Starting phenix.real_space_refine on Fri Feb 16 10:02:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgs_31978/02_2024/7vgs_31978.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgs_31978/02_2024/7vgs_31978.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgs_31978/02_2024/7vgs_31978.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgs_31978/02_2024/7vgs_31978.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgs_31978/02_2024/7vgs_31978.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgs_31978/02_2024/7vgs_31978.pdb" } resolution = 2.8 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= 0.003 sd= 0.100 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5342 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 6208 2.51 5 N 1606 2.21 5 O 1834 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 84": "OE1" <-> "OE2" Residue "E GLU 84": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9700 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1587 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "C" Number of atoms: 1683 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 218, 1657 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 205} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 Conformer: "B" Number of residues, atoms: 218, 1657 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 205} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 bond proxies already assigned to first conformer: 1662 Chain: "D" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1580 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 198} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1587 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "E" Number of atoms: 1683 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 218, 1657 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 205} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 Conformer: "B" Number of residues, atoms: 218, 1657 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 205} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 bond proxies already assigned to first conformer: 1662 Chain: "F" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1580 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 198} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 6.87, per 1000 atoms: 0.71 Number of scatterers: 9700 At special positions: 0 Unit cell: (73.455, 133.215, 141.93, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1834 8.00 N 1606 7.00 C 6208 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG ACYS C 138 " - pdb=" SG ACYS C 198 " distance=2.03 Simple disulfide: pdb=" SG BCYS C 138 " - pdb=" SG BCYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 195 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG ACYS E 138 " - pdb=" SG ACYS E 198 " distance=2.03 Simple disulfide: pdb=" SG BCYS E 138 " - pdb=" SG BCYS E 198 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 140 " - pdb=" SG CYS F 195 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.34 Conformation dependent library (CDL) restraints added in 2.7 seconds 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2360 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 20 sheets defined 16.7% alpha, 32.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 9 through 37 removed outlier: 3.631A pdb=" N LEU A 13 " --> pdb=" O THR A 9 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N PHE A 37 " --> pdb=" O CYS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 68 removed outlier: 3.640A pdb=" N ILE A 49 " --> pdb=" O PHE A 45 " (cutoff:3.500A) Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 78 through 106 removed outlier: 3.991A pdb=" N ILE A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 87 " --> pdb=" O ALA A 83 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A 88 " --> pdb=" O MET A 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 34 removed outlier: 3.525A pdb=" N ASP C 34 " --> pdb=" O TYR C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 132 removed outlier: 3.682A pdb=" N GLY C 132 " --> pdb=" O GLN C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 191 removed outlier: 4.099A pdb=" N GLU C 191 " --> pdb=" O LYS C 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 187 through 191' Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.540A pdb=" N SER D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 37 removed outlier: 4.426A pdb=" N PHE B 37 " --> pdb=" O CYS B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 68 removed outlier: 3.640A pdb=" N ILE B 49 " --> pdb=" O PHE B 45 " (cutoff:3.500A) Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 78 through 106 removed outlier: 3.992A pdb=" N ILE B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL B 88 " --> pdb=" O MET B 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 34 removed outlier: 3.525A pdb=" N ASP E 34 " --> pdb=" O TYR E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 132 removed outlier: 3.682A pdb=" N GLY E 132 " --> pdb=" O GLN E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 191 removed outlier: 4.099A pdb=" N GLU E 191 " --> pdb=" O LYS E 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 187 through 191' Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.539A pdb=" N SER F 91 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 129 through 132 removed outlier: 3.902A pdb=" N ARG A 200 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LYS A 180 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ARG A 198 " --> pdb=" O LYS A 180 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU A 149 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 11 through 13 removed outlier: 6.405A pdb=" N LEU C 11 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TRP C 39 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 19 through 21 Processing sheet with id=AA4, first strand: chain 'C' and resid 118 through 122 removed outlier: 5.101A pdb=" N SER C 135 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEU C 185 " --> pdb=" O SER C 135 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N VAL C 137 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N LEU C 183 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N PHE C 139 " --> pdb=" O SER C 181 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N SER C 181 " --> pdb=" O PHE C 139 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ASN C 141 " --> pdb=" O MET C 179 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N MET C 179 " --> pdb=" O ASN C 141 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 157 through 159 removed outlier: 4.205A pdb=" N TRP C 152 " --> pdb=" O ARG C 159 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASN C 149 " --> pdb=" O THR C 201 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.815A pdb=" N ALA D 79 " --> pdb=" O CYS D 22 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.815A pdb=" N ALA D 79 " --> pdb=" O CYS D 22 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR D 78 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP D 73 " --> pdb=" O THR D 78 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.719A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER D 40 " --> pdb=" O ASN D 44 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN D 44 " --> pdb=" O SER D 40 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 120 through 124 removed outlier: 6.309A pdb=" N TYR D 175 " --> pdb=" O GLY D 144 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU D 174 " --> pdb=" O LEU D 170 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LEU D 170 " --> pdb=" O LEU D 174 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N THR D 176 " --> pdb=" O ALA D 168 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA D 168 " --> pdb=" O THR D 176 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER D 178 " --> pdb=" O PHE D 166 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 151 through 154 Processing sheet with id=AB2, first strand: chain 'B' and resid 129 through 132 removed outlier: 3.903A pdb=" N ARG B 200 " --> pdb=" O TYR B 178 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LYS B 180 " --> pdb=" O ARG B 198 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ARG B 198 " --> pdb=" O LYS B 180 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU B 149 " --> pdb=" O LEU B 156 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 11 through 13 removed outlier: 6.406A pdb=" N LEU E 11 " --> pdb=" O GLU E 109 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TRP E 39 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 19 through 21 Processing sheet with id=AB5, first strand: chain 'E' and resid 118 through 122 removed outlier: 5.100A pdb=" N SER E 135 " --> pdb=" O LEU E 185 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU E 185 " --> pdb=" O SER E 135 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N VAL E 137 " --> pdb=" O LEU E 183 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LEU E 183 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N PHE E 139 " --> pdb=" O SER E 181 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N SER E 181 " --> pdb=" O PHE E 139 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ASN E 141 " --> pdb=" O MET E 179 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N MET E 179 " --> pdb=" O ASN E 141 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 157 through 159 removed outlier: 4.204A pdb=" N TRP E 152 " --> pdb=" O ARG E 159 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASN E 149 " --> pdb=" O THR E 201 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 3 through 6 removed outlier: 3.815A pdb=" N ALA F 79 " --> pdb=" O CYS F 22 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 3 through 6 removed outlier: 3.815A pdb=" N ALA F 79 " --> pdb=" O CYS F 22 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR F 78 " --> pdb=" O ASP F 73 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP F 73 " --> pdb=" O THR F 78 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.720A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER F 40 " --> pdb=" O ASN F 44 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN F 44 " --> pdb=" O SER F 40 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 120 through 124 removed outlier: 6.308A pdb=" N TYR F 175 " --> pdb=" O GLY F 144 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU F 174 " --> pdb=" O LEU F 170 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LEU F 170 " --> pdb=" O LEU F 174 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N THR F 176 " --> pdb=" O ALA F 168 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA F 168 " --> pdb=" O THR F 176 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER F 178 " --> pdb=" O PHE F 166 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 151 through 154 394 hydrogen bonds defined for protein. 1018 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: 2.86 Time building geometry restraints manager: 4.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3042 1.35 - 1.46: 2479 1.46 - 1.58: 4357 1.58 - 1.70: 0 1.70 - 1.82: 74 Bond restraints: 9952 Sorted by residual: bond pdb=" CA LYS A 162 " pdb=" CB LYS A 162 " ideal model delta sigma weight residual 1.522 1.553 -0.031 1.32e-02 5.74e+03 5.38e+00 bond pdb=" CA LYS B 162 " pdb=" CB LYS B 162 " ideal model delta sigma weight residual 1.522 1.553 -0.030 1.32e-02 5.74e+03 5.25e+00 bond pdb=" CB GLU A 18 " pdb=" CG GLU A 18 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.94e+00 bond pdb=" CB GLU B 18 " pdb=" CG GLU B 18 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.89e+00 bond pdb=" C ASP E 98 " pdb=" N PRO E 99 " ideal model delta sigma weight residual 1.333 1.347 -0.014 1.20e-02 6.94e+03 1.39e+00 ... (remaining 9947 not shown) Histogram of bond angle deviations from ideal: 100.09 - 106.87: 327 106.87 - 113.66: 5523 113.66 - 120.44: 3558 120.44 - 127.22: 4055 127.22 - 134.01: 129 Bond angle restraints: 13592 Sorted by residual: angle pdb=" CA LEU A 90 " pdb=" CB LEU A 90 " pdb=" CG LEU A 90 " ideal model delta sigma weight residual 116.30 125.26 -8.96 3.50e+00 8.16e-02 6.55e+00 angle pdb=" CA LEU B 90 " pdb=" CB LEU B 90 " pdb=" CG LEU B 90 " ideal model delta sigma weight residual 116.30 125.23 -8.93 3.50e+00 8.16e-02 6.51e+00 angle pdb=" N PHE B 45 " pdb=" CA PHE B 45 " pdb=" C PHE B 45 " ideal model delta sigma weight residual 113.61 109.94 3.67 1.50e+00 4.44e-01 6.00e+00 angle pdb=" N PHE A 45 " pdb=" CA PHE A 45 " pdb=" C PHE A 45 " ideal model delta sigma weight residual 113.61 109.96 3.65 1.50e+00 4.44e-01 5.92e+00 angle pdb=" N SER C 7 " pdb=" CA SER C 7 " pdb=" C SER C 7 " ideal model delta sigma weight residual 109.81 115.12 -5.31 2.21e+00 2.05e-01 5.78e+00 ... (remaining 13587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 5490 17.93 - 35.85: 368 35.85 - 53.78: 44 53.78 - 71.71: 10 71.71 - 89.63: 8 Dihedral angle restraints: 5920 sinusoidal: 2228 harmonic: 3692 Sorted by residual: dihedral pdb=" CA SER E 7 " pdb=" C SER E 7 " pdb=" N PRO E 8 " pdb=" CA PRO E 8 " ideal model delta harmonic sigma weight residual 180.00 151.11 28.89 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA SER C 7 " pdb=" C SER C 7 " pdb=" N PRO C 8 " pdb=" CA PRO C 8 " ideal model delta harmonic sigma weight residual 180.00 151.18 28.82 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CB CYS D 140 " pdb=" SG CYS D 140 " pdb=" SG CYS D 195 " pdb=" CB CYS D 195 " ideal model delta sinusoidal sigma weight residual 93.00 53.01 39.99 1 1.00e+01 1.00e-02 2.24e+01 ... (remaining 5917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1174 0.044 - 0.087: 274 0.087 - 0.131: 96 0.131 - 0.175: 12 0.175 - 0.218: 4 Chirality restraints: 1560 Sorted by residual: chirality pdb=" CA GLU A 18 " pdb=" N GLU A 18 " pdb=" C GLU A 18 " pdb=" CB GLU A 18 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA GLU B 18 " pdb=" N GLU B 18 " pdb=" C GLU B 18 " pdb=" CB GLU B 18 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB ILE C 2 " pdb=" CA ILE C 2 " pdb=" CG1 ILE C 2 " pdb=" CG2 ILE C 2 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 1557 not shown) Planarity restraints: 1708 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 164 " -0.037 5.00e-02 4.00e+02 5.56e-02 4.94e+00 pdb=" N PRO A 165 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 165 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 165 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 164 " 0.037 5.00e-02 4.00e+02 5.55e-02 4.93e+00 pdb=" N PRO B 165 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 165 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 165 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 7 " -0.036 5.00e-02 4.00e+02 5.48e-02 4.80e+00 pdb=" N PRO E 8 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO E 8 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 8 " -0.031 5.00e-02 4.00e+02 ... (remaining 1705 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1405 2.76 - 3.30: 9273 3.30 - 3.83: 15939 3.83 - 4.37: 18389 4.37 - 4.90: 31637 Nonbonded interactions: 76643 Sorted by model distance: nonbonded pdb=" OG1 THR A 116 " pdb=" O LEU A 133 " model vdw 2.230 2.440 nonbonded pdb=" OG1 THR B 116 " pdb=" O LEU B 133 " model vdw 2.231 2.440 nonbonded pdb=" O ASN C 35 " pdb=" OG1 THR C 55 " model vdw 2.241 2.440 nonbonded pdb=" O ASN E 35 " pdb=" OG1 THR E 55 " model vdw 2.241 2.440 nonbonded pdb=" OG SER D 190 " pdb=" OE1 GLU D 191 " model vdw 2.246 2.440 ... (remaining 76638 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' } ncs_group { reference = (chain 'C' and (resid 1 through 19 or resid 21 through 137 or resid 139 through \ 178 or resid 180 through 191 or resid 193 through 197 or resid 199 through 211 o \ r resid 213 through 218)) selection = (chain 'E' and (resid 1 through 19 or resid 21 through 137 or resid 139 through \ 178 or resid 180 through 191 or resid 193 through 197 or resid 199 through 211 o \ r resid 213 through 218)) } ncs_group { reference = chain 'D' selection = chain 'F' } 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=0.27 max=1.00 mean=0.99 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: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 3.420 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 30.910 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 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 : 0.002 0.042 9952 Z= 0.161 Angle : 0.660 8.959 13592 Z= 0.342 Chirality : 0.044 0.218 1560 Planarity : 0.005 0.056 1708 Dihedral : 12.190 89.633 3530 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 0.38 % Allowed : 0.56 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % 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: -1.16 (0.24), residues: 1254 helix: -0.43 (0.39), residues: 168 sheet: 0.18 (0.25), residues: 490 loop : -1.71 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 92 HIS 0.002 0.001 HIS D 41 PHE 0.008 0.001 PHE B 28 TYR 0.008 0.001 TYR C 53 ARG 0.001 0.000 ARG C 159 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 300 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.7121 (mmpt) cc_final: 0.6359 (pttt) REVERT: A 31 TRP cc_start: 0.7726 (t-100) cc_final: 0.7225 (t60) REVERT: A 127 THR cc_start: 0.7771 (p) cc_final: 0.7511 (t) REVERT: A 164 LEU cc_start: 0.7705 (pt) cc_final: 0.7239 (pp) REVERT: A 168 ILE cc_start: 0.8802 (mp) cc_final: 0.8574 (mp) REVERT: C 40 TYR cc_start: 0.8653 (m-80) cc_final: 0.8440 (m-80) REVERT: C 190 TYR cc_start: 0.7526 (t80) cc_final: 0.7289 (t80) REVERT: C 191 GLU cc_start: 0.8183 (mp0) cc_final: 0.7827 (mp0) REVERT: D 34 MET cc_start: 0.8571 (tpp) cc_final: 0.8357 (tpp) REVERT: B 127 THR cc_start: 0.7956 (p) cc_final: 0.7661 (t) REVERT: B 168 ILE cc_start: 0.8613 (mp) cc_final: 0.8398 (mp) REVERT: E 159 ARG cc_start: 0.7322 (tpt-90) cc_final: 0.7087 (ttp80) REVERT: E 191 GLU cc_start: 0.8096 (mp0) cc_final: 0.7597 (mp0) REVERT: F 57 ASP cc_start: 0.7768 (m-30) cc_final: 0.7545 (m-30) REVERT: F 82 GLU cc_start: 0.7096 (tm-30) cc_final: 0.6846 (tm-30) outliers start: 0 outliers final: 1 residues processed: 300 average time/residue: 0.9689 time to fit residues: 314.9716 Evaluate side-chains 188 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 187 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 37 optimal weight: 8.9990 chunk 58 optimal weight: 9.9990 chunk 71 optimal weight: 0.6980 chunk 110 optimal weight: 0.9980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN C 42 GLN ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 142 ASN D 39 GLN D 100 ASN E 41 GLN E 42 GLN E 128 GLN E 142 ASN ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 ASN F 39 GLN F 100 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 9952 Z= 0.339 Angle : 0.709 8.548 13592 Z= 0.362 Chirality : 0.047 0.197 1560 Planarity : 0.006 0.056 1708 Dihedral : 5.066 32.365 1380 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 4.99 % Allowed : 14.78 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.24), residues: 1254 helix: 0.28 (0.38), residues: 184 sheet: -0.03 (0.24), residues: 506 loop : -1.69 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 39 HIS 0.005 0.002 HIS B 148 PHE 0.023 0.002 PHE A 45 TYR 0.026 0.002 TYR E 53 ARG 0.012 0.001 ARG E 215 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 170 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 TRP cc_start: 0.7831 (t-100) cc_final: 0.7284 (t60) REVERT: A 87 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.7029 (pt) REVERT: A 127 THR cc_start: 0.8117 (p) cc_final: 0.7889 (t) REVERT: A 168 ILE cc_start: 0.8877 (mp) cc_final: 0.8609 (mp) REVERT: D 80 TYR cc_start: 0.6993 (m-80) cc_final: 0.6703 (m-80) REVERT: D 82 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7235 (tm-30) REVERT: D 97 GLU cc_start: 0.7545 (pp20) cc_final: 0.7267 (pp20) REVERT: B 127 THR cc_start: 0.8145 (p) cc_final: 0.7891 (t) REVERT: B 168 ILE cc_start: 0.8880 (mp) cc_final: 0.8631 (mp) REVERT: B 185 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.7305 (tm-30) REVERT: E 191 GLU cc_start: 0.7960 (mp0) cc_final: 0.7424 (mp0) REVERT: F 10 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7820 (tt0) REVERT: F 57 ASP cc_start: 0.8207 (m-30) cc_final: 0.7931 (m-30) REVERT: F 80 TYR cc_start: 0.6933 (m-80) cc_final: 0.6625 (m-80) REVERT: F 82 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7420 (tm-30) REVERT: F 97 GLU cc_start: 0.7547 (pp20) cc_final: 0.7207 (pp20) outliers start: 49 outliers final: 23 residues processed: 195 average time/residue: 1.0982 time to fit residues: 230.6848 Evaluate side-chains 181 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 155 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 195 CYS Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 135 SER Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 195 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 30 optimal weight: 0.3980 chunk 110 optimal weight: 0.9980 chunk 119 optimal weight: 0.0980 chunk 98 optimal weight: 9.9990 chunk 37 optimal weight: 20.0000 chunk 89 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 142 ASN ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN E 142 ASN ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9952 Z= 0.189 Angle : 0.641 7.647 13592 Z= 0.322 Chirality : 0.044 0.175 1560 Planarity : 0.005 0.056 1708 Dihedral : 4.951 33.835 1380 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 3.95 % Allowed : 17.80 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -0.94 (0.24), residues: 1254 helix: 0.39 (0.39), residues: 184 sheet: 0.09 (0.24), residues: 496 loop : -1.62 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 152 HIS 0.003 0.001 HIS A 125 PHE 0.017 0.001 PHE E 122 TYR 0.017 0.001 TYR E 190 ARG 0.008 0.001 ARG C 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 176 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 TRP cc_start: 0.7805 (t-100) cc_final: 0.7318 (t60) REVERT: A 87 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.7120 (pt) REVERT: A 127 THR cc_start: 0.8184 (p) cc_final: 0.7974 (t) REVERT: A 160 ASP cc_start: 0.7582 (t0) cc_final: 0.7306 (m-30) REVERT: A 167 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.7419 (pp20) REVERT: A 168 ILE cc_start: 0.8901 (mp) cc_final: 0.8330 (mp) REVERT: D 80 TYR cc_start: 0.6937 (m-80) cc_final: 0.6718 (m-80) REVERT: D 81 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.7618 (ttm) REVERT: D 82 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7232 (tm-30) REVERT: D 97 GLU cc_start: 0.7660 (pp20) cc_final: 0.7274 (pp20) REVERT: B 31 TRP cc_start: 0.7757 (t-100) cc_final: 0.7280 (t-100) REVERT: B 45 PHE cc_start: 0.7362 (m-80) cc_final: 0.7071 (m-80) REVERT: B 127 THR cc_start: 0.8125 (p) cc_final: 0.7922 (t) REVERT: B 168 ILE cc_start: 0.8812 (mp) cc_final: 0.8546 (mp) REVERT: E 158 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7257 (mm-30) REVERT: E 191 GLU cc_start: 0.8323 (mp0) cc_final: 0.8097 (mp0) REVERT: F 57 ASP cc_start: 0.8138 (m-30) cc_final: 0.7900 (m-30) REVERT: F 80 TYR cc_start: 0.6992 (m-80) cc_final: 0.6695 (m-80) REVERT: F 82 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7384 (tm-30) REVERT: F 97 GLU cc_start: 0.7685 (pp20) cc_final: 0.7318 (pp20) outliers start: 38 outliers final: 19 residues processed: 198 average time/residue: 1.0606 time to fit residues: 226.6149 Evaluate side-chains 183 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 160 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 195 CYS Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain E residue 135 SER Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 195 CYS Chi-restraints excluded: chain F residue 196 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 0.0060 chunk 57 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 52 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9952 Z= 0.219 Angle : 0.644 7.704 13592 Z= 0.326 Chirality : 0.044 0.187 1560 Planarity : 0.005 0.056 1708 Dihedral : 4.973 37.538 1380 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 5.08 % Allowed : 17.89 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -0.89 (0.24), residues: 1254 helix: 0.45 (0.39), residues: 184 sheet: 0.04 (0.24), residues: 506 loop : -1.52 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 58 HIS 0.003 0.001 HIS A 125 PHE 0.014 0.002 PHE B 193 TYR 0.017 0.001 TYR E 190 ARG 0.010 0.001 ARG E 215 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 171 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.6620 (mmmt) cc_final: 0.5612 (pttt) REVERT: A 31 TRP cc_start: 0.7784 (t-100) cc_final: 0.7258 (t60) REVERT: A 45 PHE cc_start: 0.7279 (m-80) cc_final: 0.7046 (m-80) REVERT: A 167 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.7352 (pp20) REVERT: A 168 ILE cc_start: 0.8963 (mp) cc_final: 0.8383 (mp) REVERT: D 80 TYR cc_start: 0.7070 (m-80) cc_final: 0.6811 (m-80) REVERT: D 81 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7877 (ttt) REVERT: D 82 GLU cc_start: 0.7575 (tm-30) cc_final: 0.7293 (tm-30) REVERT: D 97 GLU cc_start: 0.7695 (pp20) cc_final: 0.7391 (pp20) REVERT: D 208 LYS cc_start: 0.6993 (OUTLIER) cc_final: 0.6757 (ttmt) REVERT: B 31 TRP cc_start: 0.7798 (t-100) cc_final: 0.7328 (t-100) REVERT: B 45 PHE cc_start: 0.7296 (m-80) cc_final: 0.6921 (m-80) REVERT: B 127 THR cc_start: 0.8206 (p) cc_final: 0.7986 (t) REVERT: B 168 ILE cc_start: 0.8924 (mp) cc_final: 0.8678 (mp) REVERT: E 147 ASP cc_start: 0.8666 (OUTLIER) cc_final: 0.8057 (p0) REVERT: F 57 ASP cc_start: 0.8242 (m-30) cc_final: 0.8015 (m-30) REVERT: F 80 TYR cc_start: 0.7057 (m-80) cc_final: 0.6734 (m-80) REVERT: F 82 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7359 (tm-30) REVERT: F 97 GLU cc_start: 0.7661 (pp20) cc_final: 0.7218 (pp20) outliers start: 50 outliers final: 29 residues processed: 200 average time/residue: 1.0557 time to fit residues: 228.3205 Evaluate side-chains 188 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 155 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 195 CYS Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 208 LYS Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 135 SER Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 195 CYS Chi-restraints excluded: chain F residue 196 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 0.0670 chunk 100 optimal weight: 10.0000 chunk 81 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 overall best weight: 1.6324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN B 43 ASN ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 9952 Z= 0.312 Angle : 0.683 8.688 13592 Z= 0.347 Chirality : 0.045 0.204 1560 Planarity : 0.005 0.057 1708 Dihedral : 5.224 39.473 1380 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 5.56 % Allowed : 19.11 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -1.05 (0.25), residues: 1254 helix: 0.04 (0.37), residues: 198 sheet: -0.06 (0.24), residues: 518 loop : -1.58 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 152 HIS 0.004 0.001 HIS A 148 PHE 0.020 0.002 PHE B 193 TYR 0.021 0.002 TYR C 53 ARG 0.009 0.001 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 159 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.7356 (mmmt) cc_final: 0.6696 (pttt) REVERT: A 31 TRP cc_start: 0.7788 (t-100) cc_final: 0.7232 (t60) REVERT: A 45 PHE cc_start: 0.7201 (m-80) cc_final: 0.6967 (m-80) REVERT: A 167 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.7467 (pp20) REVERT: A 168 ILE cc_start: 0.8975 (mp) cc_final: 0.8398 (mp) REVERT: C 147 ASP cc_start: 0.8559 (OUTLIER) cc_final: 0.8046 (p0) REVERT: D 80 TYR cc_start: 0.7508 (m-80) cc_final: 0.7153 (m-80) REVERT: D 81 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.8108 (ttt) REVERT: D 82 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7414 (tm-30) REVERT: D 97 GLU cc_start: 0.7724 (pp20) cc_final: 0.7325 (pp20) REVERT: B 14 LYS cc_start: 0.6922 (OUTLIER) cc_final: 0.6675 (tmmt) REVERT: B 31 TRP cc_start: 0.7808 (t-100) cc_final: 0.7323 (t-100) REVERT: B 45 PHE cc_start: 0.7329 (m-80) cc_final: 0.6960 (m-80) REVERT: B 168 ILE cc_start: 0.8956 (mp) cc_final: 0.8706 (mp) REVERT: B 193 PHE cc_start: 0.6286 (t80) cc_final: 0.5813 (t80) REVERT: E 147 ASP cc_start: 0.8652 (OUTLIER) cc_final: 0.8024 (p0) REVERT: E 153 LYS cc_start: 0.8222 (mtmm) cc_final: 0.7828 (mtmm) REVERT: E 159 ARG cc_start: 0.7097 (tpt-90) cc_final: 0.6782 (mtp180) REVERT: F 57 ASP cc_start: 0.8278 (m-30) cc_final: 0.8007 (m-30) REVERT: F 82 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7406 (tm-30) REVERT: F 97 GLU cc_start: 0.7698 (pp20) cc_final: 0.7297 (pp20) outliers start: 55 outliers final: 35 residues processed: 192 average time/residue: 1.0905 time to fit residues: 225.9173 Evaluate side-chains 193 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 153 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 195 CYS Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 128 GLN Chi-restraints excluded: chain E residue 135 SER Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 195 CYS Chi-restraints excluded: chain F residue 196 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 69 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 54 optimal weight: 0.0020 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 113 optimal weight: 7.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 HIS E 128 GLN ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9952 Z= 0.187 Angle : 0.636 8.502 13592 Z= 0.321 Chirality : 0.043 0.186 1560 Planarity : 0.005 0.055 1708 Dihedral : 5.038 40.025 1380 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 4.33 % Allowed : 21.00 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.25), residues: 1254 helix: 0.13 (0.37), residues: 198 sheet: 0.03 (0.25), residues: 508 loop : -1.53 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 58 HIS 0.003 0.001 HIS A 125 PHE 0.012 0.001 PHE B 193 TYR 0.017 0.001 TYR E 53 ARG 0.010 0.001 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 161 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.7214 (mmmt) cc_final: 0.6413 (pttt) REVERT: A 31 TRP cc_start: 0.7659 (t-100) cc_final: 0.7240 (t60) REVERT: A 45 PHE cc_start: 0.7225 (m-80) cc_final: 0.7003 (m-80) REVERT: A 167 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.7350 (pp20) REVERT: A 168 ILE cc_start: 0.8944 (mp) cc_final: 0.8374 (mp) REVERT: C 158 GLU cc_start: 0.7591 (mm-30) cc_final: 0.6863 (mt-10) REVERT: D 80 TYR cc_start: 0.7121 (m-80) cc_final: 0.6885 (m-80) REVERT: D 81 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7876 (ttt) REVERT: D 82 GLU cc_start: 0.7587 (tm-30) cc_final: 0.7326 (tm-30) REVERT: D 97 GLU cc_start: 0.7720 (pp20) cc_final: 0.7245 (pp20) REVERT: B 31 TRP cc_start: 0.7797 (t-100) cc_final: 0.7293 (t-100) REVERT: B 45 PHE cc_start: 0.7151 (m-80) cc_final: 0.6854 (m-80) REVERT: B 168 ILE cc_start: 0.8914 (mp) cc_final: 0.8665 (mp) REVERT: E 36 TYR cc_start: 0.8488 (m-80) cc_final: 0.8180 (m-80) REVERT: E 129 LEU cc_start: 0.8042 (mt) cc_final: 0.7457 (mp) REVERT: E 147 ASP cc_start: 0.8641 (OUTLIER) cc_final: 0.8029 (p0) REVERT: E 153 LYS cc_start: 0.8070 (mtmm) cc_final: 0.7514 (mtmm) REVERT: E 159 ARG cc_start: 0.7139 (tpt-90) cc_final: 0.6929 (tpt-90) REVERT: F 57 ASP cc_start: 0.8289 (m-30) cc_final: 0.8071 (m-30) REVERT: F 82 GLU cc_start: 0.7652 (tm-30) cc_final: 0.7328 (tm-30) REVERT: F 97 GLU cc_start: 0.7684 (pp20) cc_final: 0.7227 (pp20) outliers start: 42 outliers final: 27 residues processed: 184 average time/residue: 1.0792 time to fit residues: 214.3699 Evaluate side-chains 183 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 153 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 195 CYS Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 195 CYS Chi-restraints excluded: chain F residue 196 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 0.9980 chunk 67 optimal weight: 7.9990 chunk 86 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 99 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 71 optimal weight: 0.2980 chunk 54 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN E 141 ASN ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9952 Z= 0.190 Angle : 0.638 9.890 13592 Z= 0.319 Chirality : 0.043 0.240 1560 Planarity : 0.005 0.057 1708 Dihedral : 4.944 38.632 1380 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 4.52 % Allowed : 21.56 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -0.87 (0.25), residues: 1254 helix: 0.22 (0.37), residues: 198 sheet: 0.12 (0.25), residues: 504 loop : -1.52 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 58 HIS 0.003 0.001 HIS C 193 PHE 0.011 0.001 PHE B 193 TYR 0.016 0.001 TYR E 53 ARG 0.013 0.001 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 156 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.7171 (mmmt) cc_final: 0.6434 (pttt) REVERT: A 31 TRP cc_start: 0.7662 (t-100) cc_final: 0.7244 (t60) REVERT: A 45 PHE cc_start: 0.7220 (m-80) cc_final: 0.7011 (m-80) REVERT: A 168 ILE cc_start: 0.8885 (mp) cc_final: 0.8629 (mp) REVERT: C 147 ASP cc_start: 0.8584 (OUTLIER) cc_final: 0.8066 (p0) REVERT: C 153 LYS cc_start: 0.8367 (mtpp) cc_final: 0.8137 (mtpp) REVERT: C 158 GLU cc_start: 0.7571 (mm-30) cc_final: 0.6860 (mt-10) REVERT: D 80 TYR cc_start: 0.7047 (m-80) cc_final: 0.6831 (m-80) REVERT: D 81 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7844 (ttt) REVERT: D 82 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7305 (tm-30) REVERT: D 97 GLU cc_start: 0.7713 (pp20) cc_final: 0.7320 (pp20) REVERT: B 15 LYS cc_start: 0.6982 (mmmm) cc_final: 0.6016 (pttt) REVERT: B 31 TRP cc_start: 0.7785 (t-100) cc_final: 0.7306 (t-100) REVERT: B 45 PHE cc_start: 0.7110 (m-80) cc_final: 0.6894 (m-80) REVERT: B 168 ILE cc_start: 0.8920 (mp) cc_final: 0.8665 (mp) REVERT: E 36 TYR cc_start: 0.8462 (m-80) cc_final: 0.8126 (m-80) REVERT: E 147 ASP cc_start: 0.8625 (OUTLIER) cc_final: 0.8025 (p0) REVERT: E 158 GLU cc_start: 0.7157 (mm-30) cc_final: 0.6540 (tp30) REVERT: E 159 ARG cc_start: 0.7219 (tpt-90) cc_final: 0.6979 (tpt-90) REVERT: F 82 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7307 (tm-30) REVERT: F 97 GLU cc_start: 0.7672 (pp20) cc_final: 0.7173 (pp20) outliers start: 44 outliers final: 28 residues processed: 181 average time/residue: 0.9892 time to fit residues: 194.4030 Evaluate side-chains 183 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 152 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 195 CYS Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 195 CYS Chi-restraints excluded: chain F residue 196 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 chunk 58 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 106 optimal weight: 0.0670 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 HIS E 128 GLN ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9952 Z= 0.182 Angle : 0.635 9.500 13592 Z= 0.317 Chirality : 0.043 0.221 1560 Planarity : 0.005 0.055 1708 Dihedral : 4.839 38.904 1380 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 4.14 % Allowed : 21.94 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -0.71 (0.25), residues: 1254 helix: 0.67 (0.38), residues: 186 sheet: 0.16 (0.25), residues: 516 loop : -1.46 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 58 HIS 0.003 0.001 HIS C 193 PHE 0.014 0.001 PHE A 193 TYR 0.017 0.001 TYR E 53 ARG 0.013 0.001 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 166 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.7199 (mmmt) cc_final: 0.6433 (pttt) REVERT: A 31 TRP cc_start: 0.7688 (t-100) cc_final: 0.7268 (t60) REVERT: A 45 PHE cc_start: 0.7151 (m-80) cc_final: 0.6944 (m-80) REVERT: A 168 ILE cc_start: 0.8909 (mp) cc_final: 0.8650 (mp) REVERT: C 11 LEU cc_start: 0.8877 (tt) cc_final: 0.8669 (mp) REVERT: C 147 ASP cc_start: 0.8644 (OUTLIER) cc_final: 0.8148 (p0) REVERT: C 158 GLU cc_start: 0.7559 (mm-30) cc_final: 0.6951 (mt-10) REVERT: C 159 ARG cc_start: 0.7421 (tpt-90) cc_final: 0.7203 (tpt-90) REVERT: D 80 TYR cc_start: 0.7003 (m-80) cc_final: 0.6761 (m-80) REVERT: D 81 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7755 (ttt) REVERT: D 82 GLU cc_start: 0.7581 (tm-30) cc_final: 0.7241 (tm-30) REVERT: D 97 GLU cc_start: 0.7734 (pp20) cc_final: 0.7310 (pp20) REVERT: B 15 LYS cc_start: 0.7039 (mmmm) cc_final: 0.6025 (pttt) REVERT: B 31 TRP cc_start: 0.7762 (t-100) cc_final: 0.7308 (t-100) REVERT: B 45 PHE cc_start: 0.7137 (m-80) cc_final: 0.6887 (m-80) REVERT: B 168 ILE cc_start: 0.8920 (mp) cc_final: 0.8664 (mp) REVERT: E 36 TYR cc_start: 0.8578 (m-80) cc_final: 0.8229 (m-80) REVERT: E 147 ASP cc_start: 0.8619 (OUTLIER) cc_final: 0.8018 (p0) REVERT: E 158 GLU cc_start: 0.6965 (mm-30) cc_final: 0.6422 (tp30) REVERT: E 159 ARG cc_start: 0.7096 (tpt-90) cc_final: 0.6756 (tpt-90) REVERT: F 80 TYR cc_start: 0.7241 (m-80) cc_final: 0.6737 (m-80) REVERT: F 82 GLU cc_start: 0.7624 (tm-30) cc_final: 0.7281 (tm-30) REVERT: F 97 GLU cc_start: 0.7659 (pp20) cc_final: 0.7265 (pp20) outliers start: 40 outliers final: 24 residues processed: 194 average time/residue: 0.9414 time to fit residues: 198.8264 Evaluate side-chains 183 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 156 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 195 CYS Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 195 CYS Chi-restraints excluded: chain F residue 196 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 0.0870 chunk 102 optimal weight: 0.0570 chunk 109 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 99 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 71 optimal weight: 0.1980 chunk 115 optimal weight: 0.9980 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN B 117 ASN ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 HIS E 128 GLN ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9952 Z= 0.168 Angle : 0.637 10.903 13592 Z= 0.315 Chirality : 0.043 0.264 1560 Planarity : 0.005 0.055 1708 Dihedral : 4.768 38.262 1380 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 3.01 % Allowed : 23.26 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.25), residues: 1254 helix: 0.68 (0.38), residues: 186 sheet: 0.30 (0.25), residues: 508 loop : -1.44 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 58 HIS 0.004 0.001 HIS E 80 PHE 0.012 0.001 PHE B 193 TYR 0.017 0.001 TYR E 53 ARG 0.011 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 150 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.7199 (mmmt) cc_final: 0.6459 (pttt) REVERT: A 31 TRP cc_start: 0.7692 (t-100) cc_final: 0.7306 (t60) REVERT: A 168 ILE cc_start: 0.8828 (mp) cc_final: 0.8584 (mp) REVERT: C 11 LEU cc_start: 0.8865 (tt) cc_final: 0.8661 (mp) REVERT: C 158 GLU cc_start: 0.7534 (mm-30) cc_final: 0.6985 (mt-10) REVERT: D 81 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7670 (ttt) REVERT: D 82 GLU cc_start: 0.7550 (tm-30) cc_final: 0.7208 (tm-30) REVERT: D 97 GLU cc_start: 0.7728 (pp20) cc_final: 0.7480 (pp20) REVERT: B 15 LYS cc_start: 0.6793 (mmmm) cc_final: 0.5928 (pttt) REVERT: B 31 TRP cc_start: 0.7796 (t-100) cc_final: 0.7322 (t-100) REVERT: B 168 ILE cc_start: 0.8909 (mp) cc_final: 0.8655 (mp) REVERT: E 36 TYR cc_start: 0.8515 (m-80) cc_final: 0.8236 (m-80) REVERT: E 147 ASP cc_start: 0.8613 (OUTLIER) cc_final: 0.8010 (p0) REVERT: E 158 GLU cc_start: 0.6960 (mm-30) cc_final: 0.6481 (tp30) REVERT: E 159 ARG cc_start: 0.7273 (tpt-90) cc_final: 0.6950 (tpt-90) REVERT: F 80 TYR cc_start: 0.7147 (m-80) cc_final: 0.6634 (m-80) REVERT: F 82 GLU cc_start: 0.7578 (tm-30) cc_final: 0.7223 (tm-30) REVERT: F 97 GLU cc_start: 0.7678 (pp20) cc_final: 0.7275 (pp20) outliers start: 28 outliers final: 19 residues processed: 169 average time/residue: 0.9897 time to fit residues: 181.8746 Evaluate side-chains 170 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 149 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 195 CYS Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 195 CYS Chi-restraints excluded: chain F residue 196 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 80 optimal weight: 0.0370 chunk 121 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9952 Z= 0.224 Angle : 0.657 11.953 13592 Z= 0.330 Chirality : 0.044 0.188 1560 Planarity : 0.005 0.056 1708 Dihedral : 4.856 39.085 1380 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 3.20 % Allowed : 23.16 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -0.74 (0.25), residues: 1254 helix: 0.39 (0.37), residues: 198 sheet: 0.28 (0.25), residues: 504 loop : -1.57 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 167 HIS 0.003 0.001 HIS C 193 PHE 0.017 0.002 PHE A 45 TYR 0.017 0.001 TYR C 53 ARG 0.013 0.001 ARG E 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 150 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.7220 (mmmt) cc_final: 0.6465 (pttt) REVERT: A 31 TRP cc_start: 0.7755 (t-100) cc_final: 0.7306 (t60) REVERT: A 75 TRP cc_start: 0.5141 (OUTLIER) cc_final: 0.4185 (m100) REVERT: A 167 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.7305 (pp20) REVERT: A 168 ILE cc_start: 0.8926 (mp) cc_final: 0.8344 (mp) REVERT: C 11 LEU cc_start: 0.8889 (tt) cc_final: 0.8675 (mp) REVERT: C 158 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7026 (mt-10) REVERT: D 80 TYR cc_start: 0.7448 (m-80) cc_final: 0.7013 (m-80) REVERT: D 81 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7880 (ttt) REVERT: D 82 GLU cc_start: 0.7696 (tm-30) cc_final: 0.7374 (tm-30) REVERT: B 15 LYS cc_start: 0.6748 (mmmm) cc_final: 0.5859 (pttt) REVERT: B 31 TRP cc_start: 0.7791 (t-100) cc_final: 0.7334 (t-100) REVERT: B 168 ILE cc_start: 0.8934 (mp) cc_final: 0.8676 (mp) REVERT: E 147 ASP cc_start: 0.8712 (OUTLIER) cc_final: 0.8134 (p0) REVERT: E 158 GLU cc_start: 0.7042 (mm-30) cc_final: 0.6603 (tp30) REVERT: E 159 ARG cc_start: 0.7126 (tpt-90) cc_final: 0.6772 (tpt-90) REVERT: F 82 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7343 (tm-30) REVERT: F 97 GLU cc_start: 0.7671 (pp20) cc_final: 0.7246 (pp20) outliers start: 30 outliers final: 21 residues processed: 169 average time/residue: 0.9855 time to fit residues: 181.9835 Evaluate side-chains 172 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 147 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 TRP Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 195 CYS Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 195 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 14 optimal weight: 0.0980 chunk 26 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 85 optimal weight: 0.0970 chunk 5 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN B 117 ASN ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.136892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.091559 restraints weight = 70203.731| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 5.40 r_work: 0.3138 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9952 Z= 0.179 Angle : 0.643 11.919 13592 Z= 0.320 Chirality : 0.043 0.216 1560 Planarity : 0.005 0.055 1708 Dihedral : 4.824 39.159 1380 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 3.20 % Allowed : 22.98 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -0.59 (0.25), residues: 1254 helix: 0.80 (0.37), residues: 186 sheet: 0.29 (0.25), residues: 506 loop : -1.44 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 58 HIS 0.003 0.001 HIS C 193 PHE 0.015 0.001 PHE C 213 TYR 0.015 0.001 TYR E 53 ARG 0.013 0.000 ARG E 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4153.10 seconds wall clock time: 74 minutes 35.57 seconds (4475.57 seconds total)