Starting phenix.real_space_refine on Fri Dec 8 06:58:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sip_25147/12_2023/7sip_25147_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sip_25147/12_2023/7sip_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_25147/12_2023/7sip_25147.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sip_25147/12_2023/7sip_25147.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sip_25147/12_2023/7sip_25147_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sip_25147/12_2023/7sip_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 4.88, per 1000 atoms: 0.65 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: 2.85 Conformation dependent library (CDL) restraints added in 1.1 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: 1.48 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: 1.85 Time building geometry restraints manager: 3.08 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: 1.510 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: 5.690 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 23.970 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.010 ------------------------------------------------------------------------------- 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 : 0.899 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 1.3844 time to fit residues: 179.0082 Evaluate side-chains 105 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.852 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0934 ------------------------------------------------------------------------------- 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: 1.9990 chunk 41 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.7896 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7680 Z= 0.198 Angle : 0.523 5.486 10280 Z= 0.267 Chirality : 0.039 0.126 1200 Planarity : 0.005 0.050 1192 Dihedral : 17.083 127.476 1336 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 2.01 % Allowed : 10.83 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.30), residues: 860 helix: 0.83 (0.21), residues: 712 sheet: None (None), residues: 0 loop : 0.02 (0.49), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 434 HIS 0.001 0.000 HIS B 378 PHE 0.009 0.001 PHE D 404 TYR 0.016 0.002 TYR C 483 ARG 0.005 0.001 ARG A 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 144 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 129 time to evaluate : 0.754 Fit side-chains outliers start: 15 outliers final: 2 residues processed: 130 average time/residue: 1.4869 time to fit residues: 202.4279 Evaluate side-chains 118 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 116 time to evaluate : 0.828 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1648 time to fit residues: 1.5312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 66 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 22 optimal weight: 10.0000 chunk 80 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 64 optimal weight: 0.2980 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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: 0.7929 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 7680 Z= 0.179 Angle : 0.486 5.460 10280 Z= 0.250 Chirality : 0.039 0.152 1200 Planarity : 0.005 0.050 1192 Dihedral : 14.558 122.600 1336 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 2.01 % Allowed : 12.83 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.30), residues: 860 helix: 1.00 (0.21), residues: 708 sheet: None (None), residues: 0 loop : -0.24 (0.45), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 434 HIS 0.001 0.000 HIS B 378 PHE 0.008 0.001 PHE D 404 TYR 0.013 0.002 TYR D 485 ARG 0.004 0.000 ARG D 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 107 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 0.862 Fit side-chains outliers start: 15 outliers final: 6 residues processed: 104 average time/residue: 1.7707 time to fit residues: 191.7891 Evaluate side-chains 93 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 87 time to evaluate : 0.810 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 1.0836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.4980 chunk 60 optimal weight: 0.3980 chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 0.2980 chunk 38 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 chunk 80 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 22 optimal weight: 10.0000 chunk 70 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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: 0.2061 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= 0.144 Angle : 0.451 5.450 10280 Z= 0.232 Chirality : 0.037 0.121 1200 Planarity : 0.005 0.049 1192 Dihedral : 13.476 116.526 1336 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 2.01 % Allowed : 14.17 % Favored : 83.82 % 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: 1.22 (0.30), residues: 860 helix: 1.13 (0.21), residues: 708 sheet: None (None), residues: 0 loop : -0.40 (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 D 378 PHE 0.006 0.001 PHE C 404 TYR 0.019 0.002 TYR A 483 ARG 0.005 0.000 ARG C 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 104 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 89 time to evaluate : 0.849 Fit side-chains outliers start: 15 outliers final: 8 residues processed: 100 average time/residue: 1.6746 time to fit residues: 174.9364 Evaluate side-chains 95 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 87 time to evaluate : 0.769 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 0.0905 time to fit residues: 1.4075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 0.2980 chunk 1 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 43 optimal weight: 0.4980 chunk 76 optimal weight: 0.0770 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 overall best weight: 0.5740 ------------------------------------------------------------------------------- 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: 0.7913 moved from start: 0.2273 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= 0.151 Angle : 0.454 5.435 10280 Z= 0.234 Chirality : 0.037 0.121 1200 Planarity : 0.004 0.047 1192 Dihedral : 12.907 113.220 1336 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.27 % Allowed : 15.51 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.30), residues: 860 helix: 1.15 (0.21), residues: 708 sheet: None (None), residues: 0 loop : -0.40 (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 B 378 PHE 0.007 0.001 PHE B 404 TYR 0.014 0.001 TYR D 485 ARG 0.003 0.000 ARG C 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 105 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 88 time to evaluate : 0.837 Fit side-chains outliers start: 17 outliers final: 13 residues processed: 99 average time/residue: 1.6150 time to fit residues: 167.0778 Evaluate side-chains 99 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 86 time to evaluate : 0.750 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 9 residues processed: 4 average time/residue: 0.4301 time to fit residues: 2.9535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 0.0770 chunk 16 optimal weight: 0.0070 chunk 49 optimal weight: 0.9990 chunk 20 optimal weight: 0.0970 chunk 85 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 28 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 82 optimal weight: 0.6980 overall best weight: 0.3754 ------------------------------------------------------------------------------- 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: 0.7878 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7680 Z= 0.131 Angle : 0.432 5.427 10280 Z= 0.222 Chirality : 0.036 0.118 1200 Planarity : 0.004 0.047 1192 Dihedral : 12.504 110.999 1336 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.54 % Allowed : 15.78 % 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: 1.38 (0.30), residues: 860 helix: 1.26 (0.21), residues: 708 sheet: None (None), residues: 0 loop : -0.46 (0.44), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 434 HIS 0.000 0.000 HIS A 378 PHE 0.005 0.001 PHE D 404 TYR 0.020 0.002 TYR A 483 ARG 0.003 0.000 ARG C 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 105 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 86 time to evaluate : 0.810 Fit side-chains outliers start: 19 outliers final: 13 residues processed: 96 average time/residue: 1.6458 time to fit residues: 165.0540 Evaluate side-chains 98 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 85 time to evaluate : 0.808 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 9 residues processed: 4 average time/residue: 0.2190 time to fit residues: 2.2141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 62 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 0.0050 chunk 52 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- 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: 0.7923 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7680 Z= 0.161 Angle : 0.455 5.409 10280 Z= 0.234 Chirality : 0.037 0.120 1200 Planarity : 0.004 0.048 1192 Dihedral : 12.472 111.933 1336 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.14 % Allowed : 16.18 % 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: 1.32 (0.30), residues: 860 helix: 1.21 (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 0.008 0.001 PHE A 404 TYR 0.014 0.002 TYR D 485 ARG 0.002 0.000 ARG C 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 102 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 86 time to evaluate : 0.805 Fit side-chains outliers start: 16 outliers final: 10 residues processed: 95 average time/residue: 1.6513 time to fit residues: 164.0144 Evaluate side-chains 94 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 84 time to evaluate : 0.817 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 1 average time/residue: 0.2221 time to fit residues: 1.3821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 0.0770 chunk 53 optimal weight: 8.9990 chunk 57 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 74 optimal weight: 0.2980 overall best weight: 0.7340 ------------------------------------------------------------------------------- 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: 0.7935 moved from start: 0.2556 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= 0.168 Angle : 0.458 5.414 10280 Z= 0.237 Chirality : 0.037 0.122 1200 Planarity : 0.004 0.047 1192 Dihedral : 12.519 112.461 1336 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 1.74 % Allowed : 16.31 % Favored : 81.95 % 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: 1.35 (0.30), residues: 860 helix: 1.22 (0.21), residues: 724 sheet: None (None), residues: 0 loop : -0.56 (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 0.007 0.001 PHE A 404 TYR 0.015 0.001 TYR D 485 ARG 0.002 0.000 ARG C 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 102 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 89 time to evaluate : 0.817 Fit side-chains outliers start: 13 outliers final: 12 residues processed: 100 average time/residue: 1.6679 time to fit residues: 174.3193 Evaluate side-chains 100 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 88 time to evaluate : 0.809 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 2 average time/residue: 0.2036 time to fit residues: 1.5764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 74 optimal weight: 0.3980 chunk 78 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.7945 moved from start: 0.2621 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= 0.178 Angle : 0.462 5.418 10280 Z= 0.239 Chirality : 0.037 0.122 1200 Planarity : 0.004 0.047 1192 Dihedral : 12.333 112.616 1336 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % 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: 1.20 (0.21), residues: 724 sheet: None (None), residues: 0 loop : -0.56 (0.43), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 434 HIS 0.001 0.000 HIS A 378 PHE 0.009 0.001 PHE B 404 TYR 0.021 0.002 TYR A 483 ARG 0.002 0.000 ARG A 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 99 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 85 time to evaluate : 0.822 Fit side-chains outliers start: 14 outliers final: 12 residues processed: 96 average time/residue: 1.6553 time to fit residues: 165.9481 Evaluate side-chains 96 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 84 time to evaluate : 0.797 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 2 average time/residue: 0.2156 time to fit residues: 1.6293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 42 optimal weight: 0.8980 chunk 55 optimal weight: 0.4980 chunk 74 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.7917 moved from start: 0.2660 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= 0.150 Angle : 0.443 5.431 10280 Z= 0.229 Chirality : 0.036 0.120 1200 Planarity : 0.004 0.046 1192 Dihedral : 11.936 111.399 1336 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.47 % Allowed : 17.11 % Favored : 81.42 % 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: 1.40 (0.30), residues: 860 helix: 1.25 (0.21), residues: 724 sheet: None (None), residues: 0 loop : -0.48 (0.44), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 434 HIS 0.001 0.000 HIS A 486 PHE 0.007 0.001 PHE B 404 TYR 0.015 0.001 TYR B 485 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 95 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 84 time to evaluate : 0.839 Fit side-chains outliers start: 11 outliers final: 10 residues processed: 94 average time/residue: 1.7449 time to fit residues: 171.1807 Evaluate side-chains 94 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 84 time to evaluate : 0.885 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 10 residues processed: 0 time to fit residues: 1.0396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.4765 > 50: distance: 56 - 73: 10.098 distance: 60 - 81: 9.994 distance: 68 - 73: 12.318 distance: 73 - 74: 9.776 distance: 74 - 75: 10.881 distance: 74 - 77: 27.762 distance: 75 - 76: 20.017 distance: 75 - 81: 22.388 distance: 77 - 78: 26.432 distance: 78 - 79: 8.222 distance: 78 - 80: 13.244 distance: 81 - 82: 6.420 distance: 82 - 83: 11.825 distance: 82 - 85: 16.095 distance: 83 - 84: 20.948 distance: 83 - 88: 20.535 distance: 85 - 86: 19.087 distance: 85 - 87: 11.990 distance: 88 - 89: 33.114 distance: 89 - 90: 10.371 distance: 89 - 92: 30.176 distance: 90 - 91: 26.987 distance: 90 - 99: 12.173 distance: 92 - 93: 15.669 distance: 93 - 94: 10.152 distance: 94 - 95: 15.786 distance: 95 - 96: 6.687 distance: 96 - 97: 8.105 distance: 96 - 98: 10.165 distance: 99 - 100: 23.268 distance: 100 - 101: 43.062 distance: 100 - 103: 15.496 distance: 101 - 102: 14.334 distance: 101 - 106: 24.520 distance: 103 - 104: 19.388 distance: 103 - 105: 33.112 distance: 106 - 107: 18.087 distance: 107 - 108: 21.548 distance: 107 - 110: 17.880 distance: 108 - 109: 25.682 distance: 108 - 117: 24.230 distance: 110 - 111: 32.029 distance: 111 - 112: 24.960 distance: 111 - 113: 39.071 distance: 112 - 114: 16.450 distance: 113 - 115: 6.959 distance: 114 - 116: 10.647 distance: 115 - 116: 11.745 distance: 117 - 118: 38.189 distance: 118 - 119: 33.948 distance: 118 - 121: 46.661 distance: 119 - 120: 9.846 distance: 119 - 128: 29.157 distance: 121 - 122: 35.149 distance: 122 - 123: 13.867 distance: 123 - 124: 8.645 distance: 124 - 125: 6.506 distance: 125 - 126: 6.368 distance: 125 - 127: 9.394 distance: 128 - 129: 15.672 distance: 129 - 130: 7.415 distance: 129 - 132: 40.035 distance: 130 - 131: 10.983 distance: 130 - 136: 32.621 distance: 132 - 133: 15.071 distance: 132 - 134: 8.837 distance: 133 - 135: 18.021 distance: 136 - 137: 21.149 distance: 137 - 138: 9.809 distance: 137 - 140: 13.348 distance: 138 - 139: 33.185 distance: 138 - 147: 18.976 distance: 140 - 141: 23.809 distance: 141 - 142: 3.077 distance: 141 - 143: 30.681 distance: 142 - 144: 20.803 distance: 143 - 145: 9.958 distance: 144 - 146: 23.152 distance: 145 - 146: 33.642 distance: 147 - 148: 17.999 distance: 148 - 149: 18.763 distance: 148 - 151: 30.342 distance: 149 - 150: 7.504 distance: 149 - 156: 18.407 distance: 151 - 152: 20.940 distance: 152 - 153: 12.047 distance: 153 - 154: 9.429 distance: 154 - 155: 19.912 distance: 156 - 157: 18.752 distance: 157 - 158: 15.447 distance: 157 - 160: 9.914 distance: 158 - 159: 7.853 distance: 158 - 164: 6.287 distance: 160 - 161: 3.902 distance: 161 - 162: 19.024 distance: 161 - 163: 26.129