Starting phenix.real_space_refine on Mon Mar 11 07:25:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sip_25147/03_2024/7sip_25147_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sip_25147/03_2024/7sip_25147.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sip_25147/03_2024/7sip_25147.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sip_25147/03_2024/7sip_25147.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sip_25147/03_2024/7sip_25147_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sip_25147/03_2024/7sip_25147_neut_updated.pdb" } resolution = 3.0 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= -0.001 sd= 0.093 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: 6 Type Number sf(0) Gaussians K 4 8.98 5 P 4 5.49 5 S 36 5.16 5 C 5192 2.51 5 N 1096 2.21 5 O 1228 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 447": "OD1" <-> "OD2" Residue "A TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 447": "OD1" <-> "OD2" Residue "B TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 447": "OD1" <-> "OD2" Residue "C TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 447": "OD1" <-> "OD2" Residue "D TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7560 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1747 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 214} Chain breaks: 3 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1747 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 214} Chain breaks: 3 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1747 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 214} Chain breaks: 3 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "D" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1747 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 214} Chain breaks: 3 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "A" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 169 Unusual residues: {' K': 4, 'POV': 9} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 303 Unresolved non-hydrogen angles: 371 Unresolved non-hydrogen dihedrals: 272 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 6, 'POV:plan-1': 6} Unresolved non-hydrogen planarities: 55 Chain: "B" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 137 Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 279 Unresolved non-hydrogen angles: 340 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 6, 'POV:plan-1': 6} Unresolved non-hydrogen planarities: 55 Chain: "C" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 137 Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 279 Unresolved non-hydrogen angles: 340 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 6, 'POV:plan-1': 6} Unresolved non-hydrogen planarities: 55 Chain: "D" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 109 Unusual residues: {'POV': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 255 Unresolved non-hydrogen angles: 309 Unresolved non-hydrogen dihedrals: 228 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 6, 'POV:plan-1': 6} Unresolved non-hydrogen planarities: 55 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 4.37, per 1000 atoms: 0.58 Number of scatterers: 7560 At special positions: 0 Unit cell: (98.04, 97.18, 65.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 4 19.00 S 36 16.00 P 4 15.00 O 1228 8.00 N 1096 7.00 C 5192 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 2.67 Conformation dependent library (CDL) restraints added in 1.2 seconds 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1696 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 36 helices and 0 sheets defined 78.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 213 through 218 Processing helix chain 'A' and resid 224 through 248 removed outlier: 3.705A pdb=" N VAL A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE A 231 " --> pdb=" O ARG A 227 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE A 232 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE A 237 " --> pdb=" O SER A 233 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS A 245 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU A 247 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N THR A 248 " --> pdb=" O PHE A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 252 No H-bonds generated for 'chain 'A' and resid 250 through 252' Processing helix chain 'A' and resid 281 through 299 removed outlier: 3.859A pdb=" N LEU A 285 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG A 297 " --> pdb=" O GLU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 328 removed outlier: 3.521A pdb=" N ILE A 320 " --> pdb=" O ASP A 316 " (cutoff:3.500A) Proline residue: A 322 - end of helix removed outlier: 3.518A pdb=" N THR A 326 " --> pdb=" O PRO A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 377 removed outlier: 4.174A pdb=" N ARG A 368 " --> pdb=" O ILE A 364 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N VAL A 369 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N PHE A 370 " --> pdb=" O LEU A 366 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ARG A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ILE A 372 " --> pdb=" O ARG A 368 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N PHE A 373 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LYS A 374 " --> pdb=" O PHE A 370 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU A 375 " --> pdb=" O ARG A 371 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N SER A 376 " --> pdb=" O ILE A 372 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ARG A 377 " --> pdb=" O PHE A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 416 removed outlier: 4.005A pdb=" N MET A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ARG A 394 " --> pdb=" O LYS A 390 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N GLU A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER A 412 " --> pdb=" O VAL A 408 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL A 414 " --> pdb=" O PHE A 410 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR A 415 " --> pdb=" O SER A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 440 removed outlier: 4.224A pdb=" N TRP A 434 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TRP A 435 " --> pdb=" O ALA A 432 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N MET A 440 " --> pdb=" O VAL A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 488 removed outlier: 3.704A pdb=" N ILE A 464 " --> pdb=" O SER A 460 " (cutoff:3.500A) Proline residue: A 473 - end of helix removed outlier: 5.649A pdb=" N VAL A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE A 477 " --> pdb=" O PRO A 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 218 Processing helix chain 'B' and resid 224 through 248 removed outlier: 3.706A pdb=" N VAL B 229 " --> pdb=" O ALA B 225 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA B 230 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE B 231 " --> pdb=" O ARG B 227 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE B 232 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE B 237 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS B 245 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU B 247 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N THR B 248 " --> pdb=" O PHE B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 252 No H-bonds generated for 'chain 'B' and resid 250 through 252' Processing helix chain 'B' and resid 281 through 299 removed outlier: 3.859A pdb=" N LEU B 285 " --> pdb=" O LEU B 281 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG B 297 " --> pdb=" O GLU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 328 removed outlier: 3.521A pdb=" N ILE B 320 " --> pdb=" O ASP B 316 " (cutoff:3.500A) Proline residue: B 322 - end of helix removed outlier: 3.518A pdb=" N THR B 326 " --> pdb=" O PRO B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 377 removed outlier: 4.174A pdb=" N ARG B 368 " --> pdb=" O ILE B 364 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N VAL B 369 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N PHE B 370 " --> pdb=" O LEU B 366 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ARG B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ILE B 372 " --> pdb=" O ARG B 368 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N PHE B 373 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LYS B 374 " --> pdb=" O PHE B 370 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU B 375 " --> pdb=" O ARG B 371 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N SER B 376 " --> pdb=" O ILE B 372 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ARG B 377 " --> pdb=" O PHE B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 416 removed outlier: 4.005A pdb=" N MET B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ARG B 394 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N GLU B 395 " --> pdb=" O ALA B 391 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER B 412 " --> pdb=" O VAL B 408 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA B 413 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL B 414 " --> pdb=" O PHE B 410 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR B 415 " --> pdb=" O SER B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 440 removed outlier: 4.224A pdb=" N TRP B 434 " --> pdb=" O ASP B 431 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TRP B 435 " --> pdb=" O ALA B 432 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N MET B 440 " --> pdb=" O VAL B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 488 removed outlier: 3.704A pdb=" N ILE B 464 " --> pdb=" O SER B 460 " (cutoff:3.500A) Proline residue: B 473 - end of helix removed outlier: 5.650A pdb=" N VAL B 476 " --> pdb=" O LEU B 472 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE B 477 " --> pdb=" O PRO B 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 218 Processing helix chain 'C' and resid 224 through 248 removed outlier: 3.705A pdb=" N VAL C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA C 230 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE C 231 " --> pdb=" O ARG C 227 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE C 232 " --> pdb=" O VAL C 228 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE C 237 " --> pdb=" O SER C 233 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS C 245 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU C 247 " --> pdb=" O ILE C 243 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N THR C 248 " --> pdb=" O PHE C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 252 No H-bonds generated for 'chain 'C' and resid 250 through 252' Processing helix chain 'C' and resid 281 through 299 removed outlier: 3.859A pdb=" N LEU C 285 " --> pdb=" O LEU C 281 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 328 removed outlier: 3.521A pdb=" N ILE C 320 " --> pdb=" O ASP C 316 " (cutoff:3.500A) Proline residue: C 322 - end of helix removed outlier: 3.518A pdb=" N THR C 326 " --> pdb=" O PRO C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 377 removed outlier: 4.173A pdb=" N ARG C 368 " --> pdb=" O ILE C 364 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N VAL C 369 " --> pdb=" O ARG C 365 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N PHE C 370 " --> pdb=" O LEU C 366 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ARG C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ILE C 372 " --> pdb=" O ARG C 368 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N PHE C 373 " --> pdb=" O VAL C 369 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS C 374 " --> pdb=" O PHE C 370 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU C 375 " --> pdb=" O ARG C 371 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N SER C 376 " --> pdb=" O ILE C 372 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ARG C 377 " --> pdb=" O PHE C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 416 removed outlier: 4.004A pdb=" N MET C 393 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ARG C 394 " --> pdb=" O LYS C 390 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLU C 395 " --> pdb=" O ALA C 391 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER C 412 " --> pdb=" O VAL C 408 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA C 413 " --> pdb=" O LEU C 409 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL C 414 " --> pdb=" O PHE C 410 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR C 415 " --> pdb=" O SER C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 440 removed outlier: 4.224A pdb=" N TRP C 434 " --> pdb=" O ASP C 431 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TRP C 435 " --> pdb=" O ALA C 432 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N MET C 440 " --> pdb=" O VAL C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 488 removed outlier: 3.704A pdb=" N ILE C 464 " --> pdb=" O SER C 460 " (cutoff:3.500A) Proline residue: C 473 - end of helix removed outlier: 5.650A pdb=" N VAL C 476 " --> pdb=" O LEU C 472 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE C 477 " --> pdb=" O PRO C 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 218 Processing helix chain 'D' and resid 224 through 248 removed outlier: 3.705A pdb=" N VAL D 229 " --> pdb=" O ALA D 225 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA D 230 " --> pdb=" O ALA D 226 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE D 231 " --> pdb=" O ARG D 227 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE D 232 " --> pdb=" O VAL D 228 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE D 237 " --> pdb=" O SER D 233 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS D 245 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU D 247 " --> pdb=" O ILE D 243 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N THR D 248 " --> pdb=" O PHE D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 252 No H-bonds generated for 'chain 'D' and resid 250 through 252' Processing helix chain 'D' and resid 281 through 299 removed outlier: 3.859A pdb=" N LEU D 285 " --> pdb=" O LEU D 281 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG D 297 " --> pdb=" O GLU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 328 removed outlier: 3.521A pdb=" N ILE D 320 " --> pdb=" O ASP D 316 " (cutoff:3.500A) Proline residue: D 322 - end of helix removed outlier: 3.518A pdb=" N THR D 326 " --> pdb=" O PRO D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 377 removed outlier: 4.173A pdb=" N ARG D 368 " --> pdb=" O ILE D 364 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N VAL D 369 " --> pdb=" O ARG D 365 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N PHE D 370 " --> pdb=" O LEU D 366 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ARG D 371 " --> pdb=" O VAL D 367 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ILE D 372 " --> pdb=" O ARG D 368 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N PHE D 373 " --> pdb=" O VAL D 369 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LYS D 374 " --> pdb=" O PHE D 370 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU D 375 " --> pdb=" O ARG D 371 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N SER D 376 " --> pdb=" O ILE D 372 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ARG D 377 " --> pdb=" O PHE D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 416 removed outlier: 4.005A pdb=" N MET D 393 " --> pdb=" O LEU D 389 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ARG D 394 " --> pdb=" O LYS D 390 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLU D 395 " --> pdb=" O ALA D 391 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER D 412 " --> pdb=" O VAL D 408 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA D 413 " --> pdb=" O LEU D 409 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL D 414 " --> pdb=" O PHE D 410 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR D 415 " --> pdb=" O SER D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 440 removed outlier: 4.224A pdb=" N TRP D 434 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TRP D 435 " --> pdb=" O ALA D 432 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N MET D 440 " --> pdb=" O VAL D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 488 removed outlier: 3.703A pdb=" N ILE D 464 " --> pdb=" O SER D 460 " (cutoff:3.500A) Proline residue: D 473 - end of helix removed outlier: 5.649A pdb=" N VAL D 476 " --> pdb=" O LEU D 472 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE D 477 " --> pdb=" O PRO D 473 " (cutoff:3.500A) 396 hydrogen bonds defined for protein. 1128 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: 1.76 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1032 1.31 - 1.44: 2108 1.44 - 1.56: 4364 1.56 - 1.68: 120 1.68 - 1.81: 56 Bond restraints: 7680 Sorted by residual: bond pdb=" C31 POV D 704 " pdb=" O31 POV D 704 " ideal model delta sigma weight residual 1.327 1.443 -0.116 2.00e-02 2.50e+03 3.34e+01 bond pdb=" C31 POV D 707 " pdb=" O31 POV D 707 " ideal model delta sigma weight residual 1.327 1.443 -0.116 2.00e-02 2.50e+03 3.34e+01 bond pdb=" C31 POV B 708 " pdb=" O31 POV B 708 " ideal model delta sigma weight residual 1.327 1.442 -0.115 2.00e-02 2.50e+03 3.32e+01 bond pdb=" C31 POV C 703 " pdb=" O31 POV C 703 " ideal model delta sigma weight residual 1.327 1.442 -0.115 2.00e-02 2.50e+03 3.31e+01 bond pdb=" C31 POV B 702 " pdb=" O31 POV B 702 " ideal model delta sigma weight residual 1.327 1.442 -0.115 2.00e-02 2.50e+03 3.31e+01 ... (remaining 7675 not shown) Histogram of bond angle deviations from ideal: 100.39 - 107.11: 164 107.11 - 113.83: 4556 113.83 - 120.56: 3101 120.56 - 127.28: 2387 127.28 - 134.00: 72 Bond angle restraints: 10280 Sorted by residual: angle pdb=" O11 POV B 702 " pdb=" P POV B 702 " pdb=" O12 POV B 702 " ideal model delta sigma weight residual 97.67 109.59 -11.92 3.00e+00 1.11e-01 1.58e+01 angle pdb=" O11 POV D 704 " pdb=" P POV D 704 " pdb=" O12 POV D 704 " ideal model delta sigma weight residual 97.67 109.58 -11.91 3.00e+00 1.11e-01 1.58e+01 angle pdb=" O11 POV A 701 " pdb=" P POV A 701 " pdb=" O12 POV A 701 " ideal model delta sigma weight residual 97.67 109.56 -11.89 3.00e+00 1.11e-01 1.57e+01 angle pdb=" O11 POV C 703 " pdb=" P POV C 703 " pdb=" O12 POV C 703 " ideal model delta sigma weight residual 97.67 109.56 -11.89 3.00e+00 1.11e-01 1.57e+01 angle pdb=" O13 POV C 703 " pdb=" P POV C 703 " pdb=" O14 POV C 703 " ideal model delta sigma weight residual 121.11 109.40 11.71 3.00e+00 1.11e-01 1.52e+01 ... (remaining 10275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.73: 4172 25.73 - 51.46: 256 51.46 - 77.19: 76 77.19 - 102.91: 0 102.91 - 128.64: 4 Dihedral angle restraints: 4508 sinusoidal: 1916 harmonic: 2592 Sorted by residual: dihedral pdb=" C3 POV D 704 " pdb=" C31 POV D 704 " pdb=" O31 POV D 704 " pdb=" C32 POV D 704 " ideal model delta sinusoidal sigma weight residual 172.61 43.97 128.64 1 3.00e+01 1.11e-03 1.73e+01 dihedral pdb=" C3 POV C 703 " pdb=" C31 POV C 703 " pdb=" O31 POV C 703 " pdb=" C32 POV C 703 " ideal model delta sinusoidal sigma weight residual 172.61 44.00 128.61 1 3.00e+01 1.11e-03 1.73e+01 dihedral pdb=" C3 POV A 701 " pdb=" C31 POV A 701 " pdb=" O31 POV A 701 " pdb=" C32 POV A 701 " ideal model delta sinusoidal sigma weight residual 172.61 44.00 128.61 1 3.00e+01 1.11e-03 1.73e+01 ... (remaining 4505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 708 0.027 - 0.054: 292 0.054 - 0.081: 148 0.081 - 0.109: 27 0.109 - 0.136: 25 Chirality restraints: 1200 Sorted by residual: chirality pdb=" C2 POV B 702 " pdb=" C1 POV B 702 " pdb=" C3 POV B 702 " pdb=" O21 POV B 702 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" C2 POV C 703 " pdb=" C1 POV C 703 " pdb=" C3 POV C 703 " pdb=" O21 POV C 703 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" C2 POV A 701 " pdb=" C1 POV A 701 " pdb=" C3 POV A 701 " pdb=" O21 POV A 701 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.14 2.00e-01 2.50e+01 4.60e-01 ... (remaining 1197 not shown) Planarity restraints: 1192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 472 " -0.045 5.00e-02 4.00e+02 6.80e-02 7.40e+00 pdb=" N PRO A 473 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 473 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 473 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 472 " 0.045 5.00e-02 4.00e+02 6.80e-02 7.40e+00 pdb=" N PRO C 473 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO C 473 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 473 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 472 " -0.045 5.00e-02 4.00e+02 6.78e-02 7.36e+00 pdb=" N PRO B 473 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 473 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 473 " -0.038 5.00e-02 4.00e+02 ... (remaining 1189 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.88: 2656 2.88 - 3.44: 8111 3.44 - 4.01: 12400 4.01 - 4.57: 19001 4.57 - 5.14: 26261 Nonbonded interactions: 68429 Sorted by model distance: nonbonded pdb=" O HOH C1002 " pdb=" O HOH C1005 " model vdw 2.313 2.440 nonbonded pdb=" O HOH B1002 " pdb=" O HOH B1005 " model vdw 2.313 2.440 nonbonded pdb=" O HOH A1002 " pdb=" O HOH A1005 " model vdw 2.313 2.440 nonbonded pdb=" O HOH D1002 " pdb=" O HOH D1005 " model vdw 2.313 2.440 nonbonded pdb=" O VAL C 437 " pdb=" OG1 THR C 441 " model vdw 2.353 2.440 ... (remaining 68424 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 212 through 489 or (resid 701 through 702 and (name C31 or \ name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C3 \ 8)) or (resid 703 and (name C32 or name C33 or name C34 or name C35 or name C36 \ or name C37 or name C38)) or (resid 704 through 706 and (name C32 or name C33 or \ name C34 or name C35 or name C36 or name C37 or name C38 or name C39)) or resid \ 707)) selection = (chain 'B' and (resid 212 through 489 or (resid 701 through 702 and (name C31 or \ name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C3 \ 8)) or (resid 703 and (name C32 or name C33 or name C34 or name C35 or name C36 \ or name C37 or name C38)) or (resid 704 through 706 and (name C32 or name C33 or \ name C34 or name C35 or name C36 or name C37 or name C38 or name C39)) or resid \ 707)) selection = (chain 'C' and (resid 212 through 489 or resid 701 or (resid 702 and (name C1 or \ name C2 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35) \ ) or (resid 703 and (name C32 or name C33 or name C34 or name C35 or name C36 or \ name C37 or name C38)) or (resid 704 through 706 and (name C32 or name C33 or n \ ame C34 or name C35 or name C36 or name C37 or name C38 or name C39)) or (resid \ 707 and (name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or \ name C37 or name C38)))) selection = (chain 'D' and (resid 212 through 489 or (resid 701 through 702 and (name C31 or \ name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C3 \ 8)) or (resid 703 and (name C32 or name C33 or name C34 or name C35 or name C36 \ or name C37 or name C38)) or (resid 704 through 706 and (name C32 or name C33 or \ name C34 or name C35 or name C36 or name C37 or name C38 or name C39)) or (resi \ d 707 and (name C31 or name C32 or name C33 or name C34 or name C35 or name C36 \ or name C37 or name C38)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.340 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: 5.880 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 22.500 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 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 : 0.011 0.116 7680 Z= 0.688 Angle : 1.166 11.916 10280 Z= 0.449 Chirality : 0.039 0.136 1200 Planarity : 0.005 0.068 1192 Dihedral : 17.466 128.642 2812 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.93 (0.30), residues: 860 helix: 0.81 (0.21), residues: 704 sheet: None (None), residues: 0 loop : 0.20 (0.45), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 434 HIS 0.001 0.000 HIS D 486 PHE 0.010 0.001 PHE B 290 TYR 0.003 0.001 TYR A 485 ARG 0.007 0.001 ARG B 377 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.804 Fit side-chains REVERT: A 280 PHE cc_start: 0.7654 (t80) cc_final: 0.7327 (t80) REVERT: A 390 LYS cc_start: 0.8054 (ttpp) cc_final: 0.7506 (ttpt) REVERT: B 280 PHE cc_start: 0.7628 (t80) cc_final: 0.7293 (t80) REVERT: C 280 PHE cc_start: 0.7692 (t80) cc_final: 0.7373 (t80) REVERT: C 390 LYS cc_start: 0.8067 (ttpp) cc_final: 0.7518 (ttpt) REVERT: D 390 LYS cc_start: 0.8077 (ttpp) cc_final: 0.7502 (ttpt) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 1.3846 time to fit residues: 178.7034 Evaluate side-chains 105 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 26 optimal weight: 0.0020 chunk 41 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 ASN C 313 ASN D 313 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7680 Z= 0.173 Angle : 0.517 5.505 10280 Z= 0.260 Chirality : 0.038 0.125 1200 Planarity : 0.005 0.049 1192 Dihedral : 16.922 125.639 1336 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 1.87 % Allowed : 10.43 % Favored : 87.70 % 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: 0.95 (0.30), residues: 860 helix: 0.85 (0.21), residues: 712 sheet: None (None), residues: 0 loop : 0.02 (0.48), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 434 HIS 0.001 0.000 HIS A 378 PHE 0.008 0.001 PHE A 290 TYR 0.016 0.002 TYR C 483 ARG 0.005 0.001 ARG C 362 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 128 time to evaluate : 0.716 Fit side-chains REVERT: B 390 LYS cc_start: 0.8202 (tttp) cc_final: 0.7599 (ttpm) REVERT: C 390 LYS cc_start: 0.8106 (ttpp) cc_final: 0.7658 (ttpm) REVERT: D 390 LYS cc_start: 0.8119 (ttpp) cc_final: 0.7643 (ttpm) outliers start: 14 outliers final: 1 residues processed: 129 average time/residue: 1.4658 time to fit residues: 197.7178 Evaluate side-chains 117 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 116 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 486 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 22 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 86 optimal weight: 0.0770 chunk 71 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 7680 Z= 0.165 Angle : 0.477 5.458 10280 Z= 0.244 Chirality : 0.038 0.163 1200 Planarity : 0.005 0.049 1192 Dihedral : 14.540 120.908 1336 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.20 % Allowed : 12.83 % Favored : 85.96 % 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: 1.17 (0.30), residues: 860 helix: 1.05 (0.21), residues: 708 sheet: None (None), residues: 0 loop : -0.17 (0.45), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 434 HIS 0.001 0.000 HIS B 378 PHE 0.007 0.001 PHE D 404 TYR 0.013 0.002 TYR D 485 ARG 0.004 0.000 ARG C 362 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 97 time to evaluate : 0.748 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 101 average time/residue: 1.6919 time to fit residues: 177.8140 Evaluate side-chains 97 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 93 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain D residue 360 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 53 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 70 optimal weight: 0.0040 overall best weight: 0.6794 ------------------------------------------------------------------------------- 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: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7680 Z= 0.163 Angle : 0.466 5.453 10280 Z= 0.240 Chirality : 0.038 0.123 1200 Planarity : 0.005 0.050 1192 Dihedral : 13.458 115.386 1336 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 2.01 % Allowed : 13.64 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.30), residues: 860 helix: 1.07 (0.21), residues: 708 sheet: None (None), residues: 0 loop : -0.29 (0.45), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 434 HIS 0.001 0.000 HIS B 378 PHE 0.007 0.001 PHE A 404 TYR 0.021 0.002 TYR C 483 ARG 0.005 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 87 time to evaluate : 0.830 Fit side-chains REVERT: A 316 ASP cc_start: 0.7537 (OUTLIER) cc_final: 0.7252 (m-30) REVERT: C 316 ASP cc_start: 0.7585 (OUTLIER) cc_final: 0.7359 (m-30) outliers start: 15 outliers final: 10 residues processed: 100 average time/residue: 1.6553 time to fit residues: 172.6109 Evaluate side-chains 95 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 83 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 360 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 0.0070 chunk 1 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 76 optimal weight: 0.2980 chunk 21 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- 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: 0.7897 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7680 Z= 0.141 Angle : 0.443 5.432 10280 Z= 0.228 Chirality : 0.036 0.120 1200 Planarity : 0.004 0.048 1192 Dihedral : 12.796 111.882 1336 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.87 % Allowed : 15.24 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.30), residues: 860 helix: 1.17 (0.21), residues: 708 sheet: None (None), residues: 0 loop : -0.41 (0.44), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 434 HIS 0.001 0.000 HIS C 378 PHE 0.006 0.001 PHE D 404 TYR 0.012 0.001 TYR D 485 ARG 0.004 0.000 ARG D 362 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 90 time to evaluate : 0.778 Fit side-chains REVERT: A 316 ASP cc_start: 0.7613 (OUTLIER) cc_final: 0.7379 (m-30) REVERT: B 316 ASP cc_start: 0.7616 (OUTLIER) cc_final: 0.7366 (m-30) REVERT: D 316 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.7387 (m-30) outliers start: 14 outliers final: 8 residues processed: 98 average time/residue: 1.6689 time to fit residues: 170.6084 Evaluate side-chains 97 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 86 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 486 HIS Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 486 HIS Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 486 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 0.0670 chunk 16 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 82 optimal weight: 0.4980 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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: 0.7915 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7680 Z= 0.151 Angle : 0.451 5.432 10280 Z= 0.232 Chirality : 0.037 0.120 1200 Planarity : 0.004 0.050 1192 Dihedral : 12.624 111.488 1336 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.41 % Allowed : 16.04 % Favored : 81.55 % 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: 1.27 (0.30), residues: 860 helix: 1.17 (0.21), residues: 708 sheet: None (None), residues: 0 loop : -0.42 (0.44), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 434 HIS 0.001 0.000 HIS A 378 PHE 0.007 0.001 PHE A 404 TYR 0.020 0.002 TYR C 483 ARG 0.003 0.000 ARG D 362 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 86 time to evaluate : 0.720 Fit side-chains REVERT: A 316 ASP cc_start: 0.7623 (OUTLIER) cc_final: 0.7372 (m-30) REVERT: B 316 ASP cc_start: 0.7628 (OUTLIER) cc_final: 0.7384 (m-30) REVERT: C 316 ASP cc_start: 0.7557 (OUTLIER) cc_final: 0.7332 (m-30) REVERT: D 316 ASP cc_start: 0.7614 (OUTLIER) cc_final: 0.7413 (m-30) outliers start: 18 outliers final: 12 residues processed: 98 average time/residue: 1.6447 time to fit residues: 168.1517 Evaluate side-chains 101 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 85 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 486 HIS Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 486 HIS Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 486 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 8.9990 chunk 48 optimal weight: 0.6980 chunk 62 optimal weight: 0.0010 chunk 71 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 84 optimal weight: 0.0570 chunk 53 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 52 optimal weight: 0.0040 chunk 33 optimal weight: 0.5980 overall best weight: 0.2716 ------------------------------------------------------------------------------- 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: 0.7862 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7680 Z= 0.123 Angle : 0.427 5.424 10280 Z= 0.219 Chirality : 0.036 0.116 1200 Planarity : 0.004 0.046 1192 Dihedral : 12.118 109.620 1336 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.54 % Allowed : 16.18 % Favored : 81.28 % 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: 1.44 (0.31), residues: 860 helix: 1.31 (0.22), residues: 708 sheet: None (None), residues: 0 loop : -0.44 (0.44), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 434 HIS 0.000 0.000 HIS C 378 PHE 0.004 0.001 PHE A 433 TYR 0.012 0.001 TYR D 485 ARG 0.003 0.000 ARG D 362 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 89 time to evaluate : 0.724 Fit side-chains REVERT: A 316 ASP cc_start: 0.7537 (OUTLIER) cc_final: 0.7324 (m-30) REVERT: D 316 ASP cc_start: 0.7561 (OUTLIER) cc_final: 0.7352 (m-30) REVERT: D 390 LYS cc_start: 0.8093 (tttp) cc_final: 0.7588 (tttm) outliers start: 19 outliers final: 11 residues processed: 102 average time/residue: 1.5601 time to fit residues: 166.1713 Evaluate side-chains 103 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 90 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 486 HIS Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 486 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 7.9990 chunk 25 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 53 optimal weight: 8.9990 chunk 57 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7928 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7680 Z= 0.170 Angle : 0.462 5.419 10280 Z= 0.237 Chirality : 0.037 0.120 1200 Planarity : 0.004 0.048 1192 Dihedral : 12.420 111.369 1336 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 2.41 % Allowed : 16.04 % Favored : 81.55 % 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: 1.33 (0.30), residues: 860 helix: 1.21 (0.21), residues: 708 sheet: None (None), residues: 0 loop : -0.38 (0.44), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 434 HIS 0.001 0.000 HIS A 378 PHE 0.008 0.001 PHE D 404 TYR 0.020 0.002 TYR A 483 ARG 0.003 0.000 ARG D 362 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 87 time to evaluate : 0.763 Fit side-chains REVERT: A 316 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7381 (m-30) REVERT: A 448 MET cc_start: 0.6925 (mtm) cc_final: 0.6683 (ptm) REVERT: D 316 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.7405 (m-30) outliers start: 18 outliers final: 10 residues processed: 98 average time/residue: 1.6496 time to fit residues: 168.6538 Evaluate side-chains 97 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 85 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 486 HIS Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 360 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 62 optimal weight: 0.0980 chunk 24 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7680 Z= 0.173 Angle : 0.461 5.420 10280 Z= 0.239 Chirality : 0.037 0.122 1200 Planarity : 0.004 0.048 1192 Dihedral : 12.603 112.428 1336 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 1.87 % Allowed : 16.58 % Favored : 81.55 % 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: 1.32 (0.30), residues: 860 helix: 1.19 (0.21), residues: 724 sheet: None (None), residues: 0 loop : -0.53 (0.43), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 434 HIS 0.001 0.000 HIS A 378 PHE 0.008 0.001 PHE D 404 TYR 0.020 0.002 TYR C 483 ARG 0.002 0.000 ARG D 362 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 87 time to evaluate : 0.818 Fit side-chains REVERT: A 316 ASP cc_start: 0.7635 (OUTLIER) cc_final: 0.7316 (m-30) REVERT: B 390 LYS cc_start: 0.8222 (tttm) cc_final: 0.7719 (ttpm) outliers start: 14 outliers final: 8 residues processed: 98 average time/residue: 1.6676 time to fit residues: 170.4402 Evaluate side-chains 96 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 87 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 486 HIS Chi-restraints excluded: chain D residue 360 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 42 optimal weight: 0.0570 chunk 55 optimal weight: 0.6980 chunk 74 optimal weight: 0.1980 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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: 0.7918 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7680 Z= 0.144 Angle : 0.442 5.430 10280 Z= 0.228 Chirality : 0.036 0.119 1200 Planarity : 0.004 0.047 1192 Dihedral : 12.306 111.206 1336 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 1.60 % Allowed : 17.11 % Favored : 81.28 % 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: 1.43 (0.30), residues: 860 helix: 1.27 (0.21), residues: 724 sheet: None (None), residues: 0 loop : -0.49 (0.44), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 434 HIS 0.001 0.000 HIS D 486 PHE 0.006 0.001 PHE A 404 TYR 0.021 0.002 TYR A 483 ARG 0.002 0.000 ARG B 362 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 85 time to evaluate : 0.807 Fit side-chains REVERT: A 316 ASP cc_start: 0.7635 (OUTLIER) cc_final: 0.7356 (m-30) outliers start: 12 outliers final: 11 residues processed: 95 average time/residue: 1.6779 time to fit residues: 166.4076 Evaluate side-chains 97 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 85 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 486 HIS Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 360 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 0.4980 chunk 10 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4044 r_free = 0.4044 target = 0.178435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.121978 restraints weight = 7004.134| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.17 r_work: 0.3238 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7680 Z= 0.163 Angle : 0.452 5.424 10280 Z= 0.234 Chirality : 0.037 0.119 1200 Planarity : 0.004 0.047 1192 Dihedral : 12.192 111.597 1336 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 1.74 % Allowed : 16.98 % Favored : 81.28 % 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: 1.36 (0.30), residues: 860 helix: 1.22 (0.21), residues: 724 sheet: None (None), residues: 0 loop : -0.47 (0.43), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 434 HIS 0.001 0.000 HIS A 378 PHE 0.008 0.001 PHE A 404 TYR 0.021 0.002 TYR C 483 ARG 0.002 0.000 ARG D 362 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3097.97 seconds wall clock time: 55 minutes 39.94 seconds (3339.94 seconds total)