Starting phenix.real_space_refine on Fri Mar 15 02:57:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kzx_23092/03_2024/7kzx_23092.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kzx_23092/03_2024/7kzx_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_23092/03_2024/7kzx_23092.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kzx_23092/03_2024/7kzx_23092.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kzx_23092/03_2024/7kzx_23092.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kzx_23092/03_2024/7kzx_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-dev-5265/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: 6.00, per 1000 atoms: 0.58 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: 4.18 Conformation dependent library (CDL) restraints added in 1.8 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: 3.00 Time building geometry restraints manager: 4.55 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: 2.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.970 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 30.450 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.510 ------------------------------------------------------------------------------- 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 : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.8504 (ttm) cc_final: 0.8281 (ttt) REVERT: A 99 LEU cc_start: 0.9405 (mt) cc_final: 0.9166 (mt) REVERT: B 190 CYS cc_start: 0.9491 (t) cc_final: 0.9168 (m) REVERT: D 50 TRP cc_start: 0.8398 (t60) cc_final: 0.7994 (t60) REVERT: D 93 ASP cc_start: 0.7952 (m-30) cc_final: 0.7429 (m-30) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.2683 time to fit residues: 42.8994 Evaluate side-chains 56 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 1.185 ------------------------------------------------------------------------------- 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: 10.0000 chunk 78 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 overall best weight: 1.5794 ------------------------------------------------------------------------------- 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: 0.7991 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10660 Z= 0.269 Angle : 0.681 11.398 14511 Z= 0.358 Chirality : 0.044 0.181 1689 Planarity : 0.005 0.056 1826 Dihedral : 5.858 38.754 1461 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.45 % Favored : 91.40 % Rotamer: Outliers : 1.40 % Allowed : 12.36 % Favored : 86.24 % 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: -1.72 (0.22), residues: 1337 helix: 0.51 (0.26), residues: 407 sheet: -0.85 (0.28), residues: 311 loop : -2.49 (0.23), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 179 HIS 0.008 0.001 HIS B 71 PHE 0.017 0.001 PHE F 130 TYR 0.023 0.002 TYR F 104 ARG 0.005 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 91 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 75 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.8511 (ttm) cc_final: 0.8307 (ttt) REVERT: A 93 MET cc_start: 0.8751 (mmm) cc_final: 0.8463 (tpp) REVERT: A 99 LEU cc_start: 0.9345 (mt) cc_final: 0.9118 (mt) REVERT: B 190 CYS cc_start: 0.9336 (t) cc_final: 0.9070 (m) REVERT: C 5 MET cc_start: 0.8012 (mmm) cc_final: 0.7523 (mmm) REVERT: D 50 TRP cc_start: 0.8339 (t60) cc_final: 0.8060 (t60) outliers start: 16 outliers final: 7 residues processed: 86 average time/residue: 0.2098 time to fit residues: 26.8835 Evaluate side-chains 63 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 221 ASN Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain F residue 141 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 chunk 120 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.7934 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10660 Z= 0.191 Angle : 0.629 9.414 14511 Z= 0.327 Chirality : 0.042 0.177 1689 Planarity : 0.004 0.052 1826 Dihedral : 5.402 29.289 1461 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.06 % Favored : 93.79 % Rotamer: Outliers : 1.84 % Allowed : 14.55 % Favored : 83.61 % 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: -1.34 (0.22), residues: 1337 helix: 0.89 (0.26), residues: 398 sheet: -0.91 (0.27), residues: 336 loop : -2.14 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 93 HIS 0.005 0.001 HIS B 71 PHE 0.020 0.001 PHE E 120 TYR 0.023 0.001 TYR B 156 ARG 0.006 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 90 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 69 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.8621 (mmm) cc_final: 0.8305 (tpp) REVERT: A 99 LEU cc_start: 0.9315 (mt) cc_final: 0.9111 (mt) REVERT: B 98 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8858 (tt) REVERT: B 190 CYS cc_start: 0.9341 (t) cc_final: 0.9036 (m) REVERT: C 5 MET cc_start: 0.7871 (mmm) cc_final: 0.7522 (mmm) REVERT: D 50 TRP cc_start: 0.8215 (t60) cc_final: 0.7966 (t60) REVERT: D 92 GLU cc_start: 0.7467 (tp30) cc_final: 0.7226 (tp30) outliers start: 21 outliers final: 7 residues processed: 88 average time/residue: 0.2003 time to fit residues: 26.4896 Evaluate side-chains 58 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 50 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain F residue 8 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 0.3980 chunk 91 optimal weight: 7.9990 chunk 63 optimal weight: 0.8980 chunk 13 optimal weight: 20.0000 chunk 58 optimal weight: 3.9990 chunk 81 optimal weight: 0.3980 chunk 122 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 115 optimal weight: 0.6980 chunk 34 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10660 Z= 0.177 Angle : 0.614 8.941 14511 Z= 0.317 Chirality : 0.042 0.139 1689 Planarity : 0.004 0.056 1826 Dihedral : 5.157 34.680 1461 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.21 % Favored : 93.72 % Rotamer: Outliers : 2.37 % Allowed : 15.25 % Favored : 82.38 % 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: -1.10 (0.23), residues: 1337 helix: 1.07 (0.26), residues: 398 sheet: -0.75 (0.28), residues: 325 loop : -1.96 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 50 HIS 0.004 0.001 HIS F 181 PHE 0.015 0.001 PHE F 71 TYR 0.016 0.001 TYR C 175 ARG 0.006 0.000 ARG D 22 *********************** 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 99 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 72 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.8562 (mmm) cc_final: 0.8233 (tpp) REVERT: B 45 LEU cc_start: 0.8785 (tt) cc_final: 0.8520 (tp) REVERT: B 98 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8927 (mm) REVERT: C 95 TRP cc_start: 0.7598 (t-100) cc_final: 0.7277 (t-100) outliers start: 27 outliers final: 16 residues processed: 95 average time/residue: 0.1904 time to fit residues: 27.3483 Evaluate side-chains 69 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 52 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 156 TYR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 221 ASN Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain F residue 37 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 116 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 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 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** ** 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: 0.8006 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10660 Z= 0.316 Angle : 0.666 12.682 14511 Z= 0.342 Chirality : 0.042 0.143 1689 Planarity : 0.004 0.054 1826 Dihedral : 5.211 32.266 1461 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.40 % Favored : 92.52 % Rotamer: Outliers : 3.51 % Allowed : 16.21 % Favored : 80.28 % 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: 1.16 (0.26), residues: 397 sheet: -0.74 (0.28), residues: 325 loop : -1.91 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP D 50 HIS 0.005 0.001 HIS B 71 PHE 0.032 0.002 PHE B 97 TYR 0.026 0.002 TYR C 175 ARG 0.005 0.000 ARG F 22 *********************** 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 90 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 50 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.8634 (mmm) cc_final: 0.8271 (tpp) REVERT: B 93 MET cc_start: 0.8595 (mmm) cc_final: 0.8372 (mmm) REVERT: D 50 TRP cc_start: 0.8320 (t60) cc_final: 0.8091 (t60) outliers start: 40 outliers final: 25 residues processed: 85 average time/residue: 0.2054 time to fit residues: 26.2083 Evaluate side-chains 69 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 44 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 156 TYR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 99 CYS Chi-restraints excluded: chain D residue 221 ASN Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 49 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 129 optimal weight: 0.9980 chunk 107 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 chunk 68 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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** C 168 GLN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10660 Z= 0.228 Angle : 0.622 11.222 14511 Z= 0.320 Chirality : 0.044 0.396 1689 Planarity : 0.004 0.053 1826 Dihedral : 5.064 32.453 1461 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.51 % Favored : 93.42 % Rotamer: Outliers : 3.33 % Allowed : 17.00 % Favored : 79.67 % 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: -0.89 (0.23), residues: 1337 helix: 1.30 (0.26), residues: 397 sheet: -0.70 (0.28), residues: 321 loop : -1.82 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 50 HIS 0.004 0.001 HIS F 181 PHE 0.019 0.001 PHE B 97 TYR 0.016 0.001 TYR F 104 ARG 0.003 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 89 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 51 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 41 MET cc_start: 0.8353 (mmm) cc_final: 0.8023 (mmm) REVERT: D 50 TRP cc_start: 0.8182 (t60) cc_final: 0.7775 (t60) REVERT: D 171 TRP cc_start: 0.7541 (OUTLIER) cc_final: 0.6965 (m100) REVERT: F 92 GLU cc_start: 0.8065 (pm20) cc_final: 0.7820 (pp20) outliers start: 38 outliers final: 26 residues processed: 84 average time/residue: 0.1989 time to fit residues: 25.0000 Evaluate side-chains 74 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 47 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 156 TYR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 99 CYS Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 171 TRP Chi-restraints excluded: chain D residue 221 ASN Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 49 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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** ** 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: 0.7964 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10660 Z= 0.234 Angle : 0.634 12.133 14511 Z= 0.322 Chirality : 0.043 0.329 1689 Planarity : 0.004 0.056 1826 Dihedral : 5.001 30.819 1461 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.58 % Favored : 93.34 % Rotamer: Outliers : 3.33 % Allowed : 17.00 % Favored : 79.67 % 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: -0.81 (0.23), residues: 1337 helix: 1.31 (0.27), residues: 400 sheet: -0.57 (0.28), residues: 311 loop : -1.80 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 50 HIS 0.004 0.001 HIS F 181 PHE 0.018 0.001 PHE E 120 TYR 0.016 0.001 TYR F 104 ARG 0.008 0.000 ARG B 239 *********************** 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 92 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 54 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.8902 (tpp) cc_final: 0.8257 (tpp) REVERT: B 41 MET cc_start: 0.8251 (mmm) cc_final: 0.7988 (mmm) REVERT: D 50 TRP cc_start: 0.8177 (t60) cc_final: 0.7827 (t60) REVERT: D 171 TRP cc_start: 0.7697 (OUTLIER) cc_final: 0.7075 (m100) REVERT: F 92 GLU cc_start: 0.8092 (pm20) cc_final: 0.7795 (pp20) outliers start: 38 outliers final: 28 residues processed: 87 average time/residue: 0.2076 time to fit residues: 27.2260 Evaluate side-chains 75 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 46 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 156 TYR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 99 CYS Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 171 TRP Chi-restraints excluded: chain D residue 221 ASN Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 49 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 4.9990 chunk 38 optimal weight: 30.0000 chunk 25 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 101 optimal weight: 9.9990 chunk 117 optimal weight: 0.8980 chunk 123 optimal weight: 0.5980 chunk 112 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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** ** 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: 0.7936 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10660 Z= 0.206 Angle : 0.621 14.044 14511 Z= 0.313 Chirality : 0.043 0.443 1689 Planarity : 0.004 0.053 1826 Dihedral : 4.860 29.483 1461 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.91 % Favored : 94.02 % Rotamer: Outliers : 2.98 % Allowed : 17.88 % Favored : 79.14 % 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: -0.77 (0.23), residues: 1337 helix: 1.30 (0.27), residues: 402 sheet: -0.49 (0.28), residues: 311 loop : -1.77 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 95 HIS 0.004 0.001 HIS F 181 PHE 0.018 0.001 PHE E 120 TYR 0.014 0.001 TYR F 104 ARG 0.008 0.000 ARG B 239 *********************** 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 92 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 58 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.8843 (tpp) cc_final: 0.8226 (tpp) REVERT: B 41 MET cc_start: 0.8348 (mmm) cc_final: 0.7962 (mmm) REVERT: B 225 LYS cc_start: 0.8734 (pttm) cc_final: 0.7952 (tptp) REVERT: C 95 TRP cc_start: 0.7529 (t-100) cc_final: 0.7088 (t-100) REVERT: D 50 TRP cc_start: 0.8115 (t60) cc_final: 0.7756 (t60) REVERT: D 171 TRP cc_start: 0.7913 (OUTLIER) cc_final: 0.7311 (m100) REVERT: E 187 ASP cc_start: 0.8585 (OUTLIER) cc_final: 0.8254 (m-30) REVERT: F 40 VAL cc_start: 0.9436 (t) cc_final: 0.9194 (m) REVERT: F 92 GLU cc_start: 0.8043 (pm20) cc_final: 0.7679 (pp20) outliers start: 34 outliers final: 27 residues processed: 85 average time/residue: 0.1929 time to fit residues: 25.0366 Evaluate side-chains 79 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 50 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 156 TYR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 191 HIS Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 99 CYS Chi-restraints excluded: chain D residue 171 TRP Chi-restraints excluded: chain D residue 221 ASN Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 49 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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** ** 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: 0.7955 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10660 Z= 0.232 Angle : 0.631 14.351 14511 Z= 0.319 Chirality : 0.043 0.385 1689 Planarity : 0.004 0.053 1826 Dihedral : 4.849 28.059 1461 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.43 % Favored : 93.49 % Rotamer: Outliers : 2.80 % Allowed : 18.32 % Favored : 78.88 % 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: -0.73 (0.23), residues: 1337 helix: 1.36 (0.27), residues: 402 sheet: -0.44 (0.28), residues: 312 loop : -1.80 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 95 HIS 0.004 0.001 HIS F 181 PHE 0.012 0.001 PHE F 71 TYR 0.015 0.001 TYR F 104 ARG 0.007 0.000 ARG B 239 *********************** 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 84 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 52 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.8826 (tpp) cc_final: 0.8153 (tpp) REVERT: B 41 MET cc_start: 0.8338 (mmm) cc_final: 0.7958 (mmm) REVERT: B 225 LYS cc_start: 0.8746 (pttm) cc_final: 0.7975 (tptp) REVERT: C 95 TRP cc_start: 0.7572 (t-100) cc_final: 0.7075 (t-100) REVERT: D 171 TRP cc_start: 0.7926 (OUTLIER) cc_final: 0.7334 (m100) REVERT: E 187 ASP cc_start: 0.8574 (OUTLIER) cc_final: 0.8275 (m-30) REVERT: F 40 VAL cc_start: 0.9443 (t) cc_final: 0.9196 (m) REVERT: F 92 GLU cc_start: 0.8062 (pm20) cc_final: 0.7703 (pp20) outliers start: 32 outliers final: 28 residues processed: 80 average time/residue: 0.1990 time to fit residues: 24.1129 Evaluate side-chains 79 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 49 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 156 TYR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 191 HIS Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 99 CYS Chi-restraints excluded: chain D residue 171 TRP Chi-restraints excluded: chain D residue 221 ASN Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 112 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 88 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 chunk 11 optimal weight: 0.5980 chunk 82 optimal weight: 0.2980 chunk 65 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 113 optimal weight: 5.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.7900 moved from start: 0.3587 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= 0.177 Angle : 0.618 14.161 14511 Z= 0.310 Chirality : 0.043 0.388 1689 Planarity : 0.004 0.051 1826 Dihedral : 4.728 26.311 1461 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.09 % Favored : 94.84 % Rotamer: Outliers : 2.63 % Allowed : 18.40 % Favored : 78.97 % 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: -0.63 (0.23), residues: 1337 helix: 1.40 (0.26), residues: 405 sheet: -0.44 (0.27), residues: 328 loop : -1.71 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 95 HIS 0.004 0.001 HIS F 181 PHE 0.012 0.001 PHE B 97 TYR 0.012 0.001 TYR F 55 ARG 0.007 0.000 ARG B 239 ********************** 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 88 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 58 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.8832 (tpp) cc_final: 0.8535 (tpp) REVERT: B 41 MET cc_start: 0.8297 (mmm) cc_final: 0.7909 (mmm) REVERT: B 45 LEU cc_start: 0.8662 (tt) cc_final: 0.8441 (tp) REVERT: B 225 LYS cc_start: 0.8649 (pttm) cc_final: 0.7957 (tptp) REVERT: C 95 TRP cc_start: 0.7477 (t-100) cc_final: 0.7037 (t-100) REVERT: D 171 TRP cc_start: 0.7909 (OUTLIER) cc_final: 0.7347 (m100) REVERT: E 102 GLN cc_start: 0.7803 (tp40) cc_final: 0.7527 (tp40) REVERT: E 187 ASP cc_start: 0.8566 (OUTLIER) cc_final: 0.8264 (m-30) REVERT: F 14 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7756 (pt) REVERT: F 40 VAL cc_start: 0.9410 (t) cc_final: 0.9161 (m) REVERT: F 92 GLU cc_start: 0.8035 (pm20) cc_final: 0.7670 (pp20) outliers start: 30 outliers final: 21 residues processed: 81 average time/residue: 0.2155 time to fit residues: 25.9565 Evaluate side-chains 79 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 55 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 156 TYR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 191 HIS Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 171 TRP Chi-restraints excluded: chain D residue 221 ASN Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 37 ILE 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: 0.1980 chunk 15 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 109 optimal weight: 0.8980 chunk 13 optimal weight: 0.4980 chunk 19 optimal weight: 4.9990 chunk 93 optimal weight: 0.3980 chunk 6 optimal weight: 10.0000 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.079672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.062366 restraints weight = 52189.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.063067 restraints weight = 35276.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.063121 restraints weight = 25904.101| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10660 Z= 0.180 Angle : 0.640 14.017 14511 Z= 0.317 Chirality : 0.043 0.388 1689 Planarity : 0.005 0.076 1826 Dihedral : 4.710 24.534 1461 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.46 % Favored : 94.47 % Rotamer: Outliers : 2.37 % Allowed : 18.67 % Favored : 78.97 % 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: -0.57 (0.23), residues: 1337 helix: 1.39 (0.26), residues: 405 sheet: -0.29 (0.27), residues: 334 loop : -1.71 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 95 HIS 0.004 0.001 HIS F 181 PHE 0.014 0.001 PHE E 120 TYR 0.024 0.001 TYR E 188 ARG 0.018 0.000 ARG A 229 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1873.41 seconds wall clock time: 35 minutes 4.48 seconds (2104.48 seconds total)