Starting phenix.real_space_refine on Sat Dec 9 07:40:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kzx_23092/12_2023/7kzx_23092.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kzx_23092/12_2023/7kzx_23092.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kzx_23092/12_2023/7kzx_23092.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kzx_23092/12_2023/7kzx_23092.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kzx_23092/12_2023/7kzx_23092.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kzx_23092/12_2023/7kzx_23092.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 6658 2.51 5 N 1754 2.21 5 O 1992 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 47": "OD1" <-> "OD2" Residue "A ASP 72": "OD1" <-> "OD2" Residue "A TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 81": "OE1" <-> "OE2" Residue "A PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "A TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 215": "OD1" <-> "OD2" Residue "A GLU 252": "OE1" <-> "OE2" Residue "A ASP 254": "OD1" <-> "OD2" Residue "A ASP 287": "OD1" <-> "OD2" Residue "B ASP 72": "OD1" <-> "OD2" Residue "B TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 114": "OE1" <-> "OE2" Residue "B TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 181": "OD1" <-> "OD2" Residue "B PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 215": "OD1" <-> "OD2" Residue "B ASP 267": "OD1" <-> "OD2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 71": "OD1" <-> "OD2" Residue "C PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 107": "OE1" <-> "OE2" Residue "C PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 145": "OE1" <-> "OE2" Residue "C GLU 167": "OE1" <-> "OE2" Residue "C TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4": "OE1" <-> "OE2" Residue "D GLU 9": "OE1" <-> "OE2" Residue "D PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 65": "OD1" <-> "OD2" Residue "D TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 92": "OE1" <-> "OE2" Residue "D ASP 161": "OD1" <-> "OD2" Residue "D PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 229": "OE1" <-> "OE2" Residue "E ASP 18": "OD1" <-> "OD2" Residue "E TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 71": "OD1" <-> "OD2" Residue "E GLU 82": "OE1" <-> "OE2" Residue "E PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 107": "OE1" <-> "OE2" Residue "E ASP 124": "OD1" <-> "OD2" Residue "E PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 167": "OE1" <-> "OE2" Residue "E TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 189": "OE1" <-> "OE2" Residue "E TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 65": "OD1" <-> "OD2" Residue "F PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 165": "OE1" <-> "OE2" Residue "F PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 225": "OD1" <-> "OD2" Residue "F GLU 229": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 10432 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2163 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 6, 'TRANS': 274} Chain: "B" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2163 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 6, 'TRANS': 274} Chain: "C" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1460 Classifications: {'peptide': 190} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 179} Chain breaks: 1 Chain: "D" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1589 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 196} Chain breaks: 2 Chain: "E" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1468 Classifications: {'peptide': 191} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 180} Chain breaks: 1 Chain: "F" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1589 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 196} Chain breaks: 2 Time building chain proxies: 5.88, per 1000 atoms: 0.56 Number of scatterers: 10432 At special positions: 0 Unit cell: (75.555, 151.11, 150.075, 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 28 16.00 O 1992 8.00 N 1754 7.00 C 6658 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 196 " distance=2.03 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: 4.69 Conformation dependent library (CDL) restraints added in 2.2 seconds 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2550 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 24 sheets defined 32.0% alpha, 27.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 13 through 35 removed outlier: 3.579A pdb=" N VAL A 19 " --> pdb=" O SER A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 64 Processing helix chain 'A' and resid 80 through 107 removed outlier: 3.788A pdb=" N ALA A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 138 removed outlier: 3.557A pdb=" N LYS A 138 " --> pdb=" O VAL A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 175 removed outlier: 3.826A pdb=" N SER A 153 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU A 160 " --> pdb=" O TYR A 156 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N PHE A 161 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR A 175 " --> pdb=" O VAL A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 208 removed outlier: 4.183A pdb=" N GLY A 182 " --> pdb=" O TRP A 178 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU A 183 " --> pdb=" O TRP A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 258 through 277 Processing helix chain 'B' and resid 13 through 35 removed outlier: 3.723A pdb=" N TYR B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 64 removed outlier: 3.846A pdb=" N ALA B 43 " --> pdb=" O ALA B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 109 removed outlier: 3.686A pdb=" N ALA B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA B 85 " --> pdb=" O GLU B 81 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N GLY B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASN B 109 " --> pdb=" O GLU B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 138 removed outlier: 3.704A pdb=" N LYS B 138 " --> pdb=" O VAL B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 175 removed outlier: 4.872A pdb=" N LEU B 160 " --> pdb=" O TYR B 156 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N PHE B 161 " --> pdb=" O LYS B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 208 removed outlier: 4.357A pdb=" N ASP B 181 " --> pdb=" O TRP B 177 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLY B 182 " --> pdb=" O TRP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 226 Processing helix chain 'B' and resid 258 through 277 Processing helix chain 'C' and resid 80 through 84 Processing helix chain 'C' and resid 123 through 128 Processing helix chain 'C' and resid 185 through 189 Processing helix chain 'D' and resid 65 through 68 Processing helix chain 'D' and resid 90 through 94 removed outlier: 3.709A pdb=" N THR D 94 " --> pdb=" O ALA D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 221 Processing helix chain 'E' and resid 80 through 84 Processing helix chain 'E' and resid 123 through 129 Processing helix chain 'E' and resid 186 through 190 Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 211 removed outlier: 4.511A pdb=" N ASP A 235 " --> pdb=" O HIS A 250 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N VAL A 245 " --> pdb=" O GLU A 281 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ILE A 283 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ILE A 247 " --> pdb=" O ILE A 283 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 253 through 254 removed outlier: 6.543A pdb=" N LEU A 253 " --> pdb=" O VAL A 289 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 232 through 233 Processing sheet with id=AA4, first strand: chain 'B' and resid 232 through 233 removed outlier: 6.201A pdb=" N VAL B 245 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ILE B 283 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ILE B 247 " --> pdb=" O ILE B 283 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N HIS B 285 " --> pdb=" O ILE B 247 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N PHE B 249 " --> pdb=" O HIS B 285 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 6 through 8 Processing sheet with id=AA6, first strand: chain 'C' and resid 11 through 14 removed outlier: 6.409A pdb=" N LEU C 12 " --> pdb=" O GLU C 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 54 through 55 removed outlier: 5.270A pdb=" N LEU C 47 " --> pdb=" O GLN C 38 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N GLN C 38 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 118 through 120 removed outlier: 3.949A pdb=" N ALA C 132 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU C 183 " --> pdb=" O ALA C 132 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL C 134 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN C 140 " --> pdb=" O TYR C 175 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N TYR C 175 " --> pdb=" O ASN C 140 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 8 through 9 Processing sheet with id=AB1, first strand: chain 'D' and resid 60 through 63 removed outlier: 5.200A pdb=" N TRP D 50 " --> pdb=" O ARG D 41 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ARG D 41 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N TYR D 120 " --> pdb=" O ARG D 101 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 60 through 63 removed outlier: 5.200A pdb=" N TRP D 50 " --> pdb=" O ARG D 41 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ARG D 41 " --> pdb=" O TRP D 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 106 through 108 removed outlier: 3.518A pdb=" N SER D 108 " --> pdb=" O HIS D 112 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N HIS D 112 " --> pdb=" O SER D 108 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 137 through 140 removed outlier: 3.616A pdb=" N ASP D 161 " --> pdb=" O TYR D 193 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N TYR D 193 " --> pdb=" O ASP D 161 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 137 through 140 removed outlier: 3.616A pdb=" N ASP D 161 " --> pdb=" O TYR D 193 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N TYR D 193 " --> pdb=" O ASP D 161 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 213 through 217 Processing sheet with id=AB7, first strand: chain 'E' and resid 5 through 8 removed outlier: 3.538A pdb=" N VAL E 20 " --> pdb=" O ILE E 76 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 12 through 14 removed outlier: 6.910A pdb=" N VAL E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N TYR E 50 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER E 54 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 118 through 120 removed outlier: 5.844A pdb=" N TYR E 175 " --> pdb=" O ASN E 140 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 7 through 10 Processing sheet with id=AC2, first strand: chain 'F' and resid 13 through 14 removed outlier: 6.898A pdb=" N ILE F 37 " --> pdb=" O SER F 53 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N SER F 53 " --> pdb=" O ILE F 37 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP F 39 " --> pdb=" O VAL F 51 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 106 through 107 Processing sheet with id=AC4, first strand: chain 'F' and resid 137 through 139 removed outlier: 3.512A pdb=" N ASP F 161 " --> pdb=" O TYR F 193 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N TYR F 193 " --> pdb=" O ASP F 161 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 137 through 139 removed outlier: 3.512A pdb=" N ASP F 161 " --> pdb=" O TYR F 193 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N TYR F 193 " --> pdb=" O ASP F 161 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU F 192 " --> pdb=" O GLN F 188 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 168 through 171 removed outlier: 3.555A pdb=" N SER F 170 " --> pdb=" O ASN F 214 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASN F 214 " --> pdb=" O SER F 170 " (cutoff:3.500A) 570 hydrogen bonds defined for protein. 1539 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: 3.08 Time building geometry restraints manager: 4.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3322 1.34 - 1.46: 2067 1.46 - 1.57: 5233 1.57 - 1.69: 0 1.69 - 1.81: 38 Bond restraints: 10660 Sorted by residual: bond pdb=" C LYS E 43 " pdb=" N ALA E 44 " ideal model delta sigma weight residual 1.331 1.287 0.045 1.63e-02 3.76e+03 7.46e+00 bond pdb=" CA ARG C 144 " pdb=" C ARG C 144 " ideal model delta sigma weight residual 1.524 1.471 0.053 2.25e-02 1.98e+03 5.46e+00 bond pdb=" C LYS F 218 " pdb=" N PRO F 219 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.08e-02 8.57e+03 4.16e+00 bond pdb=" C GLN C 39 " pdb=" N LYS C 40 " ideal model delta sigma weight residual 1.330 1.305 0.025 1.47e-02 4.63e+03 2.98e+00 bond pdb=" CB TRP E 93 " pdb=" CG TRP E 93 " ideal model delta sigma weight residual 1.498 1.445 0.053 3.10e-02 1.04e+03 2.89e+00 ... (remaining 10655 not shown) Histogram of bond angle deviations from ideal: 99.65 - 106.54: 282 106.54 - 113.43: 6133 113.43 - 120.33: 3643 120.33 - 127.22: 4337 127.22 - 134.12: 116 Bond angle restraints: 14511 Sorted by residual: angle pdb=" N ILE A 66 " pdb=" CA ILE A 66 " pdb=" C ILE A 66 " ideal model delta sigma weight residual 113.00 107.36 5.64 1.30e+00 5.92e-01 1.88e+01 angle pdb=" C VAL B 149 " pdb=" N GLU B 150 " pdb=" CA GLU B 150 " ideal model delta sigma weight residual 121.54 127.41 -5.87 1.91e+00 2.74e-01 9.45e+00 angle pdb=" C VAL F 51 " pdb=" N ALA F 52 " pdb=" CA ALA F 52 " ideal model delta sigma weight residual 121.63 115.87 5.76 1.92e+00 2.71e-01 9.01e+00 angle pdb=" CA ARG F 111 " pdb=" CB ARG F 111 " pdb=" CG ARG F 111 " ideal model delta sigma weight residual 114.10 119.82 -5.72 2.00e+00 2.50e-01 8.18e+00 angle pdb=" N GLY F 179 " pdb=" CA GLY F 179 " pdb=" C GLY F 179 " ideal model delta sigma weight residual 113.18 106.45 6.73 2.37e+00 1.78e-01 8.06e+00 ... (remaining 14506 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.18: 5765 18.18 - 36.35: 412 36.35 - 54.53: 79 54.53 - 72.71: 45 72.71 - 90.88: 20 Dihedral angle restraints: 6321 sinusoidal: 2362 harmonic: 3959 Sorted by residual: dihedral pdb=" CA SER C 94 " pdb=" C SER C 94 " pdb=" N TRP C 95 " pdb=" CA TRP C 95 " ideal model delta harmonic sigma weight residual -180.00 -153.91 -26.09 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA CYS C 196 " pdb=" C CYS C 196 " pdb=" N GLU C 197 " pdb=" CA GLU C 197 " ideal model delta harmonic sigma weight residual 180.00 -154.40 -25.60 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA PRO B 228 " pdb=" C PRO B 228 " pdb=" N ARG B 229 " pdb=" CA ARG B 229 " ideal model delta harmonic sigma weight residual 180.00 155.35 24.65 0 5.00e+00 4.00e-02 2.43e+01 ... (remaining 6318 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1257 0.047 - 0.094: 341 0.094 - 0.141: 82 0.141 - 0.188: 8 0.188 - 0.235: 1 Chirality restraints: 1689 Sorted by residual: chirality pdb=" CB ILE B 284 " pdb=" CA ILE B 284 " pdb=" CG1 ILE B 284 " pdb=" CG2 ILE B 284 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA ARG D 111 " pdb=" N ARG D 111 " pdb=" C ARG D 111 " pdb=" CB ARG D 111 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.71e-01 chirality pdb=" CB VAL A 230 " pdb=" CA VAL A 230 " pdb=" CG1 VAL A 230 " pdb=" CG2 VAL A 230 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.45e-01 ... (remaining 1686 not shown) Planarity restraints: 1826 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU F 165 " -0.053 5.00e-02 4.00e+02 8.02e-02 1.03e+01 pdb=" N PRO F 166 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO F 166 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO F 166 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 76 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.71e+00 pdb=" C ASP D 76 " -0.038 2.00e-02 2.50e+03 pdb=" O ASP D 76 " 0.014 2.00e-02 2.50e+03 pdb=" N THR D 77 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 195 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.24e+00 pdb=" C GLN B 195 " 0.036 2.00e-02 2.50e+03 pdb=" O GLN B 195 " -0.013 2.00e-02 2.50e+03 pdb=" N ALA B 196 " -0.012 2.00e-02 2.50e+03 ... (remaining 1823 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 141 2.61 - 3.18: 10116 3.18 - 3.75: 16628 3.75 - 4.33: 22413 4.33 - 4.90: 35955 Nonbonded interactions: 85253 Sorted by model distance: nonbonded pdb=" O SER F 34 " pdb=" OH TYR F 104 " model vdw 2.031 2.440 nonbonded pdb=" OG SER C 94 " pdb=" O LEU C 97 " model vdw 2.113 2.440 nonbonded pdb=" OH TYR F 162 " pdb=" OE1 GLU F 165 " model vdw 2.161 2.440 nonbonded pdb=" O ASP C 83 " pdb=" OH TYR C 87 " model vdw 2.161 2.440 nonbonded pdb=" O LEU B 212 " pdb=" NH1 ARG B 217 " model vdw 2.165 2.520 ... (remaining 85248 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 2 through 202) selection = (chain 'E' and (resid 2 through 149 or resid 162 through 202)) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 4.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 8.040 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 31.670 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 10660 Z= 0.406 Angle : 0.807 6.881 14511 Z= 0.457 Chirality : 0.045 0.235 1689 Planarity : 0.006 0.080 1826 Dihedral : 15.745 90.882 3759 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.27 % Favored : 90.50 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -2.29 (0.22), residues: 1337 helix: -0.18 (0.25), residues: 398 sheet: -1.17 (0.27), residues: 338 loop : -2.68 (0.23), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP B 179 HIS 0.008 0.002 HIS B 155 PHE 0.015 0.002 PHE C 72 TYR 0.028 0.002 TYR F 104 ARG 0.008 0.001 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.2703 time to fit residues: 43.3021 Evaluate side-chains 55 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 1.187 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 0.0980 chunk 101 optimal weight: 4.9990 chunk 56 optimal weight: 0.0030 chunk 34 optimal weight: 7.9990 chunk 68 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 GLN ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 GLN D 188 GLN E 38 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 GLN ** F 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 188 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10660 Z= 0.259 Angle : 0.686 11.768 14511 Z= 0.359 Chirality : 0.044 0.184 1689 Planarity : 0.005 0.055 1826 Dihedral : 5.868 38.161 1461 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.30 % Favored : 91.55 % Rotamer: Outliers : 1.14 % Allowed : 11.74 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.76 (0.22), residues: 1337 helix: 0.44 (0.26), residues: 406 sheet: -0.85 (0.28), residues: 311 loop : -2.49 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 50 HIS 0.008 0.001 HIS B 71 PHE 0.019 0.001 PHE F 130 TYR 0.023 0.002 TYR F 104 ARG 0.004 0.000 ARG F 22 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 75 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 86 average time/residue: 0.2160 time to fit residues: 27.8576 Evaluate side-chains 59 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 51 time to evaluate : 1.202 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1002 time to fit residues: 3.0449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 121 optimal weight: 0.9980 chunk 131 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 chunk 97 optimal weight: 0.8980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10660 Z= 0.238 Angle : 0.651 10.548 14511 Z= 0.338 Chirality : 0.043 0.181 1689 Planarity : 0.004 0.053 1826 Dihedral : 5.506 29.322 1461 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.03 % Favored : 92.82 % Rotamer: Outliers : 1.84 % Allowed : 14.64 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.23), residues: 1337 helix: 0.79 (0.26), residues: 399 sheet: -0.98 (0.27), residues: 336 loop : -2.18 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 50 HIS 0.006 0.001 HIS B 71 PHE 0.022 0.001 PHE E 120 TYR 0.020 0.001 TYR B 156 ARG 0.007 0.000 ARG F 90 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 63 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 6 residues processed: 81 average time/residue: 0.2013 time to fit residues: 24.9210 Evaluate side-chains 53 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 1.184 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0956 time to fit residues: 2.7189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 63 optimal weight: 0.6980 chunk 13 optimal weight: 30.0000 chunk 58 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 34 optimal weight: 0.0870 chunk 107 optimal weight: 1.9990 overall best weight: 0.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10660 Z= 0.202 Angle : 0.632 9.975 14511 Z= 0.326 Chirality : 0.043 0.394 1689 Planarity : 0.004 0.055 1826 Dihedral : 5.274 34.503 1461 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.43 % Favored : 93.42 % Rotamer: Outliers : 2.02 % Allowed : 15.95 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.23), residues: 1337 helix: 0.99 (0.26), residues: 400 sheet: -0.87 (0.27), residues: 336 loop : -2.04 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 50 HIS 0.005 0.001 HIS B 71 PHE 0.013 0.001 PHE F 71 TYR 0.016 0.001 TYR F 104 ARG 0.006 0.000 ARG F 90 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 66 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 12 residues processed: 84 average time/residue: 0.2053 time to fit residues: 26.2841 Evaluate side-chains 63 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 51 time to evaluate : 1.223 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1017 time to fit residues: 3.8228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 0.0050 chunk 116 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 GLN ** B 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10660 Z= 0.205 Angle : 0.628 12.772 14511 Z= 0.321 Chirality : 0.043 0.396 1689 Planarity : 0.004 0.053 1826 Dihedral : 5.089 31.605 1461 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.96 % Favored : 92.97 % Rotamer: Outliers : 1.67 % Allowed : 17.18 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.03 (0.23), residues: 1337 helix: 1.12 (0.26), residues: 400 sheet: -0.64 (0.28), residues: 322 loop : -1.96 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 95 HIS 0.004 0.001 HIS F 181 PHE 0.032 0.002 PHE B 97 TYR 0.016 0.001 TYR D 193 ARG 0.005 0.000 ARG F 90 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 60 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 6 residues processed: 76 average time/residue: 0.2198 time to fit residues: 24.7604 Evaluate side-chains 58 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 1.151 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0962 time to fit residues: 2.5673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 129 optimal weight: 0.8980 chunk 107 optimal weight: 0.0870 chunk 60 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 overall best weight: 1.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 GLN ** F 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10660 Z= 0.297 Angle : 0.661 11.435 14511 Z= 0.337 Chirality : 0.043 0.346 1689 Planarity : 0.004 0.054 1826 Dihedral : 5.166 32.378 1461 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.63 % Favored : 92.30 % Rotamer: Outliers : 1.75 % Allowed : 17.53 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.23), residues: 1337 helix: 1.21 (0.26), residues: 397 sheet: -0.66 (0.28), residues: 325 loop : -1.86 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP C 95 HIS 0.004 0.001 HIS C 200 PHE 0.021 0.001 PHE B 97 TYR 0.022 0.002 TYR B 156 ARG 0.004 0.000 ARG F 22 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 52 time to evaluate : 1.318 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 8 residues processed: 70 average time/residue: 0.2211 time to fit residues: 23.2998 Evaluate side-chains 56 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 48 time to evaluate : 1.183 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0929 time to fit residues: 2.9881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 51 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10660 Z= 0.233 Angle : 0.637 10.855 14511 Z= 0.324 Chirality : 0.043 0.325 1689 Planarity : 0.004 0.057 1826 Dihedral : 5.038 30.414 1461 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.18 % Favored : 92.74 % Rotamer: Outliers : 0.96 % Allowed : 18.58 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.84 (0.23), residues: 1337 helix: 1.27 (0.27), residues: 400 sheet: -0.52 (0.28), residues: 317 loop : -1.85 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 50 HIS 0.004 0.001 HIS F 181 PHE 0.019 0.001 PHE B 97 TYR 0.020 0.001 TYR B 156 ARG 0.003 0.000 ARG F 22 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 56 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 63 average time/residue: 0.2507 time to fit residues: 23.0166 Evaluate side-chains 52 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 47 time to evaluate : 1.196 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2535 time to fit residues: 3.2433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 82 optimal weight: 0.4980 chunk 87 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 101 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 112 optimal weight: 0.1980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10660 Z= 0.188 Angle : 0.637 13.017 14511 Z= 0.320 Chirality : 0.043 0.310 1689 Planarity : 0.004 0.060 1826 Dihedral : 4.857 29.047 1461 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.06 % Favored : 93.87 % Rotamer: Outliers : 1.05 % Allowed : 18.76 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.24), residues: 1337 helix: 1.37 (0.26), residues: 400 sheet: -0.46 (0.28), residues: 322 loop : -1.71 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP D 50 HIS 0.004 0.001 HIS F 181 PHE 0.017 0.001 PHE B 97 TYR 0.018 0.001 TYR B 156 ARG 0.004 0.000 ARG F 90 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 62 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 72 average time/residue: 0.2161 time to fit residues: 23.2179 Evaluate side-chains 55 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 50 time to evaluate : 1.122 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1909 time to fit residues: 2.8493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 0.4980 chunk 123 optimal weight: 0.4980 chunk 72 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 94 optimal weight: 0.1980 chunk 36 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 127 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 HIS B 285 HIS ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10660 Z= 0.182 Angle : 0.642 15.395 14511 Z= 0.319 Chirality : 0.042 0.354 1689 Planarity : 0.004 0.058 1826 Dihedral : 4.724 27.096 1461 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.61 % Favored : 94.32 % Rotamer: Outliers : 0.61 % Allowed : 19.46 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.24), residues: 1337 helix: 1.37 (0.26), residues: 405 sheet: -0.27 (0.28), residues: 322 loop : -1.66 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 50 HIS 0.004 0.001 HIS F 181 PHE 0.022 0.001 PHE F 71 TYR 0.021 0.001 TYR F 193 ARG 0.006 0.000 ARG B 229 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 61 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 65 average time/residue: 0.2408 time to fit residues: 23.1995 Evaluate side-chains 55 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 53 time to evaluate : 1.216 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1049 time to fit residues: 1.9063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 3.9990 chunk 60 optimal weight: 0.3980 chunk 88 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 chunk 122 optimal weight: 0.0770 chunk 106 optimal weight: 6.9990 chunk 11 optimal weight: 0.5980 chunk 82 optimal weight: 6.9990 chunk 65 optimal weight: 0.2980 chunk 84 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10660 Z= 0.172 Angle : 0.645 15.222 14511 Z= 0.318 Chirality : 0.043 0.385 1689 Planarity : 0.004 0.057 1826 Dihedral : 4.613 25.333 1461 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.53 % Favored : 94.39 % Rotamer: Outliers : 0.18 % Allowed : 20.51 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.24), residues: 1337 helix: 1.45 (0.26), residues: 405 sheet: -0.09 (0.28), residues: 329 loop : -1.67 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 50 HIS 0.003 0.001 HIS F 181 PHE 0.016 0.001 PHE F 71 TYR 0.024 0.001 TYR E 188 ARG 0.006 0.000 ARG B 229 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 60 average time/residue: 0.2807 time to fit residues: 25.5008 Evaluate side-chains 55 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 1.222 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1027 time to fit residues: 1.7882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 7.9990 chunk 98 optimal weight: 0.8980 chunk 15 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 93 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.077930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.061628 restraints weight = 52562.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.061387 restraints weight = 35485.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.061910 restraints weight = 32751.189| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10660 Z= 0.315 Angle : 0.681 14.551 14511 Z= 0.343 Chirality : 0.043 0.348 1689 Planarity : 0.005 0.052 1826 Dihedral : 4.849 25.463 1461 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.03 % Favored : 92.89 % Rotamer: Outliers : 0.26 % Allowed : 20.51 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.24), residues: 1337 helix: 1.43 (0.26), residues: 402 sheet: -0.34 (0.28), residues: 343 loop : -1.72 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 171 HIS 0.004 0.001 HIS D 217 PHE 0.020 0.002 PHE E 120 TYR 0.018 0.002 TYR D 162 ARG 0.004 0.000 ARG F 22 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1924.55 seconds wall clock time: 36 minutes 25.78 seconds (2185.78 seconds total)