Starting phenix.real_space_refine on Tue Apr 9 04:17:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ubs_20714/04_2024/6ubs_20714_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ubs_20714/04_2024/6ubs_20714.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ubs_20714/04_2024/6ubs_20714_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ubs_20714/04_2024/6ubs_20714_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ubs_20714/04_2024/6ubs_20714_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ubs_20714/04_2024/6ubs_20714.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ubs_20714/04_2024/6ubs_20714.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ubs_20714/04_2024/6ubs_20714_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ubs_20714/04_2024/6ubs_20714_updated.pdb" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 100 5.16 5 C 9950 2.51 5 N 2440 2.21 5 O 2770 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 53": "NH1" <-> "NH2" Residue "A ARG 96": "NH1" <-> "NH2" Residue "A ASP 121": "OD1" <-> "OD2" Residue "A GLU 134": "OE1" <-> "OE2" Residue "A ARG 143": "NH1" <-> "NH2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A ASP 308": "OD1" <-> "OD2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A ARG 409": "NH1" <-> "NH2" Residue "A GLU 439": "OE1" <-> "OE2" Residue "A ASP 440": "OD1" <-> "OD2" Residue "B ARG 53": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ASP 121": "OD1" <-> "OD2" Residue "B GLU 134": "OE1" <-> "OE2" Residue "B ARG 143": "NH1" <-> "NH2" Residue "B GLU 181": "OE1" <-> "OE2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B ASP 308": "OD1" <-> "OD2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B ARG 409": "NH1" <-> "NH2" Residue "B GLU 439": "OE1" <-> "OE2" Residue "B ASP 440": "OD1" <-> "OD2" Residue "C ARG 53": "NH1" <-> "NH2" Residue "C ARG 96": "NH1" <-> "NH2" Residue "C ASP 121": "OD1" <-> "OD2" Residue "C GLU 134": "OE1" <-> "OE2" Residue "C ARG 143": "NH1" <-> "NH2" Residue "C GLU 181": "OE1" <-> "OE2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C ASP 308": "OD1" <-> "OD2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C ARG 409": "NH1" <-> "NH2" Residue "C GLU 439": "OE1" <-> "OE2" Residue "C ASP 440": "OD1" <-> "OD2" Residue "D ARG 53": "NH1" <-> "NH2" Residue "D ARG 96": "NH1" <-> "NH2" Residue "D ASP 121": "OD1" <-> "OD2" Residue "D GLU 134": "OE1" <-> "OE2" Residue "D ARG 143": "NH1" <-> "NH2" Residue "D GLU 181": "OE1" <-> "OE2" Residue "D ARG 237": "NH1" <-> "NH2" Residue "D ASP 308": "OD1" <-> "OD2" Residue "D GLU 324": "OE1" <-> "OE2" Residue "D ARG 409": "NH1" <-> "NH2" Residue "D GLU 439": "OE1" <-> "OE2" Residue "D ASP 440": "OD1" <-> "OD2" Residue "E ARG 53": "NH1" <-> "NH2" Residue "E ARG 96": "NH1" <-> "NH2" Residue "E ASP 121": "OD1" <-> "OD2" Residue "E GLU 134": "OE1" <-> "OE2" Residue "E ARG 143": "NH1" <-> "NH2" Residue "E GLU 181": "OE1" <-> "OE2" Residue "E ARG 237": "NH1" <-> "NH2" Residue "E ASP 308": "OD1" <-> "OD2" Residue "E GLU 324": "OE1" <-> "OE2" Residue "E ARG 409": "NH1" <-> "NH2" Residue "E GLU 439": "OE1" <-> "OE2" Residue "E ASP 440": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 15270 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2949 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 16, 'TRANS': 345} Chain breaks: 1 Chain: "B" Number of atoms: 2949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2949 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 16, 'TRANS': 345} Chain breaks: 1 Chain: "C" Number of atoms: 2949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2949 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 16, 'TRANS': 345} Chain breaks: 1 Chain: "D" Number of atoms: 2949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2949 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 16, 'TRANS': 345} Chain breaks: 1 Chain: "E" Number of atoms: 2949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2949 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 16, 'TRANS': 345} Chain breaks: 1 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Unusual residues: {'PIO': 1, 'PX4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 106 Unusual residues: {'PIO': 1, 'PX4': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 77 Unusual residues: {'PIO': 1, 'PX4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 6 Chain: "D" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 77 Unusual residues: {'PIO': 1, 'PX4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 77 Unusual residues: {'PIO': 1, 'PX4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 8.20, per 1000 atoms: 0.54 Number of scatterers: 15270 At special positions: 0 Unit cell: (99.828, 100.89, 139.122, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 100 16.00 P 10 15.00 O 2770 8.00 N 2440 7.00 C 9950 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 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG F 1 " - " ASN A 62 " " NAG G 1 " - " ASN B 62 " " NAG H 1 " - " ASN C 62 " " NAG I 1 " - " ASN D 62 " " NAG J 1 " - " ASN E 62 " Time building additional restraints: 5.56 Conformation dependent library (CDL) restraints added in 2.7 seconds 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3480 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 20 sheets defined 38.1% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.77 Creating SS restraints... Processing helix chain 'A' and resid 34 through 41 removed outlier: 3.879A pdb=" N LEU A 38 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ASP A 39 " --> pdb=" O GLU A 36 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU A 41 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 116 No H-bonds generated for 'chain 'A' and resid 114 through 116' Processing helix chain 'A' and resid 169 through 171 No H-bonds generated for 'chain 'A' and resid 169 through 171' Processing helix chain 'A' and resid 245 through 249 Processing helix chain 'A' and resid 253 through 266 removed outlier: 4.522A pdb=" N SER A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N PHE A 266 " --> pdb=" O SER A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 294 removed outlier: 3.799A pdb=" N SER A 294 " --> pdb=" O GLN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 340 removed outlier: 3.577A pdb=" N TRP A 310 " --> pdb=" O ALA A 306 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 318 " --> pdb=" O CYS A 314 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A 322 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 442 removed outlier: 3.851A pdb=" N MET A 399 " --> pdb=" O THR A 395 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ARG A 400 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS A 401 " --> pdb=" O GLU A 397 " (cutoff:3.500A) Proline residue: A 419 - end of helix removed outlier: 3.709A pdb=" N PHE A 422 " --> pdb=" O PHE A 418 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE A 436 " --> pdb=" O THR A 432 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 441 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N HIS A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 41 removed outlier: 3.878A pdb=" N LEU B 38 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ASP B 39 " --> pdb=" O GLU B 36 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU B 41 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 116 No H-bonds generated for 'chain 'B' and resid 114 through 116' Processing helix chain 'B' and resid 169 through 171 No H-bonds generated for 'chain 'B' and resid 169 through 171' Processing helix chain 'B' and resid 245 through 249 Processing helix chain 'B' and resid 253 through 266 removed outlier: 4.524A pdb=" N SER B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N PHE B 266 " --> pdb=" O SER B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 294 removed outlier: 3.799A pdb=" N SER B 294 " --> pdb=" O GLN B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 340 removed outlier: 3.577A pdb=" N TRP B 310 " --> pdb=" O ALA B 306 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B 318 " --> pdb=" O CYS B 314 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU B 322 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR B 325 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE B 331 " --> pdb=" O ALA B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 442 removed outlier: 3.850A pdb=" N MET B 399 " --> pdb=" O THR B 395 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ARG B 400 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B 401 " --> pdb=" O GLU B 397 " (cutoff:3.500A) Proline residue: B 419 - end of helix removed outlier: 3.708A pdb=" N PHE B 422 " --> pdb=" O PHE B 418 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE B 436 " --> pdb=" O THR B 432 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE B 441 " --> pdb=" O ARG B 437 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N HIS B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 41 removed outlier: 3.879A pdb=" N LEU C 38 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ASP C 39 " --> pdb=" O GLU C 36 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU C 41 " --> pdb=" O LEU C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 116 No H-bonds generated for 'chain 'C' and resid 114 through 116' Processing helix chain 'C' and resid 169 through 171 No H-bonds generated for 'chain 'C' and resid 169 through 171' Processing helix chain 'C' and resid 245 through 249 Processing helix chain 'C' and resid 253 through 266 removed outlier: 4.524A pdb=" N SER C 265 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N PHE C 266 " --> pdb=" O SER C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 294 removed outlier: 3.799A pdb=" N SER C 294 " --> pdb=" O GLN C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 340 removed outlier: 3.577A pdb=" N TRP C 310 " --> pdb=" O ALA C 306 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL C 318 " --> pdb=" O CYS C 314 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU C 322 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR C 325 " --> pdb=" O ALA C 321 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE C 331 " --> pdb=" O ALA C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 442 removed outlier: 3.851A pdb=" N MET C 399 " --> pdb=" O THR C 395 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ARG C 400 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS C 401 " --> pdb=" O GLU C 397 " (cutoff:3.500A) Proline residue: C 419 - end of helix removed outlier: 3.708A pdb=" N PHE C 422 " --> pdb=" O PHE C 418 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE C 436 " --> pdb=" O THR C 432 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE C 441 " --> pdb=" O ARG C 437 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N HIS C 442 " --> pdb=" O SER C 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 41 removed outlier: 3.879A pdb=" N LEU D 38 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ASP D 39 " --> pdb=" O GLU D 36 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU D 41 " --> pdb=" O LEU D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 116 No H-bonds generated for 'chain 'D' and resid 114 through 116' Processing helix chain 'D' and resid 169 through 171 No H-bonds generated for 'chain 'D' and resid 169 through 171' Processing helix chain 'D' and resid 245 through 249 Processing helix chain 'D' and resid 253 through 266 removed outlier: 4.523A pdb=" N SER D 265 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N PHE D 266 " --> pdb=" O SER D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 294 removed outlier: 3.798A pdb=" N SER D 294 " --> pdb=" O GLN D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 340 removed outlier: 3.578A pdb=" N TRP D 310 " --> pdb=" O ALA D 306 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL D 318 " --> pdb=" O CYS D 314 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU D 322 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR D 325 " --> pdb=" O ALA D 321 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE D 331 " --> pdb=" O ALA D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 442 removed outlier: 3.850A pdb=" N MET D 399 " --> pdb=" O THR D 395 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ARG D 400 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS D 401 " --> pdb=" O GLU D 397 " (cutoff:3.500A) Proline residue: D 419 - end of helix removed outlier: 3.709A pdb=" N PHE D 422 " --> pdb=" O PHE D 418 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE D 436 " --> pdb=" O THR D 432 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE D 441 " --> pdb=" O ARG D 437 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N HIS D 442 " --> pdb=" O SER D 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 41 removed outlier: 3.879A pdb=" N LEU E 38 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ASP E 39 " --> pdb=" O GLU E 36 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU E 41 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 116 No H-bonds generated for 'chain 'E' and resid 114 through 116' Processing helix chain 'E' and resid 169 through 171 No H-bonds generated for 'chain 'E' and resid 169 through 171' Processing helix chain 'E' and resid 245 through 249 Processing helix chain 'E' and resid 253 through 266 removed outlier: 4.523A pdb=" N SER E 265 " --> pdb=" O LEU E 261 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N PHE E 266 " --> pdb=" O SER E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 294 removed outlier: 3.798A pdb=" N SER E 294 " --> pdb=" O GLN E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 340 removed outlier: 3.577A pdb=" N TRP E 310 " --> pdb=" O ALA E 306 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL E 318 " --> pdb=" O CYS E 314 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU E 322 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR E 325 " --> pdb=" O ALA E 321 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE E 331 " --> pdb=" O ALA E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 442 removed outlier: 3.851A pdb=" N MET E 399 " --> pdb=" O THR E 395 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ARG E 400 " --> pdb=" O VAL E 396 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS E 401 " --> pdb=" O GLU E 397 " (cutoff:3.500A) Proline residue: E 419 - end of helix removed outlier: 3.708A pdb=" N PHE E 422 " --> pdb=" O PHE E 418 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE E 436 " --> pdb=" O THR E 432 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE E 441 " --> pdb=" O ARG E 437 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N HIS E 442 " --> pdb=" O SER E 438 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 190 through 194 removed outlier: 6.515A pdb=" N VAL A 61 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLU A 193 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VAL A 63 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ASN A 62 " --> pdb=" O ASN A 93 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ASN A 93 " --> pdb=" O ASN A 62 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 200 through 202 removed outlier: 6.412A pdb=" N ILE A 67 " --> pdb=" O GLN A 201 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ASN A 85 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N PHE A 72 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ARG A 83 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY A 129 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ALA A 161 " --> pdb=" O GLU A 127 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N GLU A 127 " --> pdb=" O ALA A 161 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 122 through 124 removed outlier: 3.670A pdb=" N ILE A 234 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 220 through 225 Processing sheet with id= E, first strand: chain 'B' and resid 190 through 194 removed outlier: 6.515A pdb=" N VAL B 61 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLU B 193 " --> pdb=" O VAL B 61 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL B 63 " --> pdb=" O GLU B 193 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ASN B 62 " --> pdb=" O ASN B 93 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ASN B 93 " --> pdb=" O ASN B 62 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 200 through 202 removed outlier: 6.412A pdb=" N ILE B 67 " --> pdb=" O GLN B 201 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ASN B 85 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N PHE B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ARG B 83 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY B 129 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N ALA B 161 " --> pdb=" O GLU B 127 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N GLU B 127 " --> pdb=" O ALA B 161 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 122 through 124 removed outlier: 3.670A pdb=" N ILE B 234 " --> pdb=" O LEU B 180 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 220 through 225 Processing sheet with id= I, first strand: chain 'C' and resid 190 through 194 removed outlier: 6.514A pdb=" N VAL C 61 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLU C 193 " --> pdb=" O VAL C 61 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N VAL C 63 " --> pdb=" O GLU C 193 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ASN C 62 " --> pdb=" O ASN C 93 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ASN C 93 " --> pdb=" O ASN C 62 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 200 through 202 removed outlier: 6.412A pdb=" N ILE C 67 " --> pdb=" O GLN C 201 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASN C 85 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N PHE C 72 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ARG C 83 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY C 129 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ALA C 161 " --> pdb=" O GLU C 127 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N GLU C 127 " --> pdb=" O ALA C 161 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 122 through 124 removed outlier: 3.670A pdb=" N ILE C 234 " --> pdb=" O LEU C 180 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 220 through 225 Processing sheet with id= M, first strand: chain 'D' and resid 190 through 194 removed outlier: 6.514A pdb=" N VAL D 61 " --> pdb=" O ILE D 191 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N GLU D 193 " --> pdb=" O VAL D 61 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VAL D 63 " --> pdb=" O GLU D 193 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ASN D 62 " --> pdb=" O ASN D 93 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ASN D 93 " --> pdb=" O ASN D 62 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 200 through 202 removed outlier: 6.412A pdb=" N ILE D 67 " --> pdb=" O GLN D 201 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASN D 85 " --> pdb=" O ASN D 70 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N PHE D 72 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ARG D 83 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY D 129 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ALA D 161 " --> pdb=" O GLU D 127 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N GLU D 127 " --> pdb=" O ALA D 161 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 122 through 124 removed outlier: 3.670A pdb=" N ILE D 234 " --> pdb=" O LEU D 180 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 220 through 225 Processing sheet with id= Q, first strand: chain 'E' and resid 190 through 194 removed outlier: 6.515A pdb=" N VAL E 61 " --> pdb=" O ILE E 191 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLU E 193 " --> pdb=" O VAL E 61 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL E 63 " --> pdb=" O GLU E 193 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ASN E 62 " --> pdb=" O ASN E 93 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ASN E 93 " --> pdb=" O ASN E 62 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 200 through 202 removed outlier: 6.412A pdb=" N ILE E 67 " --> pdb=" O GLN E 201 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ASN E 85 " --> pdb=" O ASN E 70 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N PHE E 72 " --> pdb=" O ARG E 83 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ARG E 83 " --> pdb=" O PHE E 72 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY E 129 " --> pdb=" O VAL E 159 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ALA E 161 " --> pdb=" O GLU E 127 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N GLU E 127 " --> pdb=" O ALA E 161 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 122 through 124 removed outlier: 3.670A pdb=" N ILE E 234 " --> pdb=" O LEU E 180 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 220 through 225 625 hydrogen bonds defined for protein. 1800 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: 5.72 Time building geometry restraints manager: 6.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2370 1.31 - 1.44: 4282 1.44 - 1.56: 8768 1.56 - 1.69: 30 1.69 - 1.82: 170 Bond restraints: 15620 Sorted by residual: bond pdb=" C9 PX4 D 601 " pdb=" O5 PX4 D 601 " ideal model delta sigma weight residual 1.327 1.431 -0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" C9 PX4 C 601 " pdb=" O5 PX4 C 601 " ideal model delta sigma weight residual 1.327 1.431 -0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" C9 PX4 E 902 " pdb=" O5 PX4 E 902 " ideal model delta sigma weight residual 1.327 1.431 -0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" C9 PX4 B 603 " pdb=" O5 PX4 B 603 " ideal model delta sigma weight residual 1.327 1.430 -0.103 2.00e-02 2.50e+03 2.68e+01 bond pdb=" C9 PX4 C 605 " pdb=" O5 PX4 C 605 " ideal model delta sigma weight residual 1.327 1.430 -0.103 2.00e-02 2.50e+03 2.67e+01 ... (remaining 15615 not shown) Histogram of bond angle deviations from ideal: 100.32 - 107.06: 503 107.06 - 113.80: 8668 113.80 - 120.54: 6481 120.54 - 127.28: 5280 127.28 - 134.02: 163 Bond angle restraints: 21095 Sorted by residual: angle pdb=" O3 PX4 D 605 " pdb=" P1 PX4 D 605 " pdb=" O4 PX4 D 605 " ideal model delta sigma weight residual 93.64 110.38 -16.74 3.00e+00 1.11e-01 3.11e+01 angle pdb=" O3 PX4 C 605 " pdb=" P1 PX4 C 605 " pdb=" O4 PX4 C 605 " ideal model delta sigma weight residual 93.64 110.38 -16.74 3.00e+00 1.11e-01 3.11e+01 angle pdb=" O3 PX4 E 901 " pdb=" P1 PX4 E 901 " pdb=" O4 PX4 E 901 " ideal model delta sigma weight residual 93.64 110.38 -16.74 3.00e+00 1.11e-01 3.11e+01 angle pdb=" O3 PX4 B 603 " pdb=" P1 PX4 B 603 " pdb=" O4 PX4 B 603 " ideal model delta sigma weight residual 93.64 110.36 -16.72 3.00e+00 1.11e-01 3.11e+01 angle pdb=" O3 PX4 B 606 " pdb=" P1 PX4 B 606 " pdb=" O4 PX4 B 606 " ideal model delta sigma weight residual 93.64 110.36 -16.72 3.00e+00 1.11e-01 3.11e+01 ... (remaining 21090 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.19: 9061 29.19 - 58.37: 459 58.37 - 87.56: 20 87.56 - 116.74: 0 116.74 - 145.93: 5 Dihedral angle restraints: 9545 sinusoidal: 4190 harmonic: 5355 Sorted by residual: dihedral pdb=" O5 PX4 D 601 " pdb=" C7 PX4 D 601 " pdb=" C8 PX4 D 601 " pdb=" O7 PX4 D 601 " ideal model delta sinusoidal sigma weight residual 59.95 -85.98 145.93 1 3.00e+01 1.11e-03 1.95e+01 dihedral pdb=" O5 PX4 E 902 " pdb=" C7 PX4 E 902 " pdb=" C8 PX4 E 902 " pdb=" O7 PX4 E 902 " ideal model delta sinusoidal sigma weight residual 59.95 -85.97 145.92 1 3.00e+01 1.11e-03 1.95e+01 dihedral pdb=" O5 PX4 A 601 " pdb=" C7 PX4 A 601 " pdb=" C8 PX4 A 601 " pdb=" O7 PX4 A 601 " ideal model delta sinusoidal sigma weight residual 59.95 -85.97 145.92 1 3.00e+01 1.11e-03 1.95e+01 ... (remaining 9542 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1586 0.046 - 0.093: 523 0.093 - 0.139: 178 0.139 - 0.186: 48 0.186 - 0.232: 20 Chirality restraints: 2355 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN B 62 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN D 62 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" C4 NAG H 1 " pdb=" C3 NAG H 1 " pdb=" C5 NAG H 1 " pdb=" O4 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.30 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 2352 not shown) Planarity restraints: 2605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP E 411 " -0.020 2.00e-02 2.50e+03 3.99e-02 1.59e+01 pdb=" C ASP E 411 " 0.069 2.00e-02 2.50e+03 pdb=" O ASP E 411 " -0.026 2.00e-02 2.50e+03 pdb=" N THR E 412 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 411 " -0.020 2.00e-02 2.50e+03 3.98e-02 1.58e+01 pdb=" C ASP D 411 " 0.069 2.00e-02 2.50e+03 pdb=" O ASP D 411 " -0.026 2.00e-02 2.50e+03 pdb=" N THR D 412 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 411 " 0.020 2.00e-02 2.50e+03 3.97e-02 1.58e+01 pdb=" C ASP C 411 " -0.069 2.00e-02 2.50e+03 pdb=" O ASP C 411 " 0.026 2.00e-02 2.50e+03 pdb=" N THR C 412 " 0.023 2.00e-02 2.50e+03 ... (remaining 2602 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 1102 2.74 - 3.28: 14637 3.28 - 3.82: 24136 3.82 - 4.36: 29010 4.36 - 4.90: 49295 Nonbonded interactions: 118180 Sorted by model distance: nonbonded pdb=" O GLY D 278 " pdb=" OG1 THR D 282 " model vdw 2.194 2.440 nonbonded pdb=" O GLY C 278 " pdb=" OG1 THR C 282 " model vdw 2.194 2.440 nonbonded pdb=" O GLY B 278 " pdb=" OG1 THR B 282 " model vdw 2.194 2.440 nonbonded pdb=" O GLY A 278 " pdb=" OG1 THR A 282 " model vdw 2.195 2.440 nonbonded pdb=" O GLY E 278 " pdb=" OG1 THR E 282 " model vdw 2.195 2.440 ... (remaining 118175 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 31 through 444 or resid 601)) selection = (chain 'B' and (resid 31 through 444 or resid 601)) selection = (chain 'C' and (resid 31 through 444 or resid 601)) selection = (chain 'D' and (resid 31 through 444 or resid 601)) selection = (chain 'E' and (resid 31 through 444 or (resid 901 and (name C10 or name C11 or \ name C12 or name C13 or name C14 or name C23 or name C24 or name C25 or name C26 \ or name C27 or name C28 or name C6 or name C7 or name C8 or name C9 or name O4 \ or name O5 or name O6 or name O7 or name O8 )))) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 1.210 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: 0.020 Extract box with map and model: 6.440 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 42.060 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.120 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 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 : 0.006 0.104 15620 Z= 0.406 Angle : 0.978 16.743 21095 Z= 0.491 Chirality : 0.056 0.232 2355 Planarity : 0.008 0.044 2600 Dihedral : 16.045 145.925 6065 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.22 % Allowed : 11.87 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.10 (0.16), residues: 1790 helix: -3.28 (0.14), residues: 600 sheet: -1.67 (0.23), residues: 460 loop : -2.74 (0.18), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 263 HIS 0.004 0.001 HIS A 133 PHE 0.018 0.001 PHE B 319 TYR 0.017 0.002 TYR C 433 ARG 0.005 0.000 ARG D 51 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 268 time to evaluate : 1.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 258 ILE cc_start: 0.9350 (pt) cc_final: 0.8671 (pt) REVERT: D 258 ILE cc_start: 0.9414 (pt) cc_final: 0.8775 (pt) outliers start: 20 outliers final: 8 residues processed: 284 average time/residue: 0.2385 time to fit residues: 104.9663 Evaluate side-chains 170 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 162 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain E residue 62 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 7.9990 chunk 136 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 92 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 141 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 163 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 290 GLN B 70 ASN D 290 GLN E 290 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15620 Z= 0.214 Angle : 0.605 7.020 21095 Z= 0.313 Chirality : 0.044 0.157 2355 Planarity : 0.004 0.027 2600 Dihedral : 13.055 148.055 2473 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.30 % Allowed : 15.29 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.19), residues: 1790 helix: -0.31 (0.19), residues: 600 sheet: -0.95 (0.24), residues: 485 loop : -2.21 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 263 HIS 0.004 0.001 HIS B 133 PHE 0.027 0.001 PHE D 319 TYR 0.015 0.002 TYR D 433 ARG 0.004 0.000 ARG B 409 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 152 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASP cc_start: 0.7852 (OUTLIER) cc_final: 0.7511 (p0) REVERT: A 187 MET cc_start: 0.9103 (mmm) cc_final: 0.8812 (tpt) REVERT: B 121 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7460 (p0) REVERT: C 121 ASP cc_start: 0.7511 (OUTLIER) cc_final: 0.7124 (p0) REVERT: C 187 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8252 (tpp) REVERT: D 121 ASP cc_start: 0.7959 (OUTLIER) cc_final: 0.7675 (p0) REVERT: D 244 MET cc_start: 0.7784 (ttp) cc_final: 0.7553 (ttp) REVERT: E 121 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7839 (p0) outliers start: 54 outliers final: 30 residues processed: 188 average time/residue: 0.1985 time to fit residues: 61.7215 Evaluate side-chains 165 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 129 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 308 ASP Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 99 TYR Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 308 ASP Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 323 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 136 optimal weight: 0.5980 chunk 111 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 chunk 176 optimal weight: 0.9990 chunk 145 optimal weight: 0.0470 chunk 162 optimal weight: 0.0770 chunk 55 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 overall best weight: 0.5440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 290 GLN C 70 ASN D 70 ASN D 290 GLN E 70 ASN E 290 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15620 Z= 0.148 Angle : 0.526 6.526 21095 Z= 0.275 Chirality : 0.043 0.142 2355 Planarity : 0.003 0.024 2600 Dihedral : 12.177 143.582 2472 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.79 % Allowed : 15.72 % Favored : 80.49 % 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: -1.00 (0.20), residues: 1790 helix: 0.78 (0.21), residues: 605 sheet: -0.63 (0.25), residues: 485 loop : -1.95 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 92 HIS 0.005 0.001 HIS C 335 PHE 0.023 0.001 PHE D 319 TYR 0.015 0.001 TYR D 325 ARG 0.010 0.000 ARG C 400 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 141 time to evaluate : 1.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.7561 (p0) REVERT: A 187 MET cc_start: 0.9073 (mmm) cc_final: 0.8850 (mmm) REVERT: B 121 ASP cc_start: 0.7852 (OUTLIER) cc_final: 0.7411 (p0) REVERT: B 187 MET cc_start: 0.9078 (mmm) cc_final: 0.8701 (mmm) REVERT: C 121 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.7269 (p0) REVERT: C 187 MET cc_start: 0.8729 (mmt) cc_final: 0.8277 (tpp) REVERT: D 121 ASP cc_start: 0.7912 (OUTLIER) cc_final: 0.7646 (p0) REVERT: D 187 MET cc_start: 0.9129 (tpt) cc_final: 0.8832 (tpt) REVERT: D 244 MET cc_start: 0.7787 (ttp) cc_final: 0.7528 (ttp) REVERT: E 121 ASP cc_start: 0.8045 (OUTLIER) cc_final: 0.7799 (p0) outliers start: 62 outliers final: 33 residues processed: 185 average time/residue: 0.2045 time to fit residues: 63.3589 Evaluate side-chains 164 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 126 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 308 ASP Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 99 TYR Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 308 ASP Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 323 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 109 optimal weight: 0.0980 chunk 164 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 290 GLN C 290 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15620 Z= 0.283 Angle : 0.590 7.691 21095 Z= 0.311 Chirality : 0.045 0.176 2355 Planarity : 0.004 0.054 2600 Dihedral : 12.010 140.287 2470 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.40 % Allowed : 17.13 % Favored : 78.47 % 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: -0.42 (0.20), residues: 1790 helix: 1.38 (0.21), residues: 610 sheet: -0.23 (0.25), residues: 485 loop : -1.83 (0.22), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 267 HIS 0.005 0.001 HIS D 335 PHE 0.024 0.002 PHE B 319 TYR 0.021 0.002 TYR E 325 ARG 0.008 0.000 ARG C 89 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 118 time to evaluate : 1.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.7858 (p0) REVERT: A 187 MET cc_start: 0.9112 (mmm) cc_final: 0.8860 (mmm) REVERT: A 323 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.8955 (mm) REVERT: B 121 ASP cc_start: 0.8113 (OUTLIER) cc_final: 0.7811 (p0) REVERT: B 187 MET cc_start: 0.9026 (mmm) cc_final: 0.8605 (mmm) REVERT: C 121 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7578 (p0) REVERT: C 180 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8731 (pp) REVERT: D 113 MET cc_start: 0.8716 (pmm) cc_final: 0.8284 (pmm) REVERT: D 121 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7914 (p0) REVERT: D 244 MET cc_start: 0.7864 (ttp) cc_final: 0.7538 (ttp) REVERT: E 121 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.8012 (p0) REVERT: E 134 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7874 (tp30) outliers start: 72 outliers final: 44 residues processed: 173 average time/residue: 0.2076 time to fit residues: 59.3777 Evaluate side-chains 162 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 111 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 102 TYR Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 308 ASP Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 99 TYR Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 308 ASP Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 323 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 0.2980 chunk 98 optimal weight: 3.9990 chunk 2 optimal weight: 0.0870 chunk 129 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 148 optimal weight: 0.8980 chunk 120 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 overall best weight: 1.0560 ------------------------------------------------------------------------------- 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: 0.8336 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15620 Z= 0.192 Angle : 0.539 8.362 21095 Z= 0.281 Chirality : 0.043 0.154 2355 Planarity : 0.003 0.036 2600 Dihedral : 11.627 136.489 2470 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.00 % Allowed : 18.29 % Favored : 78.72 % 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: -0.30 (0.20), residues: 1790 helix: 1.59 (0.21), residues: 610 sheet: -0.01 (0.27), residues: 410 loop : -1.85 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 267 HIS 0.004 0.001 HIS A 335 PHE 0.016 0.001 PHE B 319 TYR 0.017 0.001 TYR D 325 ARG 0.001 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 120 time to evaluate : 1.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASP cc_start: 0.8225 (OUTLIER) cc_final: 0.7936 (p0) REVERT: A 323 LEU cc_start: 0.9413 (mm) cc_final: 0.8958 (mm) REVERT: B 121 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7787 (p0) REVERT: B 187 MET cc_start: 0.9036 (mmm) cc_final: 0.8610 (mmm) REVERT: C 42 MET cc_start: 0.8858 (mpp) cc_final: 0.8539 (ptp) REVERT: C 121 ASP cc_start: 0.8079 (OUTLIER) cc_final: 0.7751 (p0) REVERT: C 180 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8808 (pp) REVERT: C 187 MET cc_start: 0.8877 (tpt) cc_final: 0.8451 (tpp) REVERT: D 121 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.7988 (p0) REVERT: D 244 MET cc_start: 0.7813 (ttp) cc_final: 0.7532 (ttp) REVERT: E 80 MET cc_start: 0.9105 (mmm) cc_final: 0.8674 (mmt) REVERT: E 121 ASP cc_start: 0.8339 (OUTLIER) cc_final: 0.8104 (p0) outliers start: 49 outliers final: 38 residues processed: 154 average time/residue: 0.2106 time to fit residues: 53.2669 Evaluate side-chains 155 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 111 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 308 ASP Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 99 TYR Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 308 ASP Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 323 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 0.8980 chunk 156 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 174 optimal weight: 1.9990 chunk 144 optimal weight: 0.0870 chunk 80 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- 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: 0.8331 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15620 Z= 0.160 Angle : 0.515 7.096 21095 Z= 0.267 Chirality : 0.043 0.156 2355 Planarity : 0.003 0.035 2600 Dihedral : 11.216 132.450 2470 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.49 % Allowed : 17.92 % Favored : 78.59 % 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: 0.06 (0.21), residues: 1790 helix: 1.74 (0.21), residues: 610 sheet: 0.12 (0.25), residues: 485 loop : -1.60 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 92 HIS 0.005 0.001 HIS B 335 PHE 0.017 0.001 PHE D 319 TYR 0.016 0.001 TYR E 325 ARG 0.001 0.000 ARG D 406 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 116 time to evaluate : 1.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.7892 (p0) REVERT: A 134 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7716 (tp30) REVERT: A 323 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.8992 (mm) REVERT: B 121 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7816 (p0) REVERT: B 187 MET cc_start: 0.9034 (mmm) cc_final: 0.8592 (mmm) REVERT: C 42 MET cc_start: 0.8852 (mpp) cc_final: 0.8527 (ptp) REVERT: C 80 MET cc_start: 0.9019 (mmm) cc_final: 0.8761 (mmm) REVERT: C 121 ASP cc_start: 0.8027 (OUTLIER) cc_final: 0.7707 (p0) REVERT: C 187 MET cc_start: 0.8870 (tpt) cc_final: 0.8210 (tpp) REVERT: D 121 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.8004 (p0) REVERT: D 164 MET cc_start: 0.9166 (mtp) cc_final: 0.8952 (mtp) REVERT: E 79 THR cc_start: 0.9010 (OUTLIER) cc_final: 0.8677 (p) REVERT: E 121 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.8020 (p0) outliers start: 57 outliers final: 47 residues processed: 155 average time/residue: 0.2166 time to fit residues: 55.5149 Evaluate side-chains 162 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 108 time to evaluate : 1.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 308 ASP Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 99 TYR Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 308 ASP Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 323 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 99 optimal weight: 4.9990 chunk 127 optimal weight: 7.9990 chunk 98 optimal weight: 0.6980 chunk 146 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 173 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 105 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 133 HIS ** E 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 15620 Z= 0.234 Angle : 0.542 6.929 21095 Z= 0.281 Chirality : 0.043 0.157 2355 Planarity : 0.003 0.033 2600 Dihedral : 11.184 128.100 2470 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.73 % Allowed : 18.17 % Favored : 78.10 % 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: 0.07 (0.21), residues: 1790 helix: 1.91 (0.21), residues: 610 sheet: 0.36 (0.28), residues: 410 loop : -1.76 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 92 HIS 0.004 0.001 HIS B 335 PHE 0.030 0.001 PHE B 319 TYR 0.018 0.002 TYR D 325 ARG 0.001 0.000 ARG C 437 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 111 time to evaluate : 1.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASP cc_start: 0.8323 (OUTLIER) cc_final: 0.8016 (p0) REVERT: A 134 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7684 (tp30) REVERT: A 323 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.8980 (mm) REVERT: B 121 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.7977 (p0) REVERT: B 187 MET cc_start: 0.9054 (mmm) cc_final: 0.8798 (mmm) REVERT: C 42 MET cc_start: 0.8945 (mpp) cc_final: 0.8622 (ptp) REVERT: C 121 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7769 (p0) REVERT: C 187 MET cc_start: 0.8958 (tpt) cc_final: 0.8261 (tpp) REVERT: C 323 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9197 (mm) REVERT: D 121 ASP cc_start: 0.8469 (OUTLIER) cc_final: 0.8159 (p0) REVERT: E 104 ASP cc_start: 0.7045 (OUTLIER) cc_final: 0.6664 (p0) REVERT: E 121 ASP cc_start: 0.8507 (OUTLIER) cc_final: 0.8089 (p0) REVERT: E 251 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.8003 (pmm) outliers start: 61 outliers final: 44 residues processed: 151 average time/residue: 0.2216 time to fit residues: 55.2614 Evaluate side-chains 162 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 109 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 308 ASP Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 99 TYR Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 308 ASP Chi-restraints excluded: chain E residue 323 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 110 optimal weight: 0.0870 chunk 118 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 136 optimal weight: 0.5980 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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: 0.8344 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15620 Z= 0.143 Angle : 0.512 9.446 21095 Z= 0.263 Chirality : 0.043 0.157 2355 Planarity : 0.003 0.025 2600 Dihedral : 10.857 124.341 2470 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.43 % Allowed : 18.23 % Favored : 78.35 % 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: 0.17 (0.21), residues: 1790 helix: 1.95 (0.21), residues: 610 sheet: 0.44 (0.28), residues: 410 loop : -1.67 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 92 HIS 0.005 0.001 HIS B 335 PHE 0.019 0.001 PHE B 319 TYR 0.015 0.001 TYR E 325 ARG 0.001 0.000 ARG B 400 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 109 time to evaluate : 1.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.8426 (ptm) cc_final: 0.8084 (ptm) REVERT: A 121 ASP cc_start: 0.8300 (OUTLIER) cc_final: 0.7969 (p0) REVERT: A 323 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.8981 (mm) REVERT: B 121 ASP cc_start: 0.8208 (OUTLIER) cc_final: 0.7879 (p0) REVERT: B 187 MET cc_start: 0.9049 (mmm) cc_final: 0.8822 (mmm) REVERT: C 42 MET cc_start: 0.8943 (mpp) cc_final: 0.8639 (ptp) REVERT: C 121 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7772 (p0) REVERT: C 187 MET cc_start: 0.8970 (tpt) cc_final: 0.8365 (tpp) REVERT: C 323 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.9198 (mm) REVERT: D 121 ASP cc_start: 0.8431 (OUTLIER) cc_final: 0.8099 (p0) REVERT: E 79 THR cc_start: 0.8991 (OUTLIER) cc_final: 0.8640 (p) REVERT: E 80 MET cc_start: 0.9079 (mmm) cc_final: 0.8736 (mmt) REVERT: E 121 ASP cc_start: 0.8491 (OUTLIER) cc_final: 0.8017 (p0) REVERT: E 187 MET cc_start: 0.9008 (mmm) cc_final: 0.8795 (mmm) REVERT: E 189 ASP cc_start: 0.8725 (OUTLIER) cc_final: 0.8380 (t70) outliers start: 56 outliers final: 42 residues processed: 150 average time/residue: 0.2063 time to fit residues: 51.2197 Evaluate side-chains 155 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 104 time to evaluate : 1.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 271 ASP Chi-restraints excluded: chain D residue 308 ASP Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 99 TYR Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 308 ASP Chi-restraints excluded: chain E residue 323 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 0.5980 chunk 166 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 161 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 126 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 146 optimal weight: 0.5980 chunk 152 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.8347 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15620 Z= 0.155 Angle : 0.517 9.326 21095 Z= 0.265 Chirality : 0.043 0.151 2355 Planarity : 0.003 0.026 2600 Dihedral : 10.682 121.207 2470 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.24 % Allowed : 18.84 % Favored : 77.92 % 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: 0.23 (0.21), residues: 1790 helix: 1.97 (0.21), residues: 610 sheet: 0.47 (0.28), residues: 415 loop : -1.62 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 92 HIS 0.005 0.001 HIS B 335 PHE 0.022 0.001 PHE B 319 TYR 0.016 0.001 TYR E 325 ARG 0.001 0.000 ARG A 415 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 107 time to evaluate : 1.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.8424 (ptm) cc_final: 0.8085 (ptm) REVERT: A 121 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.7897 (p0) REVERT: A 134 GLU cc_start: 0.8075 (tp30) cc_final: 0.7638 (tp30) REVERT: A 323 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9006 (mm) REVERT: B 121 ASP cc_start: 0.8208 (OUTLIER) cc_final: 0.7887 (p0) REVERT: B 187 MET cc_start: 0.9042 (mmm) cc_final: 0.8824 (mmm) REVERT: C 42 MET cc_start: 0.8974 (mpp) cc_final: 0.8703 (ptp) REVERT: C 121 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.7685 (p0) REVERT: C 187 MET cc_start: 0.8976 (tpt) cc_final: 0.8359 (tpp) REVERT: D 121 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.8066 (p0) REVERT: E 121 ASP cc_start: 0.8481 (OUTLIER) cc_final: 0.7991 (p0) outliers start: 53 outliers final: 45 residues processed: 145 average time/residue: 0.2156 time to fit residues: 51.4508 Evaluate side-chains 156 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 105 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 271 ASP Chi-restraints excluded: chain D residue 308 ASP Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 99 TYR Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 308 ASP Chi-restraints excluded: chain E residue 323 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 0.0050 chunk 104 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 179 optimal weight: 0.9990 chunk 165 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 110 optimal weight: 0.0270 chunk 87 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 overall best weight: 0.4652 ------------------------------------------------------------------------------- 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: 0.8334 moved from start: 0.4965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15620 Z= 0.136 Angle : 0.512 9.206 21095 Z= 0.263 Chirality : 0.043 0.192 2355 Planarity : 0.003 0.025 2600 Dihedral : 10.479 117.857 2470 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.06 % Allowed : 18.90 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.21), residues: 1790 helix: 2.00 (0.21), residues: 610 sheet: 0.50 (0.28), residues: 415 loop : -1.59 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 92 HIS 0.004 0.001 HIS B 335 PHE 0.021 0.001 PHE B 319 TYR 0.024 0.001 TYR E 102 ARG 0.001 0.000 ARG C 89 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 108 time to evaluate : 1.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.8407 (ptm) cc_final: 0.8081 (ptm) REVERT: A 121 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7836 (p0) REVERT: A 134 GLU cc_start: 0.8143 (tp30) cc_final: 0.7659 (tp30) REVERT: A 323 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9010 (mm) REVERT: B 121 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.7843 (p0) REVERT: B 187 MET cc_start: 0.9009 (mmm) cc_final: 0.8791 (mmm) REVERT: C 42 MET cc_start: 0.9004 (mpp) cc_final: 0.8727 (ptp) REVERT: C 121 ASP cc_start: 0.8019 (OUTLIER) cc_final: 0.7670 (p0) REVERT: C 187 MET cc_start: 0.8947 (tpt) cc_final: 0.8409 (tpp) REVERT: D 121 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.7987 (p0) REVERT: E 121 ASP cc_start: 0.8379 (OUTLIER) cc_final: 0.8020 (p0) outliers start: 50 outliers final: 43 residues processed: 143 average time/residue: 0.2240 time to fit residues: 53.4898 Evaluate side-chains 152 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 103 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 271 ASP Chi-restraints excluded: chain D residue 308 ASP Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 99 TYR Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 323 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 0.2980 chunk 43 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 146 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 chunk 125 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3410 r_free = 0.3410 target = 0.085421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.065536 restraints weight = 40405.083| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 3.43 r_work: 0.2841 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.5057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15620 Z= 0.158 Angle : 0.517 8.906 21095 Z= 0.265 Chirality : 0.043 0.152 2355 Planarity : 0.003 0.025 2600 Dihedral : 10.414 116.117 2470 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.24 % Allowed : 18.84 % Favored : 77.92 % 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: 0.23 (0.21), residues: 1790 helix: 1.91 (0.21), residues: 640 sheet: 0.55 (0.28), residues: 415 loop : -1.75 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 92 HIS 0.004 0.001 HIS B 335 PHE 0.020 0.001 PHE B 319 TYR 0.016 0.001 TYR E 102 ARG 0.000 0.000 ARG A 53 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2699.18 seconds wall clock time: 50 minutes 44.82 seconds (3044.82 seconds total)