 83 average time/residue: 0.2518 time to fit residues: 34.5848 Evaluate side-chains 70 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 43 time to evaluate : 2.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 116 TYR Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 262 TYR Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 439 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 175 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 19 optimal weight: 0.1980 chunk 84 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 188 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 168 optimal weight: 0.5980 chunk 50 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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: 0.7906 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17160 Z= 0.209 Angle : 0.969 20.869 23460 Z= 0.376 Chirality : 0.093 1.945 2750 Planarity : 0.004 0.044 2850 Dihedral : 17.000 171.406 2565 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.84 % Allowed : 13.39 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.51 (0.20), residues: 1955 helix: 1.10 (0.19), residues: 850 sheet: -0.34 (0.24), residues: 435 loop : -2.24 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 331 HIS 0.003 0.001 HIS A 119 PHE 0.033 0.001 PHE E 265 TYR 0.013 0.001 TYR A 67 ARG 0.003 0.000 ARG D 420 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 49 time to evaluate : 1.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 400 ARG cc_start: 0.4216 (mmp-170) cc_final: 0.3529 (mmt180) REVERT: C 400 ARG cc_start: 0.4026 (mmp-170) cc_final: 0.3598 (mmt180) outliers start: 34 outliers final: 23 residues processed: 81 average time/residue: 0.2541 time to fit residues: 34.1805 Evaluate side-chains 71 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 48 time to evaluate : 2.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 286 TYR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 262 TYR Chi-restraints excluded: chain E residue 280 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 156 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 160 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 chunk 169 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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: 0.7986 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 17160 Z= 0.322 Angle : 1.014 21.140 23460 Z= 0.406 Chirality : 0.093 1.926 2750 Planarity : 0.005 0.042 2850 Dihedral : 17.161 171.616 2565 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.38 % Allowed : 13.98 % Favored : 83.63 % 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: -0.70 (0.19), residues: 1955 helix: 0.91 (0.18), residues: 840 sheet: -0.66 (0.24), residues: 460 loop : -2.10 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 331 HIS 0.004 0.001 HIS A 119 PHE 0.024 0.001 PHE D 265 TYR 0.018 0.002 TYR E 67 ARG 0.004 0.000 ARG E 424 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 50 time to evaluate : 2.036 Fit side-chains REVERT: A 223 TYR cc_start: 0.7444 (OUTLIER) cc_final: 0.6636 (t80) REVERT: B 223 TYR cc_start: 0.7499 (OUTLIER) cc_final: 0.6792 (t80) REVERT: B 400 ARG cc_start: 0.4402 (mmp-170) cc_final: 0.3647 (mmt180) REVERT: C 400 ARG cc_start: 0.3946 (mmp-170) cc_final: 0.3119 (mmt180) REVERT: D 223 TYR cc_start: 0.7525 (OUTLIER) cc_final: 0.6856 (t80) outliers start: 44 outliers final: 36 residues processed: 90 average time/residue: 0.2767 time to fit residues: 40.5586 Evaluate side-chains 85 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 46 time to evaluate : 2.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 265 PHE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 223 TYR Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 262 TYR Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 439 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 63 optimal weight: 9.9990 chunk 169 optimal weight: 0.0070 chunk 37 optimal weight: 6.9990 chunk 110 optimal weight: 0.0470 chunk 46 optimal weight: 3.9990 chunk 188 optimal weight: 0.0020 chunk 156 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 overall best weight: 0.8106 ------------------------------------------------------------------------------- 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: 0.7912 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17160 Z= 0.180 Angle : 0.964 20.690 23460 Z= 0.373 Chirality : 0.093 1.954 2750 Planarity : 0.004 0.043 2850 Dihedral : 17.033 171.373 2565 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.79 % Allowed : 15.50 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.20), residues: 1955 helix: 1.15 (0.19), residues: 845 sheet: -0.57 (0.24), residues: 455 loop : -1.91 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 331 HIS 0.002 0.001 HIS B 118 PHE 0.021 0.001 PHE E 265 TYR 0.010 0.001 TYR B 67 ARG 0.002 0.000 ARG B 424 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 48 time to evaluate : 1.814 Fit side-chains revert: symmetry clash REVERT: B 400 ARG cc_start: 0.4400 (mmp-170) cc_final: 0.3718 (mmt180) REVERT: C 400 ARG cc_start: 0.4019 (mmp-170) cc_final: 0.3261 (mmt180) outliers start: 33 outliers final: 27 residues processed: 76 average time/residue: 0.2496 time to fit residues: 31.6349 Evaluate side-chains 73 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 46 time to evaluate : 1.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 262 TYR Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 321 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 181 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 137 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 158 optimal weight: 0.9980 chunk 105 optimal weight: 8.9990 chunk 187 optimal weight: 9.9990 chunk 117 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 HIS B 119 HIS C 119 HIS D 119 HIS E 119 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 17160 Z= 0.419 Angle : 1.051 21.266 23460 Z= 0.430 Chirality : 0.094 1.928 2750 Planarity : 0.005 0.050 2850 Dihedral : 17.308 172.891 2565 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.41 % Allowed : 14.42 % Favored : 82.17 % 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: -0.87 (0.19), residues: 1955 helix: 0.76 (0.18), residues: 835 sheet: -0.76 (0.23), residues: 460 loop : -2.14 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 331 HIS 0.005 0.001 HIS B 119 PHE 0.026 0.002 PHE E 265 TYR 0.022 0.002 TYR E 67 ARG 0.005 0.001 ARG D 306 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 48 time to evaluate : 2.035 Fit side-chains REVERT: A 223 TYR cc_start: 0.7428 (OUTLIER) cc_final: 0.6620 (t80) REVERT: A 258 LEU cc_start: 0.6722 (OUTLIER) cc_final: 0.6254 (pp) REVERT: B 223 TYR cc_start: 0.7602 (OUTLIER) cc_final: 0.6922 (t80) REVERT: B 400 ARG cc_start: 0.4493 (mmp-170) cc_final: 0.3763 (mmt180) REVERT: C 400 ARG cc_start: 0.4459 (mmp-170) cc_final: 0.3594 (mmt180) REVERT: D 223 TYR cc_start: 0.7500 (OUTLIER) cc_final: 0.6652 (t80) outliers start: 63 outliers final: 50 residues processed: 101 average time/residue: 0.2613 time to fit residues: 43.1597 Evaluate side-chains 100 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 46 time to evaluate : 1.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 265 PHE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 441 TYR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 441 TYR Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 223 TYR Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 262 TYR Chi-restraints excluded: chain D residue 265 PHE Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 441 TYR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 101 ASN Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 262 TYR Chi-restraints excluded: chain E residue 265 PHE Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 441 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 116 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 119 optimal weight: 0.3980 chunk 128 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 147 optimal weight: 9.9990 chunk 170 optimal weight: 4.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- 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: 0.8014 moved from start: 0.4468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 17160 Z= 0.343 Angle : 1.026 21.224 23460 Z= 0.413 Chirality : 0.094 1.938 2750 Planarity : 0.005 0.051 2850 Dihedral : 17.290 171.905 2565 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.25 % Allowed : 15.34 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.19), residues: 1955 helix: 0.73 (0.18), residues: 840 sheet: -0.89 (0.23), residues: 460 loop : -2.06 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 331 HIS 0.003 0.001 HIS B 158 PHE 0.030 0.001 PHE B 265 TYR 0.015 0.002 TYR D 67 ARG 0.004 0.000 ARG D 306 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 49 time to evaluate : 2.094 Fit side-chains REVERT: A 258 LEU cc_start: 0.6548 (OUTLIER) cc_final: 0.6140 (pp) REVERT: B 400 ARG cc_start: 0.4443 (mmt180) cc_final: 0.3770 (mmt180) REVERT: C 400 ARG cc_start: 0.4567 (mmt180) cc_final: 0.3867 (mmt180) REVERT: D 223 TYR cc_start: 0.7501 (OUTLIER) cc_final: 0.6842 (t80) REVERT: D 400 ARG cc_start: 0.4123 (mmp-170) cc_final: 0.3327 (mmt180) outliers start: 60 outliers final: 53 residues processed: 105 average time/residue: 0.2769 time to fit residues: 46.0909 Evaluate side-chains 102 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 47 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 265 PHE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 441 TYR Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 223 TYR Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 262 TYR Chi-restraints excluded: chain D residue 265 PHE Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 101 ASN Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 262 TYR Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 439 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 180 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 chunk 175 optimal weight: 0.9980 chunk 105 optimal weight: 8.9990 chunk 76 optimal weight: 6.9990 chunk 137 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 158 optimal weight: 5.9990 chunk 165 optimal weight: 0.8980 chunk 174 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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: 0.7959 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17160 Z= 0.206 Angle : 0.986 20.795 23460 Z= 0.386 Chirality : 0.094 1.952 2750 Planarity : 0.004 0.044 2850 Dihedral : 17.133 171.633 2565 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.38 % Allowed : 16.26 % Favored : 81.36 % 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: -0.57 (0.20), residues: 1955 helix: 0.99 (0.19), residues: 845 sheet: -0.76 (0.23), residues: 460 loop : -1.86 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 331 HIS 0.002 0.001 HIS A 158 PHE 0.030 0.001 PHE B 265 TYR 0.011 0.001 TYR A 67 ARG 0.007 0.000 ARG C 424 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 50 time to evaluate : 2.009 Fit side-chains revert: symmetry clash REVERT: A 258 LEU cc_start: 0.6509 (OUTLIER) cc_final: 0.6126 (pp) REVERT: B 400 ARG cc_start: 0.4439 (mmt180) cc_final: 0.3801 (mmt180) REVERT: C 400 ARG cc_start: 0.4511 (mmt180) cc_final: 0.3837 (mmt180) REVERT: D 400 ARG cc_start: 0.4098 (mmp-170) cc_final: 0.3431 (mmt180) outliers start: 44 outliers final: 39 residues processed: 91 average time/residue: 0.2800 time to fit residues: 40.5955 Evaluate side-chains 87 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 47 time to evaluate : 1.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 262 TYR Chi-restraints excluded: chain D residue 265 PHE Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 265 PHE Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 439 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 185 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 chunk 194 optimal weight: 2.9990 chunk 178 optimal weight: 8.9990 chunk 154 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 119 optimal weight: 0.4980 chunk 94 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- 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: 0.7992 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17160 Z= 0.277 Angle : 1.012 21.051 23460 Z= 0.403 Chirality : 0.093 1.936 2750 Planarity : 0.004 0.048 2850 Dihedral : 17.181 172.139 2565 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.38 % Allowed : 16.37 % Favored : 81.25 % 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: -0.56 (0.20), residues: 1955 helix: 1.01 (0.19), residues: 835 sheet: -0.80 (0.23), residues: 460 loop : -1.78 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 331 HIS 0.003 0.001 HIS C 158 PHE 0.033 0.001 PHE B 265 TYR 0.015 0.001 TYR D 67 ARG 0.005 0.000 ARG C 424 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 48 time to evaluate : 2.071 Fit side-chains revert: symmetry clash REVERT: A 258 LEU cc_start: 0.6642 (OUTLIER) cc_final: 0.6204 (pp) REVERT: B 400 ARG cc_start: 0.4398 (mmt180) cc_final: 0.3772 (mmt180) REVERT: C 400 ARG cc_start: 0.4507 (mmt180) cc_final: 0.3815 (mmt180) REVERT: D 400 ARG cc_start: 0.4290 (mmp-170) cc_final: 0.3503 (mmt180) REVERT: E 258 LEU cc_start: 0.6816 (OUTLIER) cc_final: 0.6478 (pp) outliers start: 44 outliers final: 40 residues processed: 89 average time/residue: 0.2833 time to fit residues: 40.1407 Evaluate side-chains 90 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 48 time to evaluate : 1.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 262 TYR Chi-restraints excluded: chain D residue 265 PHE Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 101 ASN Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 262 TYR Chi-restraints excluded: chain E residue 265 PHE Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 439 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 142 optimal weight: 20.0000 chunk 22 optimal weight: 0.0010 chunk 42 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 136 optimal weight: 0.8980 overall best weight: 1.1190 ------------------------------------------------------------------------------- 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 = 0.3692 r_free = 0.3692 target = 0.081912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.058187 restraints weight = 66286.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.058459 restraints weight = 43580.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.059167 restraints weight = 30379.770| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17160 Z= 0.198 Angle : 0.991 20.822 23460 Z= 0.389 Chirality : 0.093 1.945 2750 Planarity : 0.004 0.042 2850 Dihedral : 17.078 171.460 2565 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.17 % Allowed : 16.59 % Favored : 81.25 % 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: -0.39 (0.20), residues: 1955 helix: 1.17 (0.19), residues: 840 sheet: -0.69 (0.23), residues: 455 loop : -1.78 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 331 HIS 0.002 0.001 HIS B 118 PHE 0.028 0.001 PHE B 265 TYR 0.010 0.001 TYR A 67 ARG 0.005 0.000 ARG C 424 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2431.33 seconds wall clock time: 45 minutes 58.74 seconds (2758.74 seconds total)