Starting phenix.real_space_refine on Thu Mar 21 23:41:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kox_22983/03_2024/7kox_22983_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kox_22983/03_2024/7kox_22983.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kox_22983/03_2024/7kox_22983_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kox_22983/03_2024/7kox_22983_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kox_22983/03_2024/7kox_22983_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kox_22983/03_2024/7kox_22983.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kox_22983/03_2024/7kox_22983.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kox_22983/03_2024/7kox_22983_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kox_22983/03_2024/7kox_22983_trim_updated.pdb" } resolution = 2.7 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= 0.001 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: 7 Type Number sf(0) Gaussians Ca 5 9.91 5 S 110 5.16 5 Cl 5 4.86 5 C 10390 2.51 5 N 2535 2.21 5 O 2895 1.98 5 H 15410 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A LEU 249": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23" Residue "B LEU 249": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23" Residue "C LEU 249": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23" Residue "D LEU 249": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23" Residue "E LEU 249": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 31350 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 6198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 6198 Classifications: {'peptide': 386} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 365} Chain breaks: 1 Chain: "B" Number of atoms: 6198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 6198 Classifications: {'peptide': 386} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 365} Chain breaks: 1 Chain: "C" Number of atoms: 6198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 6198 Classifications: {'peptide': 386} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 365} Chain breaks: 1 Chain: "D" Number of atoms: 6198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 6198 Classifications: {'peptide': 386} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 365} Chain breaks: 1 Chain: "E" Number of atoms: 6198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 6198 Classifications: {'peptide': 386} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 365} 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: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' CA': 1, 'EPJ': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' CA': 1, 'EPJ': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' CA': 1, 'EPJ': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' CA': 1, 'EPJ': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' CA': 1, 'EPJ': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 13.70, per 1000 atoms: 0.44 Number of scatterers: 31350 At special positions: 0 Unit cell: (95.45, 97.11, 154.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 5 19.99 Cl 5 17.00 S 110 16.00 O 2895 8.00 N 2535 7.00 C 10390 6.00 H 15410 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 190 " distance=2.05 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 190 " distance=2.05 Simple disulfide: pdb=" SG CYS C 127 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 189 " - pdb=" SG CYS C 190 " distance=2.05 Simple disulfide: pdb=" SG CYS D 127 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 189 " - pdb=" SG CYS D 190 " distance=2.05 Simple disulfide: pdb=" SG CYS E 127 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 189 " - pdb=" SG CYS E 190 " distance=2.05 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 A 501 " - " ASN A 67 " " NAG A 502 " - " ASN A 23 " " NAG B 501 " - " ASN B 67 " " NAG B 502 " - " ASN B 23 " " NAG C 501 " - " ASN C 67 " " NAG C 502 " - " ASN C 23 " " NAG D 501 " - " ASN D 67 " " NAG D 502 " - " ASN D 23 " " NAG E 501 " - " ASN E 67 " " NAG E 502 " - " ASN E 23 " " NAG F 1 " - " ASN A 110 " " NAG G 1 " - " ASN B 110 " " NAG H 1 " - " ASN C 110 " " NAG I 1 " - " ASN D 110 " " NAG J 1 " - " ASN E 110 " Time building additional restraints: 23.57 Conformation dependent library (CDL) restraints added in 2.9 seconds 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3680 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 25 sheets defined 38.1% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.83 Creating SS restraints... Processing helix chain 'A' and resid 2 through 10 Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 215 through 230 Processing helix chain 'A' and resid 238 through 259 removed outlier: 3.694A pdb=" N ILE A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 293 Processing helix chain 'A' and resid 306 through 319 Processing helix chain 'A' and resid 414 through 431 Processing helix chain 'A' and resid 436 through 464 Processing helix chain 'A' and resid 470 through 477 Processing helix chain 'B' and resid 2 through 10 Processing helix chain 'B' and resid 208 through 213 Processing helix chain 'B' and resid 215 through 230 Processing helix chain 'B' and resid 238 through 259 removed outlier: 3.694A pdb=" N ILE B 259 " --> pdb=" O LEU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 293 Processing helix chain 'B' and resid 306 through 319 Processing helix chain 'B' and resid 414 through 431 Processing helix chain 'B' and resid 436 through 464 Processing helix chain 'B' and resid 470 through 477 Processing helix chain 'C' and resid 2 through 10 Processing helix chain 'C' and resid 208 through 213 Processing helix chain 'C' and resid 215 through 230 Processing helix chain 'C' and resid 238 through 259 removed outlier: 3.694A pdb=" N ILE C 259 " --> pdb=" O LEU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 293 Processing helix chain 'C' and resid 306 through 319 Processing helix chain 'C' and resid 414 through 431 Processing helix chain 'C' and resid 436 through 464 Processing helix chain 'C' and resid 470 through 477 Processing helix chain 'D' and resid 2 through 10 Processing helix chain 'D' and resid 208 through 213 Processing helix chain 'D' and resid 215 through 230 Processing helix chain 'D' and resid 238 through 259 removed outlier: 3.694A pdb=" N ILE D 259 " --> pdb=" O LEU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 293 Processing helix chain 'D' and resid 306 through 319 Processing helix chain 'D' and resid 414 through 431 Processing helix chain 'D' and resid 436 through 464 Processing helix chain 'D' and resid 470 through 477 Processing helix chain 'E' and resid 2 through 10 Processing helix chain 'E' and resid 208 through 213 Processing helix chain 'E' and resid 215 through 230 Processing helix chain 'E' and resid 238 through 259 removed outlier: 3.693A pdb=" N ILE E 259 " --> pdb=" O LEU E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 293 Processing helix chain 'E' and resid 306 through 319 Processing helix chain 'E' and resid 414 through 431 Processing helix chain 'E' and resid 436 through 464 Processing helix chain 'E' and resid 470 through 477 Processing sheet with id= A, first strand: chain 'A' and resid 155 through 159 removed outlier: 6.338A pdb=" N LEU A 28 " --> pdb=" O ASP A 156 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLN A 158 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL A 30 " --> pdb=" O GLN A 158 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ASN A 52 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ILE A 39 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N THR A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 41 through 43 Processing sheet with id= C, first strand: chain 'A' and resid 57 through 60 Processing sheet with id= D, first strand: chain 'A' and resid 77 through 79 Processing sheet with id= E, first strand: chain 'A' and resid 89 through 91 removed outlier: 6.627A pdb=" N ARG A 204 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N LEU A 175 " --> pdb=" O ARG A 204 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 155 through 159 removed outlier: 6.338A pdb=" N LEU B 28 " --> pdb=" O ASP B 156 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLN B 158 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL B 30 " --> pdb=" O GLN B 158 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ASN B 52 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ILE B 39 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N THR B 50 " --> pdb=" O ILE B 39 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 41 through 43 Processing sheet with id= H, first strand: chain 'B' and resid 57 through 60 Processing sheet with id= I, first strand: chain 'B' and resid 77 through 79 Processing sheet with id= J, first strand: chain 'B' and resid 89 through 91 removed outlier: 6.627A pdb=" N ARG B 204 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N LEU B 175 " --> pdb=" O ARG B 204 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 155 through 159 removed outlier: 6.337A pdb=" N LEU C 28 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLN C 158 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL C 30 " --> pdb=" O GLN C 158 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ASN C 52 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ILE C 39 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N THR C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 41 through 43 Processing sheet with id= M, first strand: chain 'C' and resid 57 through 60 Processing sheet with id= N, first strand: chain 'C' and resid 77 through 79 Processing sheet with id= O, first strand: chain 'C' and resid 89 through 91 removed outlier: 6.627A pdb=" N ARG C 204 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N LEU C 175 " --> pdb=" O ARG C 204 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 155 through 159 removed outlier: 6.339A pdb=" N LEU D 28 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLN D 158 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL D 30 " --> pdb=" O GLN D 158 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ASN D 52 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ILE D 39 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N THR D 50 " --> pdb=" O ILE D 39 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 41 through 43 Processing sheet with id= R, first strand: chain 'D' and resid 57 through 60 Processing sheet with id= S, first strand: chain 'D' and resid 77 through 79 Processing sheet with id= T, first strand: chain 'D' and resid 89 through 91 removed outlier: 6.628A pdb=" N ARG D 204 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N LEU D 175 " --> pdb=" O ARG D 204 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 155 through 159 removed outlier: 6.338A pdb=" N LEU E 28 " --> pdb=" O ASP E 156 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLN E 158 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL E 30 " --> pdb=" O GLN E 158 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN E 52 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ILE E 39 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N THR E 50 " --> pdb=" O ILE E 39 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 41 through 43 Processing sheet with id= W, first strand: chain 'E' and resid 57 through 60 Processing sheet with id= X, first strand: chain 'E' and resid 77 through 79 Processing sheet with id= Y, first strand: chain 'E' and resid 89 through 91 removed outlier: 6.627A pdb=" N ARG E 204 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N LEU E 175 " --> pdb=" O ARG E 204 " (cutoff:3.500A) 760 hydrogen bonds defined for protein. 2190 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.21 Time building geometry restraints manager: 24.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 15370 1.03 - 1.24: 1921 1.24 - 1.44: 5304 1.44 - 1.65: 9025 1.65 - 1.85: 165 Bond restraints: 31785 Sorted by residual: bond pdb=" C3 EPJ B 503 " pdb=" N1 EPJ B 503 " ideal model delta sigma weight residual 1.718 1.472 0.246 2.00e-02 2.50e+03 1.51e+02 bond pdb=" C3 EPJ C 503 " pdb=" N1 EPJ C 503 " ideal model delta sigma weight residual 1.718 1.473 0.245 2.00e-02 2.50e+03 1.50e+02 bond pdb=" C3 EPJ D 503 " pdb=" N1 EPJ D 503 " ideal model delta sigma weight residual 1.718 1.473 0.245 2.00e-02 2.50e+03 1.50e+02 bond pdb=" C3 EPJ A 503 " pdb=" N1 EPJ A 503 " ideal model delta sigma weight residual 1.718 1.473 0.245 2.00e-02 2.50e+03 1.50e+02 bond pdb=" C3 EPJ E 503 " pdb=" N1 EPJ E 503 " ideal model delta sigma weight residual 1.718 1.473 0.245 2.00e-02 2.50e+03 1.50e+02 ... (remaining 31780 not shown) Histogram of bond angle deviations from ideal: 76.01 - 87.61: 135 87.61 - 99.22: 40 99.22 - 110.82: 32857 110.82 - 122.42: 19513 122.42 - 134.03: 4765 Bond angle restraints: 57310 Sorted by residual: angle pdb=" CG LEU A 254 " pdb=" CD1 LEU A 254 " pdb="HD12 LEU A 254 " ideal model delta sigma weight residual 109.00 76.01 32.99 3.00e+00 1.11e-01 1.21e+02 angle pdb=" CG LEU D 254 " pdb=" CD1 LEU D 254 " pdb="HD12 LEU D 254 " ideal model delta sigma weight residual 109.00 76.03 32.97 3.00e+00 1.11e-01 1.21e+02 angle pdb=" CG LEU C 254 " pdb=" CD1 LEU C 254 " pdb="HD12 LEU C 254 " ideal model delta sigma weight residual 109.00 76.03 32.97 3.00e+00 1.11e-01 1.21e+02 angle pdb=" CG LEU E 254 " pdb=" CD1 LEU E 254 " pdb="HD12 LEU E 254 " ideal model delta sigma weight residual 109.00 76.03 32.97 3.00e+00 1.11e-01 1.21e+02 angle pdb=" CG LEU B 254 " pdb=" CD1 LEU B 254 " pdb="HD12 LEU B 254 " ideal model delta sigma weight residual 109.00 76.05 32.95 3.00e+00 1.11e-01 1.21e+02 ... (remaining 57305 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.66: 13610 15.66 - 31.31: 1255 31.31 - 46.97: 300 46.97 - 62.63: 160 62.63 - 78.29: 25 Dihedral angle restraints: 15350 sinusoidal: 8335 harmonic: 7015 Sorted by residual: dihedral pdb=" CB CYS C 127 " pdb=" SG CYS C 127 " pdb=" SG CYS C 141 " pdb=" CB CYS C 141 " ideal model delta sinusoidal sigma weight residual 93.00 33.07 59.93 1 1.00e+01 1.00e-02 4.79e+01 dihedral pdb=" CB CYS E 127 " pdb=" SG CYS E 127 " pdb=" SG CYS E 141 " pdb=" CB CYS E 141 " ideal model delta sinusoidal sigma weight residual 93.00 33.07 59.93 1 1.00e+01 1.00e-02 4.79e+01 dihedral pdb=" CB CYS D 127 " pdb=" SG CYS D 127 " pdb=" SG CYS D 141 " pdb=" CB CYS D 141 " ideal model delta sinusoidal sigma weight residual 93.00 33.08 59.92 1 1.00e+01 1.00e-02 4.79e+01 ... (remaining 15347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.568: 2535 0.568 - 1.135: 0 1.135 - 1.703: 15 1.703 - 2.270: 15 2.270 - 2.838: 5 Chirality restraints: 2570 Sorted by residual: chirality pdb=" CG LEU E 249 " pdb=" CB LEU E 249 " pdb=" CD1 LEU E 249 " pdb=" CD2 LEU E 249 " both_signs ideal model delta sigma weight residual False -2.59 0.25 -2.84 2.00e-01 2.50e+01 2.01e+02 chirality pdb=" CG LEU B 249 " pdb=" CB LEU B 249 " pdb=" CD1 LEU B 249 " pdb=" CD2 LEU B 249 " both_signs ideal model delta sigma weight residual False -2.59 0.25 -2.84 2.00e-01 2.50e+01 2.01e+02 chirality pdb=" CG LEU A 249 " pdb=" CB LEU A 249 " pdb=" CD1 LEU A 249 " pdb=" CD2 LEU A 249 " both_signs ideal model delta sigma weight residual False -2.59 0.24 -2.83 2.00e-01 2.50e+01 2.01e+02 ... (remaining 2567 not shown) Planarity restraints: 4575 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 213 " -0.013 2.00e-02 2.50e+03 4.14e-02 2.57e+01 pdb=" CG ASN B 213 " -0.052 2.00e-02 2.50e+03 pdb=" OD1 ASN B 213 " 0.042 2.00e-02 2.50e+03 pdb=" ND2 ASN B 213 " 0.048 2.00e-02 2.50e+03 pdb="HD21 ASN B 213 " 0.027 2.00e-02 2.50e+03 pdb="HD22 ASN B 213 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 213 " -0.014 2.00e-02 2.50e+03 4.12e-02 2.55e+01 pdb=" CG ASN C 213 " -0.052 2.00e-02 2.50e+03 pdb=" OD1 ASN C 213 " 0.042 2.00e-02 2.50e+03 pdb=" ND2 ASN C 213 " 0.047 2.00e-02 2.50e+03 pdb="HD21 ASN C 213 " 0.027 2.00e-02 2.50e+03 pdb="HD22 ASN C 213 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 213 " 0.013 2.00e-02 2.50e+03 4.12e-02 2.55e+01 pdb=" CG ASN E 213 " 0.052 2.00e-02 2.50e+03 pdb=" OD1 ASN E 213 " -0.042 2.00e-02 2.50e+03 pdb=" ND2 ASN E 213 " -0.047 2.00e-02 2.50e+03 pdb="HD21 ASN E 213 " -0.027 2.00e-02 2.50e+03 pdb="HD22 ASN E 213 " 0.051 2.00e-02 2.50e+03 ... (remaining 4572 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.09: 613 2.09 - 2.72: 51895 2.72 - 3.35: 87796 3.35 - 3.97: 113416 3.97 - 4.60: 177339 Nonbonded interactions: 431059 Sorted by model distance: nonbonded pdb=" HG SER C 183 " pdb=" OD1 ASP C 196 " model vdw 1.468 1.850 nonbonded pdb=" HG SER B 183 " pdb=" OD1 ASP B 196 " model vdw 1.469 1.850 nonbonded pdb=" HG SER E 183 " pdb=" OD1 ASP E 196 " model vdw 1.469 1.850 nonbonded pdb=" HG SER D 183 " pdb=" OD1 ASP D 196 " model vdw 1.469 1.850 nonbonded pdb=" HG SER A 183 " pdb=" OD1 ASP A 196 " model vdw 1.469 1.850 ... (remaining 431054 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 2.330 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: 0.480 Extract box with map and model: 10.930 Check model and map are aligned: 0.360 Set scattering table: 0.240 Process input model: 94.190 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.180 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:11.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 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 : 0.013 0.246 16375 Z= 0.876 Angle : 1.190 13.431 22325 Z= 0.671 Chirality : 0.228 2.838 2570 Planarity : 0.005 0.047 2745 Dihedral : 13.507 75.109 6190 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.57 % Allowed : 1.15 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.69 (0.18), residues: 1910 helix: 0.55 (0.17), residues: 815 sheet: -1.10 (0.25), residues: 390 loop : -1.13 (0.21), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 315 HIS 0.003 0.001 HIS D 295 PHE 0.041 0.002 PHE C 252 TYR 0.037 0.002 TYR C 210 ARG 0.007 0.001 ARG D 132 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 188 time to evaluate : 2.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 448 CYS cc_start: 0.6906 (m) cc_final: 0.6502 (m) REVERT: D 448 CYS cc_start: 0.6832 (m) cc_final: 0.6450 (m) REVERT: E 97 GLU cc_start: 0.7822 (pp20) cc_final: 0.7602 (pp20) outliers start: 10 outliers final: 9 residues processed: 194 average time/residue: 1.5219 time to fit residues: 353.3295 Evaluate side-chains 149 residues out of total 1745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 140 time to evaluate : 2.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 287 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 0.5980 chunk 144 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 90 optimal weight: 0.5980 chunk 110 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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: 0.7908 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16375 Z= 0.239 Angle : 0.773 11.919 22325 Z= 0.354 Chirality : 0.185 1.779 2570 Planarity : 0.004 0.044 2745 Dihedral : 7.009 78.212 2554 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.18 % Allowed : 5.62 % Favored : 92.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.19), residues: 1910 helix: 1.19 (0.18), residues: 810 sheet: -0.92 (0.25), residues: 390 loop : -1.09 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 59 HIS 0.004 0.001 HIS C 295 PHE 0.028 0.002 PHE C 252 TYR 0.008 0.001 TYR C 209 ARG 0.004 0.000 ARG C 132 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 147 time to evaluate : 2.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 ILE cc_start: 0.6956 (mm) cc_final: 0.6702 (mm) REVERT: C 213 ASN cc_start: 0.8206 (t0) cc_final: 0.7941 (t0) REVERT: C 448 CYS cc_start: 0.6710 (m) cc_final: 0.6474 (m) REVERT: E 97 GLU cc_start: 0.7773 (pp20) cc_final: 0.7544 (pp20) REVERT: E 213 ASN cc_start: 0.8297 (t0) cc_final: 0.7966 (t0) REVERT: E 448 CYS cc_start: 0.7111 (m) cc_final: 0.6821 (m) outliers start: 38 outliers final: 12 residues processed: 165 average time/residue: 1.3895 time to fit residues: 281.2345 Evaluate side-chains 148 residues out of total 1745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 136 time to evaluate : 2.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 287 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 95 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 143 optimal weight: 7.9990 chunk 117 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 186 optimal weight: 8.9990 chunk 153 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 138 optimal weight: 7.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 16375 Z= 0.395 Angle : 0.784 11.868 22325 Z= 0.362 Chirality : 0.185 1.751 2570 Planarity : 0.004 0.046 2745 Dihedral : 7.146 89.014 2554 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.83 % Allowed : 6.53 % Favored : 91.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.00 (0.18), residues: 1910 helix: 1.45 (0.18), residues: 810 sheet: -1.04 (0.24), residues: 415 loop : -0.99 (0.21), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 148 HIS 0.006 0.001 HIS E 295 PHE 0.021 0.002 PHE E 252 TYR 0.008 0.001 TYR C 209 ARG 0.004 0.000 ARG E 205 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 129 time to evaluate : 2.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 213 ASN cc_start: 0.8411 (t0) cc_final: 0.8058 (t0) REVERT: E 213 ASN cc_start: 0.8338 (t0) cc_final: 0.8115 (t0) outliers start: 32 outliers final: 19 residues processed: 153 average time/residue: 1.3827 time to fit residues: 258.0760 Evaluate side-chains 140 residues out of total 1745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 121 time to evaluate : 2.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 448 CYS Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 287 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 173 optimal weight: 0.1980 chunk 183 optimal weight: 10.0000 chunk 90 optimal weight: 0.5980 chunk 164 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.7942 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16375 Z= 0.192 Angle : 0.735 11.727 22325 Z= 0.332 Chirality : 0.184 1.737 2570 Planarity : 0.003 0.045 2745 Dihedral : 6.960 89.453 2554 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.66 % Allowed : 8.31 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.31 (0.19), residues: 1910 helix: 1.79 (0.18), residues: 810 sheet: -0.97 (0.24), residues: 410 loop : -0.89 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 59 HIS 0.006 0.001 HIS E 295 PHE 0.014 0.001 PHE A 252 TYR 0.007 0.001 TYR D 14 ARG 0.001 0.000 ARG A 446 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 126 time to evaluate : 2.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 212 LEU cc_start: 0.8699 (tt) cc_final: 0.8345 (tm) REVERT: C 278 MET cc_start: 0.7823 (ttm) cc_final: 0.7574 (ttm) REVERT: D 229 PHE cc_start: 0.7556 (m-10) cc_final: 0.7257 (m-80) REVERT: E 213 ASN cc_start: 0.8322 (t0) cc_final: 0.8105 (t0) outliers start: 29 outliers final: 21 residues processed: 148 average time/residue: 1.5484 time to fit residues: 275.1635 Evaluate side-chains 140 residues out of total 1745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 119 time to evaluate : 2.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 448 CYS Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 290 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 136 optimal weight: 4.9990 chunk 75 optimal weight: 9.9990 chunk 156 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 164 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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: 0.7961 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16375 Z= 0.267 Angle : 0.745 11.724 22325 Z= 0.339 Chirality : 0.183 1.725 2570 Planarity : 0.003 0.043 2745 Dihedral : 6.917 89.633 2554 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.43 % Allowed : 9.17 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.44 (0.19), residues: 1910 helix: 1.90 (0.18), residues: 810 sheet: -0.86 (0.25), residues: 405 loop : -0.86 (0.22), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 437 HIS 0.005 0.001 HIS E 295 PHE 0.011 0.001 PHE D 252 TYR 0.006 0.001 TYR D 14 ARG 0.002 0.000 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 127 time to evaluate : 2.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 LEU cc_start: 0.8732 (tt) cc_final: 0.8413 (tm) REVERT: A 229 PHE cc_start: 0.7285 (m-10) cc_final: 0.7061 (m-80) REVERT: B 212 LEU cc_start: 0.8741 (tt) cc_final: 0.8417 (tm) REVERT: C 212 LEU cc_start: 0.8747 (tt) cc_final: 0.8461 (tm) REVERT: D 212 LEU cc_start: 0.8629 (tt) cc_final: 0.8296 (tm) REVERT: D 229 PHE cc_start: 0.7668 (m-10) cc_final: 0.7437 (m-80) outliers start: 25 outliers final: 23 residues processed: 145 average time/residue: 1.5284 time to fit residues: 266.5267 Evaluate side-chains 142 residues out of total 1745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 119 time to evaluate : 2.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 416 GLU Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 416 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 61 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 183 optimal weight: 10.0000 chunk 152 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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: 0.7997 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 16375 Z= 0.413 Angle : 0.770 11.780 22325 Z= 0.354 Chirality : 0.184 1.724 2570 Planarity : 0.004 0.046 2745 Dihedral : 7.017 88.853 2553 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.18 % Allowed : 9.05 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.54 (0.19), residues: 1910 helix: 2.21 (0.18), residues: 775 sheet: -0.83 (0.24), residues: 425 loop : -0.94 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 59 HIS 0.006 0.001 HIS E 295 PHE 0.016 0.002 PHE A 99 TYR 0.007 0.001 TYR D 187 ARG 0.005 0.000 ARG E 205 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 130 time to evaluate : 2.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 LEU cc_start: 0.8875 (tt) cc_final: 0.8592 (tm) REVERT: B 212 LEU cc_start: 0.8796 (tt) cc_final: 0.8516 (tm) REVERT: C 212 LEU cc_start: 0.8825 (tt) cc_final: 0.8550 (tm) REVERT: D 212 LEU cc_start: 0.8749 (tt) cc_final: 0.8467 (tm) outliers start: 38 outliers final: 31 residues processed: 153 average time/residue: 1.4265 time to fit residues: 261.4529 Evaluate side-chains 150 residues out of total 1745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 119 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 448 CYS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 465 MET Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 416 GLU Chi-restraints excluded: chain E residue 465 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 177 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 154 optimal weight: 0.0670 chunk 102 optimal weight: 2.9990 chunk 183 optimal weight: 9.9990 chunk 114 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 84 optimal weight: 0.7980 chunk 113 optimal weight: 10.0000 overall best weight: 1.7724 ------------------------------------------------------------------------------- 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: 0.7990 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 16375 Z= 0.344 Angle : 0.762 11.763 22325 Z= 0.349 Chirality : 0.183 1.725 2570 Planarity : 0.003 0.043 2745 Dihedral : 6.913 87.504 2553 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.55 % Allowed : 10.66 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.58 (0.19), residues: 1910 helix: 2.22 (0.18), residues: 775 sheet: -0.83 (0.24), residues: 425 loop : -0.86 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 59 HIS 0.006 0.001 HIS B 295 PHE 0.018 0.001 PHE D 229 TYR 0.008 0.001 TYR A 14 ARG 0.003 0.000 ARG E 205 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 120 time to evaluate : 2.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 LEU cc_start: 0.8878 (tt) cc_final: 0.8603 (tm) REVERT: A 252 PHE cc_start: 0.7975 (OUTLIER) cc_final: 0.7693 (t80) REVERT: B 212 LEU cc_start: 0.8795 (tt) cc_final: 0.8549 (tm) REVERT: C 212 LEU cc_start: 0.8717 (tt) cc_final: 0.8488 (tm) REVERT: D 212 LEU cc_start: 0.8784 (tt) cc_final: 0.8519 (tm) REVERT: D 252 PHE cc_start: 0.8015 (OUTLIER) cc_final: 0.6773 (t80) outliers start: 27 outliers final: 23 residues processed: 139 average time/residue: 1.5602 time to fit residues: 258.2995 Evaluate side-chains 141 residues out of total 1745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 116 time to evaluate : 2.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 416 GLU Chi-restraints excluded: chain E residue 465 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 73 optimal weight: 10.0000 chunk 109 optimal weight: 9.9990 chunk 55 optimal weight: 0.0980 chunk 35 optimal weight: 7.9990 chunk 116 optimal weight: 0.9980 chunk 124 optimal weight: 0.1980 chunk 90 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 143 optimal weight: 10.0000 chunk 166 optimal weight: 1.9990 chunk 175 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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: 0.7966 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16375 Z= 0.222 Angle : 0.737 11.696 22325 Z= 0.334 Chirality : 0.183 1.723 2570 Planarity : 0.003 0.042 2745 Dihedral : 6.633 85.367 2551 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.49 % Allowed : 11.23 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.19), residues: 1910 helix: 2.32 (0.18), residues: 775 sheet: -0.81 (0.24), residues: 425 loop : -0.78 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 59 HIS 0.005 0.001 HIS B 295 PHE 0.023 0.001 PHE D 229 TYR 0.009 0.001 TYR D 14 ARG 0.002 0.000 ARG E 418 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 117 time to evaluate : 2.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 LEU cc_start: 0.8901 (tt) cc_final: 0.8653 (tm) REVERT: A 252 PHE cc_start: 0.7995 (OUTLIER) cc_final: 0.7644 (t80) REVERT: B 212 LEU cc_start: 0.8790 (tt) cc_final: 0.8564 (tm) REVERT: D 212 LEU cc_start: 0.8800 (tt) cc_final: 0.8513 (tm) REVERT: D 252 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.6688 (t80) REVERT: E 212 LEU cc_start: 0.8821 (tt) cc_final: 0.8548 (tm) outliers start: 26 outliers final: 19 residues processed: 135 average time/residue: 1.6485 time to fit residues: 264.6340 Evaluate side-chains 133 residues out of total 1745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 112 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 416 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 0.2980 chunk 170 optimal weight: 0.1980 chunk 175 optimal weight: 5.9990 chunk 102 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 154 optimal weight: 0.7980 chunk 161 optimal weight: 0.8980 chunk 112 optimal weight: 9.9990 chunk 180 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.7953 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16375 Z= 0.201 Angle : 0.728 11.685 22325 Z= 0.328 Chirality : 0.182 1.717 2570 Planarity : 0.003 0.042 2745 Dihedral : 6.436 83.681 2551 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.38 % Allowed : 11.23 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.86 (0.19), residues: 1910 helix: 2.45 (0.18), residues: 775 sheet: -0.66 (0.25), residues: 415 loop : -0.73 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 59 HIS 0.004 0.001 HIS B 295 PHE 0.014 0.001 PHE D 229 TYR 0.008 0.001 TYR D 14 ARG 0.004 0.000 ARG C 418 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 120 time to evaluate : 2.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 LEU cc_start: 0.8881 (tt) cc_final: 0.8659 (tm) REVERT: A 252 PHE cc_start: 0.7978 (OUTLIER) cc_final: 0.7554 (t80) REVERT: B 212 LEU cc_start: 0.8777 (tt) cc_final: 0.8569 (tm) REVERT: C 252 PHE cc_start: 0.7935 (OUTLIER) cc_final: 0.6670 (t80) REVERT: D 212 LEU cc_start: 0.8806 (tt) cc_final: 0.8576 (tm) REVERT: D 252 PHE cc_start: 0.7945 (OUTLIER) cc_final: 0.6762 (t80) REVERT: E 212 LEU cc_start: 0.8841 (tt) cc_final: 0.8588 (tm) outliers start: 24 outliers final: 16 residues processed: 135 average time/residue: 1.5920 time to fit residues: 256.4484 Evaluate side-chains 135 residues out of total 1745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 116 time to evaluate : 2.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 252 PHE Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 290 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 110 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 189 optimal weight: 5.9990 chunk 174 optimal weight: 7.9990 chunk 150 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 160 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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: 0.7966 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16375 Z= 0.257 Angle : 0.742 11.687 22325 Z= 0.335 Chirality : 0.183 1.714 2570 Planarity : 0.003 0.042 2745 Dihedral : 6.413 84.566 2550 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.20 % Allowed : 11.52 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.19), residues: 1910 helix: 2.49 (0.18), residues: 775 sheet: -0.60 (0.25), residues: 415 loop : -0.73 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 59 HIS 0.004 0.001 HIS B 295 PHE 0.020 0.001 PHE D 229 TYR 0.006 0.001 TYR A 14 ARG 0.003 0.000 ARG B 418 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 114 time to evaluate : 2.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 LEU cc_start: 0.8877 (tt) cc_final: 0.8676 (tm) REVERT: A 252 PHE cc_start: 0.7982 (OUTLIER) cc_final: 0.7553 (t80) REVERT: C 252 PHE cc_start: 0.7940 (OUTLIER) cc_final: 0.6776 (t80) REVERT: D 212 LEU cc_start: 0.8821 (tt) cc_final: 0.8562 (tm) REVERT: E 212 LEU cc_start: 0.8851 (tt) cc_final: 0.8619 (tm) outliers start: 21 outliers final: 14 residues processed: 125 average time/residue: 1.6345 time to fit residues: 244.1530 Evaluate side-chains 129 residues out of total 1745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 113 time to evaluate : 2.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 287 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 46 optimal weight: 0.4980 chunk 138 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 150 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 8 optimal weight: 0.4980 overall best weight: 0.7184 ------------------------------------------------------------------------------- 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 = 0.3886 r_free = 0.3886 target = 0.141415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.084085 restraints weight = 63486.587| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.41 r_work: 0.2842 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16375 Z= 0.207 Angle : 0.732 11.654 22325 Z= 0.328 Chirality : 0.183 1.727 2570 Planarity : 0.003 0.042 2745 Dihedral : 6.297 83.453 2550 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.92 % Allowed : 11.86 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.97 (0.19), residues: 1910 helix: 2.48 (0.18), residues: 780 sheet: -0.59 (0.25), residues: 415 loop : -0.63 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 133 HIS 0.003 0.001 HIS A 295 PHE 0.017 0.001 PHE D 229 TYR 0.007 0.001 TYR D 14 ARG 0.002 0.000 ARG C 418 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7550.83 seconds wall clock time: 133 minutes 38.21 seconds (8018.21 seconds total)