Starting phenix.real_space_refine on Mon Nov 18 15:21:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fsz_29422/11_2024/8fsz_29422.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fsz_29422/11_2024/8fsz_29422.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fsz_29422/11_2024/8fsz_29422.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fsz_29422/11_2024/8fsz_29422.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fsz_29422/11_2024/8fsz_29422.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fsz_29422/11_2024/8fsz_29422.cif" } 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. Time to flip 15 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 16690 Number of models: 1 Model: "" Number of chains: 6 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: "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: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'Y7H': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'Y7H': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, D, E Time building chain proxies: 10.32, per 1000 atoms: 0.62 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=2, 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 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: 4.88 Conformation dependent library (CDL) restraints added in 2.3 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... Secondary structure from input PDB file: 50 helices and 15 sheets defined 44.6% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 10 through 20 Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 220 through 234 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 Processing helix chain 'A' and resid 236 through 241 Processing helix chain 'A' and resid 247 through 262 removed outlier: 4.307A pdb=" N LEU A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 273 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 281 through 310 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) removed outlier: 3.889A pdb=" N LYS A 310 " --> pdb=" O ARG A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 332 Processing helix chain 'A' and resid 398 through 425 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 427 through 462 removed outlier: 4.051A pdb=" N TYR A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) 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) Processing helix chain 'B' and resid 10 through 20 Processing helix chain 'B' and resid 170 through 176 Processing helix chain 'B' and resid 220 through 234 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 Processing helix chain 'B' and resid 236 through 241 Processing helix chain 'B' and resid 247 through 262 removed outlier: 4.306A pdb=" N LEU B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 273 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 281 through 310 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) removed outlier: 3.889A pdb=" N LYS B 310 " --> pdb=" O ARG B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 332 Processing helix chain 'B' and resid 398 through 425 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 427 through 462 removed outlier: 4.050A pdb=" N TYR B 431 " --> pdb=" O LEU B 427 " (cutoff:3.500A) 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) Processing helix chain 'C' and resid 10 through 20 Processing helix chain 'C' and resid 170 through 176 Processing helix chain 'C' and resid 220 through 234 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 Processing helix chain 'C' and resid 236 through 241 Processing helix chain 'C' and resid 247 through 262 removed outlier: 4.307A pdb=" N LEU C 260 " --> pdb=" O ILE C 256 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR C 262 " --> pdb=" O LEU C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 273 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 281 through 310 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) removed outlier: 3.889A pdb=" N LYS C 310 " --> pdb=" O ARG C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 332 Processing helix chain 'C' and resid 398 through 425 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 427 through 462 removed outlier: 4.050A pdb=" N TYR C 431 " --> pdb=" O LEU C 427 " (cutoff:3.500A) 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) Processing helix chain 'D' and resid 10 through 20 Processing helix chain 'D' and resid 170 through 176 Processing helix chain 'D' and resid 220 through 234 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 Processing helix chain 'D' and resid 236 through 241 Processing helix chain 'D' and resid 247 through 262 removed outlier: 4.306A pdb=" N LEU D 260 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR D 262 " --> pdb=" O LEU D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 273 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 281 through 310 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) removed outlier: 3.890A pdb=" N LYS D 310 " --> pdb=" O ARG D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 332 Processing helix chain 'D' and resid 398 through 425 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 427 through 462 removed outlier: 4.051A pdb=" N TYR D 431 " --> pdb=" O LEU D 427 " (cutoff:3.500A) 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) Processing helix chain 'E' and resid 10 through 20 Processing helix chain 'E' and resid 170 through 176 Processing helix chain 'E' and resid 220 through 234 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 Processing helix chain 'E' and resid 236 through 241 Processing helix chain 'E' and resid 247 through 262 removed outlier: 4.307A pdb=" N LEU E 260 " --> pdb=" O ILE E 256 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR E 262 " --> pdb=" O LEU E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 273 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 281 through 310 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) removed outlier: 3.888A pdb=" N LYS E 310 " --> pdb=" O ARG E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 332 Processing helix chain 'E' and resid 398 through 425 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 427 through 462 removed outlier: 4.051A pdb=" N TYR E 431 " --> pdb=" O LEU E 427 " (cutoff:3.500A) 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) Processing sheet with id=AA1, first strand: chain 'A' and resid 129 through 133 removed outlier: 3.909A pdb=" N ASN A 50 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N TYR A 61 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ILE A 48 " --> pdb=" O TYR A 61 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N TRP A 63 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N TYR A 46 " --> pdb=" O TRP A 63 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N ARG A 65 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N ILE A 44 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N TYR A 67 " --> pdb=" O ASP A 42 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N ASP A 42 " --> pdb=" O TYR A 67 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE A 41 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 89 Processing sheet with id=AA3, 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=AA4, first strand: chain 'B' and resid 129 through 133 removed outlier: 3.909A pdb=" N ASN B 50 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N TYR B 61 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ILE B 48 " --> pdb=" O TYR B 61 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N TRP B 63 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N TYR B 46 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N ARG B 65 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N ILE B 44 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N TYR B 67 " --> pdb=" O ASP B 42 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N ASP B 42 " --> pdb=" O TYR B 67 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE B 41 " --> pdb=" O THR B 166 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 85 through 89 Processing sheet with id=AA6, 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=AA7, first strand: chain 'C' and resid 129 through 133 removed outlier: 3.909A pdb=" N ASN C 50 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N TYR C 61 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ILE C 48 " --> pdb=" O TYR C 61 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N TRP C 63 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N TYR C 46 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N ARG C 65 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N ILE C 44 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N TYR C 67 " --> pdb=" O ASP C 42 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N ASP C 42 " --> pdb=" O TYR C 67 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE C 41 " --> pdb=" O THR C 166 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 85 through 89 Processing sheet with id=AA9, 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=AB1, first strand: chain 'D' and resid 129 through 133 removed outlier: 3.909A pdb=" N ASN D 50 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N TYR D 61 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ILE D 48 " --> pdb=" O TYR D 61 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N TRP D 63 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N TYR D 46 " --> pdb=" O TRP D 63 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N ARG D 65 " --> pdb=" O ILE D 44 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ILE D 44 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N TYR D 67 " --> pdb=" O ASP D 42 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N ASP D 42 " --> pdb=" O TYR D 67 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE D 41 " --> pdb=" O THR D 166 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 85 through 89 Processing sheet with id=AB3, 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=AB4, first strand: chain 'E' and resid 129 through 133 removed outlier: 3.909A pdb=" N ASN E 50 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N TYR E 61 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ILE E 48 " --> pdb=" O TYR E 61 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N TRP E 63 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N TYR E 46 " --> pdb=" O TRP E 63 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N ARG E 65 " --> pdb=" O ILE E 44 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N ILE E 44 " --> pdb=" O ARG E 65 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N TYR E 67 " --> pdb=" O ASP E 42 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N ASP E 42 " --> pdb=" O TYR E 67 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE E 41 " --> pdb=" O THR E 166 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 85 through 89 Processing sheet with id=AB6, 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) 745 hydrogen bonds defined for protein. 2190 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.29 Time building geometry restraints manager: 5.20 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=" CA ARG C 28 " pdb=" C ARG C 28 " ideal model delta sigma weight residual 1.527 1.476 0.051 1.02e-02 9.61e+03 2.50e+01 bond pdb=" CA ARG A 28 " pdb=" C ARG A 28 " ideal model delta sigma weight residual 1.527 1.477 0.050 1.02e-02 9.61e+03 2.43e+01 bond pdb=" CA ARG E 28 " pdb=" C ARG E 28 " ideal model delta sigma weight residual 1.527 1.477 0.050 1.02e-02 9.61e+03 2.41e+01 bond pdb=" CA ARG B 28 " pdb=" C ARG B 28 " ideal model delta sigma weight residual 1.527 1.477 0.050 1.02e-02 9.61e+03 2.38e+01 bond pdb=" CA ARG D 28 " pdb=" C ARG D 28 " ideal model delta sigma weight residual 1.527 1.478 0.049 1.02e-02 9.61e+03 2.34e+01 ... (remaining 17155 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 22162 2.27 - 4.55: 1113 4.55 - 6.82: 145 6.82 - 9.09: 30 9.09 - 11.36: 10 Bond angle restraints: 23460 Sorted by residual: angle pdb=" N ARG B 28 " pdb=" CA ARG B 28 " pdb=" C ARG B 28 " ideal model delta sigma weight residual 109.64 102.08 7.56 1.27e+00 6.20e-01 3.54e+01 angle pdb=" N ARG E 28 " pdb=" CA ARG E 28 " pdb=" C ARG E 28 " ideal model delta sigma weight residual 109.64 102.10 7.54 1.27e+00 6.20e-01 3.53e+01 angle pdb=" N ARG C 28 " pdb=" CA ARG C 28 " pdb=" C ARG C 28 " ideal model delta sigma weight residual 109.64 102.10 7.54 1.27e+00 6.20e-01 3.52e+01 angle pdb=" N ARG A 28 " pdb=" CA ARG A 28 " pdb=" C ARG A 28 " ideal model delta sigma weight residual 109.64 102.11 7.53 1.27e+00 6.20e-01 3.52e+01 angle pdb=" N ARG D 28 " pdb=" CA ARG D 28 " pdb=" C ARG D 28 " ideal model delta sigma weight residual 109.64 102.11 7.53 1.27e+00 6.20e-01 3.52e+01 ... (remaining 23455 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 9417 17.93 - 35.85: 794 35.85 - 53.78: 130 53.78 - 71.71: 20 71.71 - 89.64: 20 Dihedral angle restraints: 10381 sinusoidal: 4486 harmonic: 5895 Sorted by residual: dihedral pdb=" C PHE D 242 " pdb=" N PHE D 242 " pdb=" CA PHE D 242 " pdb=" CB PHE D 242 " ideal model delta harmonic sigma weight residual -122.60 -131.75 9.15 0 2.50e+00 1.60e-01 1.34e+01 dihedral pdb=" C PHE C 242 " pdb=" N PHE C 242 " pdb=" CA PHE C 242 " pdb=" CB PHE C 242 " ideal model delta harmonic sigma weight residual -122.60 -131.69 9.09 0 2.50e+00 1.60e-01 1.32e+01 dihedral pdb=" C PHE B 242 " pdb=" N PHE B 242 " pdb=" CA PHE B 242 " pdb=" CB PHE B 242 " ideal model delta harmonic sigma weight residual -122.60 -131.68 9.08 0 2.50e+00 1.60e-01 1.32e+01 ... (remaining 10378 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2140 0.064 - 0.129: 519 0.129 - 0.193: 76 0.193 - 0.257: 10 0.257 - 0.322: 5 Chirality restraints: 2750 Sorted by residual: chirality pdb=" CA PHE D 242 " pdb=" N PHE D 242 " pdb=" C PHE D 242 " pdb=" CB PHE D 242 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CA PHE B 242 " pdb=" N PHE B 242 " pdb=" C PHE B 242 " pdb=" CB PHE B 242 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CA PHE C 242 " pdb=" N PHE C 242 " pdb=" C PHE C 242 " pdb=" CB PHE C 242 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.56e+00 ... (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: 2.03 - 2.60: 78 2.60 - 3.18: 13896 3.18 - 3.75: 25073 3.75 - 4.33: 32973 4.33 - 4.90: 53715 Nonbonded interactions: 125735 Sorted by model distance: nonbonded pdb=" SG CYS C 135 " pdb=" SG CYS C 149 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS D 135 " pdb=" SG CYS D 149 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS E 135 " pdb=" SG CYS E 149 " model vdw 2.032 3.760 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 ... (remaining 125730 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' 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: 8.880 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 40.240 Find NCS groups from input model: 2.570 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.010 ------------------------------------------------------------------------------- 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 : 0.007 0.056 17160 Z= 0.480 Angle : 1.061 11.364 23460 Z= 0.646 Chirality : 0.057 0.322 2750 Planarity : 0.006 0.057 2850 Dihedral : 13.520 89.636 6535 Min Nonbonded Distance : 2.030 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 to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 2.039 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: 0.3578 time to fit residues: 71.0616 Evaluate side-chains 47 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 1.951 ------------------------------------------------------------------------------- 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: 0.9990 chunk 147 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 chunk 99 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 152 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 177 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN A 119 HIS A 311 GLN B 66 GLN B 119 HIS B 311 GLN C 66 GLN C 119 HIS C 311 GLN D 66 GLN D 311 GLN E 66 GLN E 311 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2212 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= 0.253 Angle : 0.609 8.560 23460 Z= 0.308 Chirality : 0.044 0.184 2750 Planarity : 0.005 0.050 2850 Dihedral : 4.636 17.890 2645 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.54 % Allowed : 10.35 % Favored : 89.11 % 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: -1.07 (0.19), residues: 1955 helix: 0.56 (0.18), residues: 860 sheet: -0.56 (0.24), residues: 440 loop : -2.51 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP D 331 HIS 0.004 0.001 HIS A 119 PHE 0.016 0.001 PHE B 199 TYR 0.019 0.002 TYR C 262 ARG 0.007 0.000 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 57 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 2.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 291 MET cc_start: 0.7759 (mmm) cc_final: 0.7103 (mmp) outliers start: 10 outliers final: 7 residues processed: 55 average time/residue: 0.2410 time to fit residues: 24.0684 Evaluate side-chains 52 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 2.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 232 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 120 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 177 optimal weight: 0.7980 chunk 191 optimal weight: 0.9980 chunk 157 optimal weight: 8.9990 chunk 175 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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: 0.7868 moved from start: 0.2688 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= 0.202 Angle : 0.551 7.909 23460 Z= 0.277 Chirality : 0.042 0.131 2750 Planarity : 0.004 0.038 2850 Dihedral : 4.269 16.479 2645 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.41 % Allowed : 12.14 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.63 (0.20), residues: 1955 helix: 0.91 (0.18), residues: 865 sheet: -0.36 (0.25), residues: 435 loop : -2.27 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 331 HIS 0.003 0.001 HIS E 119 PHE 0.027 0.001 PHE A 265 TYR 0.014 0.001 TYR A 67 ARG 0.004 0.000 ARG B 424 *********************** 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 70 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 44 time to evaluate : 2.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.7082 (tp) REVERT: A 291 MET cc_start: 0.7416 (mmp) cc_final: 0.6407 (mmp) REVERT: B 273 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7148 (tt) outliers start: 26 outliers final: 14 residues processed: 67 average time/residue: 0.2407 time to fit residues: 27.9918 Evaluate side-chains 59 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 43 time to evaluate : 2.121 ------------------------------------------------------------------------------- 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 273 LEU 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 273 LEU Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain D residue 100 ILE 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 262 TYR Chi-restraints excluded: chain E residue 286 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 175 optimal weight: 0.4980 chunk 133 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 chunk 178 optimal weight: 0.6980 chunk 188 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 168 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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: 0.7846 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17160 Z= 0.153 Angle : 0.517 7.575 23460 Z= 0.256 Chirality : 0.042 0.130 2750 Planarity : 0.004 0.040 2850 Dihedral : 4.138 16.171 2645 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.08 % Allowed : 13.88 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.20), residues: 1955 helix: 1.13 (0.19), residues: 865 sheet: -0.17 (0.25), residues: 435 loop : -2.15 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 331 HIS 0.002 0.001 HIS E 119 PHE 0.021 0.001 PHE A 265 TYR 0.021 0.001 TYR B 262 ARG 0.003 0.000 ARG B 424 *********************** 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 63 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 43 time to evaluate : 1.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 265 PHE cc_start: 0.4328 (p90) cc_final: 0.4093 (p90) outliers start: 20 outliers final: 9 residues processed: 63 average time/residue: 0.2537 time to fit residues: 27.7918 Evaluate side-chains 51 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 2.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 286 TYR Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 286 TYR Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 286 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 156 optimal weight: 8.9990 chunk 106 optimal weight: 10.0000 chunk 2 optimal weight: 0.7980 chunk 140 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 160 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 96 optimal weight: 8.9990 chunk 169 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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: 0.7967 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17160 Z= 0.325 Angle : 0.626 6.615 23460 Z= 0.314 Chirality : 0.044 0.133 2750 Planarity : 0.005 0.048 2850 Dihedral : 4.769 21.742 2645 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.52 % Allowed : 14.36 % Favored : 84.12 % 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: -0.60 (0.20), residues: 1955 helix: 0.92 (0.18), residues: 865 sheet: -0.27 (0.25), residues: 440 loop : -2.29 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 331 HIS 0.004 0.001 HIS D 119 PHE 0.031 0.001 PHE E 265 TYR 0.020 0.002 TYR A 67 ARG 0.003 0.000 ARG C 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 74 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 46 time to evaluate : 2.124 Fit side-chains revert: symmetry clash REVERT: B 400 ARG cc_start: 0.4338 (mmp-170) cc_final: 0.3588 (mmt180) REVERT: C 400 ARG cc_start: 0.4003 (mmp-170) cc_final: 0.3171 (mmt180) REVERT: E 45 MET cc_start: 0.8263 (mmm) cc_final: 0.8043 (tpt) outliers start: 28 outliers final: 23 residues processed: 70 average time/residue: 0.2769 time to fit residues: 32.0488 Evaluate side-chains 66 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 43 time to evaluate : 2.152 ------------------------------------------------------------------------------- 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 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 232 ILE Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 321 LEU 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 262 TYR Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 177 ASP 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 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: 3.9990 chunk 169 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 110 optimal weight: 0.2980 chunk 46 optimal weight: 4.9990 chunk 188 optimal weight: 0.2980 chunk 156 optimal weight: 0.6980 chunk 87 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 62 optimal weight: 20.0000 chunk 99 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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: 0.7920 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17160 Z= 0.185 Angle : 0.546 6.786 23460 Z= 0.272 Chirality : 0.042 0.130 2750 Planarity : 0.004 0.044 2850 Dihedral : 4.521 23.177 2645 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.03 % Allowed : 15.72 % Favored : 83.25 % 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: -0.41 (0.20), residues: 1955 helix: 1.10 (0.19), residues: 865 sheet: -0.23 (0.25), residues: 440 loop : -2.18 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 331 HIS 0.002 0.001 HIS E 119 PHE 0.026 0.001 PHE E 265 TYR 0.012 0.001 TYR A 67 ARG 0.003 0.000 ARG B 306 *********************** 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 64 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 45 time to evaluate : 2.064 Fit side-chains REVERT: B 400 ARG cc_start: 0.4329 (mmp-170) cc_final: 0.3642 (mmt180) REVERT: C 400 ARG cc_start: 0.4031 (mmp-170) cc_final: 0.3256 (mmt180) REVERT: E 45 MET cc_start: 0.8265 (mmm) cc_final: 0.8026 (tpt) REVERT: E 262 TYR cc_start: 0.0017 (p90) cc_final: -0.0218 (p90) REVERT: E 291 MET cc_start: 0.7213 (mmp) cc_final: 0.6376 (mmp) outliers start: 19 outliers final: 13 residues processed: 62 average time/residue: 0.2744 time to fit residues: 28.6740 Evaluate side-chains 57 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 2.043 ------------------------------------------------------------------------------- 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 265 PHE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 100 ILE 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: 7.9990 chunk 21 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 105 optimal weight: 8.9990 chunk 187 optimal weight: 9.9990 chunk 117 optimal weight: 7.9990 chunk 114 optimal weight: 7.9990 chunk 86 optimal weight: 0.3980 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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: 0.7926 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17160 Z= 0.196 Angle : 0.548 6.795 23460 Z= 0.273 Chirality : 0.042 0.168 2750 Planarity : 0.004 0.044 2850 Dihedral : 4.528 24.607 2645 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.57 % Allowed : 15.72 % 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: -0.38 (0.20), residues: 1955 helix: 1.11 (0.19), residues: 865 sheet: -0.23 (0.26), residues: 440 loop : -2.14 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 331 HIS 0.003 0.001 HIS E 119 PHE 0.024 0.001 PHE E 265 TYR 0.012 0.001 TYR A 67 ARG 0.003 0.000 ARG B 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 75 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 46 time to evaluate : 2.042 Fit side-chains revert: symmetry clash REVERT: A 258 LEU cc_start: 0.6174 (OUTLIER) cc_final: 0.5972 (pp) REVERT: B 223 TYR cc_start: 0.7211 (OUTLIER) cc_final: 0.6417 (t80) REVERT: B 400 ARG cc_start: 0.4413 (mmp-170) cc_final: 0.3716 (mmt180) REVERT: C 400 ARG cc_start: 0.4075 (mmp-170) cc_final: 0.3291 (mmt180) REVERT: D 223 TYR cc_start: 0.7227 (OUTLIER) cc_final: 0.6656 (t80) REVERT: E 45 MET cc_start: 0.8293 (mmm) cc_final: 0.8059 (tpt) REVERT: E 400 ARG cc_start: 0.3880 (mmp-170) cc_final: 0.3134 (mmt180) outliers start: 29 outliers final: 21 residues processed: 73 average time/residue: 0.2950 time to fit residues: 34.6473 Evaluate side-chains 69 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 45 time to evaluate : 1.916 ------------------------------------------------------------------------------- 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 258 LEU 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 223 TYR 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 321 LEU Chi-restraints excluded: chain C residue 203 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 D residue 100 ILE Chi-restraints excluded: chain D residue 223 TYR 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 280 THR Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 439 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 116 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 147 optimal weight: 0.2980 chunk 170 optimal weight: 7.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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: 0.7914 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17160 Z= 0.183 Angle : 0.555 9.018 23460 Z= 0.272 Chirality : 0.042 0.145 2750 Planarity : 0.004 0.042 2850 Dihedral : 4.486 25.348 2645 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.90 % Allowed : 15.77 % Favored : 82.33 % 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: -0.34 (0.20), residues: 1955 helix: 1.10 (0.19), residues: 870 sheet: -0.19 (0.26), residues: 435 loop : -2.07 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 331 HIS 0.002 0.001 HIS E 119 PHE 0.022 0.001 PHE E 265 TYR 0.011 0.001 TYR A 67 ARG 0.002 0.000 ARG B 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 83 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 48 time to evaluate : 2.127 Fit side-chains revert: symmetry clash REVERT: B 223 TYR cc_start: 0.7119 (OUTLIER) cc_final: 0.6328 (t80) REVERT: B 400 ARG cc_start: 0.4462 (mmp-170) cc_final: 0.3751 (mmt180) REVERT: C 400 ARG cc_start: 0.4001 (mmp-170) cc_final: 0.3236 (mmt180) REVERT: D 223 TYR cc_start: 0.7218 (OUTLIER) cc_final: 0.6651 (t80) REVERT: E 45 MET cc_start: 0.8292 (mmm) cc_final: 0.8047 (tpt) REVERT: E 258 LEU cc_start: 0.6756 (OUTLIER) cc_final: 0.6425 (pp) REVERT: E 291 MET cc_start: 0.7198 (mmp) cc_final: 0.6454 (mmp) REVERT: E 400 ARG cc_start: 0.3904 (mmp-170) cc_final: 0.3186 (mmt180) outliers start: 35 outliers final: 25 residues processed: 80 average time/residue: 0.2780 time to fit residues: 36.1199 Evaluate side-chains 73 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 45 time to evaluate : 2.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 203 ILE 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 223 TYR 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 203 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 D residue 100 ILE Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 223 TYR Chi-restraints excluded: chain D residue 258 LEU 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 100 ILE Chi-restraints excluded: chain E residue 258 LEU 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: 9.9990 chunk 164 optimal weight: 0.0980 chunk 175 optimal weight: 0.0000 chunk 105 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 137 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 158 optimal weight: 0.0970 chunk 165 optimal weight: 0.7980 chunk 174 optimal weight: 0.7980 chunk 115 optimal weight: 7.9990 overall best weight: 0.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS E 118 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17160 Z= 0.141 Angle : 0.546 11.191 23460 Z= 0.262 Chirality : 0.042 0.130 2750 Planarity : 0.004 0.039 2850 Dihedral : 4.218 23.161 2645 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.25 % Allowed : 16.75 % Favored : 82.01 % 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: -0.26 (0.20), residues: 1955 helix: 1.24 (0.19), residues: 860 sheet: -0.13 (0.26), residues: 435 loop : -2.12 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 331 HIS 0.002 0.000 HIS B 118 PHE 0.019 0.001 PHE E 265 TYR 0.022 0.001 TYR E 262 ARG 0.002 0.000 ARG C 428 *********************** 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 72 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 49 time to evaluate : 2.115 Fit side-chains REVERT: B 223 TYR cc_start: 0.7094 (OUTLIER) cc_final: 0.6305 (t80) REVERT: B 400 ARG cc_start: 0.4497 (mmp-170) cc_final: 0.3815 (mmt180) REVERT: C 400 ARG cc_start: 0.3985 (mmp-170) cc_final: 0.3237 (mmt180) REVERT: E 45 MET cc_start: 0.8271 (mmm) cc_final: 0.7984 (tpt) REVERT: E 258 LEU cc_start: 0.6706 (OUTLIER) cc_final: 0.6422 (pp) REVERT: E 400 ARG cc_start: 0.3977 (mmp-170) cc_final: 0.3293 (mmt180) outliers start: 23 outliers final: 19 residues processed: 70 average time/residue: 0.2929 time to fit residues: 33.1930 Evaluate side-chains 69 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 48 time to evaluate : 1.969 ------------------------------------------------------------------------------- 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 280 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 223 TYR 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 321 LEU 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 D residue 117 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 258 LEU 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: 9.9990 chunk 113 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 194 optimal weight: 5.9990 chunk 178 optimal weight: 0.0060 chunk 154 optimal weight: 20.0000 chunk 16 optimal weight: 0.8980 chunk 119 optimal weight: 0.5980 chunk 94 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 overall best weight: 2.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17160 Z= 0.260 Angle : 0.606 10.047 23460 Z= 0.298 Chirality : 0.043 0.150 2750 Planarity : 0.004 0.044 2850 Dihedral : 4.712 28.238 2645 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.25 % Allowed : 16.96 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.20), residues: 1955 helix: 1.01 (0.18), residues: 870 sheet: -0.23 (0.26), residues: 440 loop : -2.06 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 331 HIS 0.004 0.001 HIS D 119 PHE 0.022 0.001 PHE A 265 TYR 0.030 0.002 TYR E 262 ARG 0.003 0.000 ARG B 306 ********************** 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 68 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 45 time to evaluate : 2.071 Fit side-chains REVERT: A 223 TYR cc_start: 0.7237 (OUTLIER) cc_final: 0.6323 (t80) REVERT: B 223 TYR cc_start: 0.7281 (OUTLIER) cc_final: 0.6653 (t80) REVERT: B 400 ARG cc_start: 0.4548 (mmp-170) cc_final: 0.3549 (mmt180) REVERT: C 400 ARG cc_start: 0.4336 (mmp-170) cc_final: 0.3572 (mmt180) REVERT: D 240 VAL cc_start: 0.8041 (t) cc_final: 0.7813 (t) REVERT: E 45 MET cc_start: 0.8264 (mmm) cc_final: 0.8044 (tpt) REVERT: E 258 LEU cc_start: 0.6674 (OUTLIER) cc_final: 0.6424 (pp) outliers start: 23 outliers final: 19 residues processed: 67 average time/residue: 0.2753 time to fit residues: 30.9116 Evaluate side-chains 66 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 44 time to evaluate : 1.999 ------------------------------------------------------------------------------- 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 280 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 223 TYR 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 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 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 280 THR Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 258 LEU 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: 2.9990 chunk 47 optimal weight: 0.2980 chunk 142 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 154 optimal weight: 20.0000 chunk 64 optimal weight: 0.8980 chunk 159 optimal weight: 0.9990 chunk 19 optimal weight: 0.0470 chunk 28 optimal weight: 20.0000 chunk 136 optimal weight: 0.0020 overall best weight: 0.4486 ------------------------------------------------------------------------------- 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 = 0.3732 r_free = 0.3732 target = 0.083872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.065341 restraints weight = 65869.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.063706 restraints weight = 59013.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.064118 restraints weight = 61964.381| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17160 Z= 0.144 Angle : 0.551 8.790 23460 Z= 0.268 Chirality : 0.042 0.183 2750 Planarity : 0.004 0.042 2850 Dihedral : 4.360 25.083 2645 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.08 % Allowed : 17.24 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.20), residues: 1955 helix: 1.20 (0.19), residues: 865 sheet: -0.14 (0.26), residues: 435 loop : -2.04 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 331 HIS 0.002 0.001 HIS B 118 PHE 0.018 0.001 PHE E 265 TYR 0.028 0.001 TYR E 262 ARG 0.002 0.000 ARG B 424 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2327.64 seconds wall clock time: 44 minutes 43.43 seconds (2683.43 seconds total)