Starting phenix.real_space_refine on Sun Apr 7 14:03:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v69_31739/04_2024/7v69_31739.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v69_31739/04_2024/7v69_31739.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v69_31739/04_2024/7v69_31739.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v69_31739/04_2024/7v69_31739.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v69_31739/04_2024/7v69_31739.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v69_31739/04_2024/7v69_31739.pdb" } resolution = 3.4 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= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2134 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 65 5.16 5 C 5468 2.51 5 N 1446 2.21 5 O 1560 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 26": "OD1" <-> "OD2" Residue "S TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8539 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1649 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 69 Chain: "B" Number of atoms: 2553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2553 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 4, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Chain: "C" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 435 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "S" Number of atoms: 1746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1746 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "R" Number of atoms: 2156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2156 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 266} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 19 Time building chain proxies: 4.88, per 1000 atoms: 0.57 Number of scatterers: 8539 At special positions: 0 Unit cell: (90.48, 121.68, 122.72, 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 65 16.00 O 1560 8.00 N 1446 7.00 C 5468 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 105 " - pdb=" SG CYS R 185 " distance=2.03 Simple disulfide: pdb=" SG CYS R 426 " - pdb=" SG CYS R 429 " 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: 3.23 Conformation dependent library (CDL) restraints added in 1.7 seconds 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2104 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 13 sheets defined 39.1% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.964A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.620A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 removed outlier: 4.207A pdb=" N GLY A 203 " --> pdb=" O ASP A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.726A pdb=" N TRP A 211 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 282 through 286 removed outlier: 4.138A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.536A pdb=" N LYS A 345 " --> pdb=" O ASP A 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.616A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'C' and resid 9 through 24 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 34 through 43 Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.565A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 56 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.833A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 60 removed outlier: 3.707A pdb=" N THR R 37 " --> pdb=" O VAL R 33 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL R 38 " --> pdb=" O PHE R 34 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU R 52 " --> pdb=" O VAL R 48 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL R 53 " --> pdb=" O GLY R 49 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU R 55 " --> pdb=" O ILE R 51 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS R 58 " --> pdb=" O MET R 54 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN R 60 " --> pdb=" O SER R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 64 Processing helix chain 'R' and resid 65 through 66 No H-bonds generated for 'chain 'R' and resid 65 through 66' Processing helix chain 'R' and resid 67 through 95 removed outlier: 4.206A pdb=" N LEU R 71 " --> pdb=" O ASN R 67 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE R 84 " --> pdb=" O ILE R 80 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N MET R 86 " --> pdb=" O GLY R 82 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ASN R 87 " --> pdb=" O ALA R 83 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LYS R 95 " --> pdb=" O VAL R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 136 removed outlier: 3.594A pdb=" N CYS R 105 " --> pdb=" O GLY R 101 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ALA R 110 " --> pdb=" O ASP R 106 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR R 113 " --> pdb=" O LEU R 109 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL R 114 " --> pdb=" O ALA R 110 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL R 115 " --> pdb=" O LEU R 111 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL R 120 " --> pdb=" O SER R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 144 Processing helix chain 'R' and resid 145 through 170 removed outlier: 3.805A pdb=" N MET R 152 " --> pdb=" O MET R 148 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA R 155 " --> pdb=" O LEU R 151 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TRP R 157 " --> pdb=" O ILE R 153 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER R 160 " --> pdb=" O ALA R 156 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE R 161 " --> pdb=" O TRP R 157 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA R 165 " --> pdb=" O PHE R 161 " (cutoff:3.500A) Proline residue: R 166 - end of helix removed outlier: 3.638A pdb=" N LEU R 169 " --> pdb=" O ALA R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 170 through 176 removed outlier: 3.745A pdb=" N VAL R 175 " --> pdb=" O TRP R 171 " (cutoff:3.500A) Processing helix chain 'R' and resid 192 through 202 removed outlier: 3.734A pdb=" N GLY R 198 " --> pdb=" O ALA R 194 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA R 202 " --> pdb=" O GLY R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 204 through 222 removed outlier: 3.826A pdb=" N VAL R 213 " --> pdb=" O VAL R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 392 through 423 removed outlier: 3.705A pdb=" N ALA R 404 " --> pdb=" O ARG R 400 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA R 408 " --> pdb=" O ALA R 404 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE R 409 " --> pdb=" O ILE R 405 " (cutoff:3.500A) Proline residue: R 415 - end of helix Processing helix chain 'R' and resid 432 through 439 removed outlier: 4.029A pdb=" N SER R 436 " --> pdb=" O ASP R 432 " (cutoff:3.500A) Processing helix chain 'R' and resid 440 through 455 Proline residue: R 450 - end of helix Processing helix chain 'R' and resid 457 through 471 Processing sheet with id=AA1, first strand: chain 'A' and resid 196 through 199 removed outlier: 6.851A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.850A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.725A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 328 " --> pdb=" O GLY B 319 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY B 319 " --> pdb=" O ALA B 328 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 61 removed outlier: 6.777A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105 removed outlier: 3.607A pdb=" N ALA B 104 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 150 removed outlier: 6.836A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.631A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.370A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278 Processing sheet with id=AA9, first strand: chain 'S' and resid 4 through 7 removed outlier: 4.089A pdb=" N VAL S 5 " --> pdb=" O SER S 23 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.859A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 135 through 136 removed outlier: 6.626A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'S' and resid 144 through 148 removed outlier: 3.534A pdb=" N PHE S 200 " --> pdb=" O CYS S 147 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 174 through 177 removed outlier: 6.782A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N MET S 218 " --> pdb=" O TYR S 163 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR S 216 " --> pdb=" O PHE S 165 " (cutoff:3.500A) 363 hydrogen bonds defined for protein. 1017 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.17 Time building geometry restraints manager: 3.53 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: 2717 1.34 - 1.46: 2006 1.46 - 1.58: 3905 1.58 - 1.70: 0 1.70 - 1.81: 94 Bond restraints: 8722 Sorted by residual: bond pdb=" C GLY B 116 " pdb=" O GLY B 116 " ideal model delta sigma weight residual 1.239 1.230 0.009 8.50e-03 1.38e+04 1.08e+00 bond pdb=" C SER R 191 " pdb=" N ASN R 192 " ideal model delta sigma weight residual 1.326 1.343 -0.017 1.66e-02 3.63e+03 1.01e+00 bond pdb=" CA THR B 263 " pdb=" CB THR B 263 " ideal model delta sigma weight residual 1.529 1.542 -0.013 1.38e-02 5.25e+03 9.53e-01 bond pdb=" CA ASP B 247 " pdb=" CB ASP B 247 " ideal model delta sigma weight residual 1.529 1.546 -0.017 1.78e-02 3.16e+03 8.77e-01 bond pdb=" N GLY B 185 " pdb=" CA GLY B 185 " ideal model delta sigma weight residual 1.446 1.456 -0.010 1.08e-02 8.57e+03 8.71e-01 ... (remaining 8717 not shown) Histogram of bond angle deviations from ideal: 98.51 - 105.63: 136 105.63 - 112.75: 4686 112.75 - 119.87: 2890 119.87 - 126.99: 4042 126.99 - 134.11: 105 Bond angle restraints: 11859 Sorted by residual: angle pdb=" N SER R 428 " pdb=" CA SER R 428 " pdb=" C SER R 428 " ideal model delta sigma weight residual 114.64 109.07 5.57 1.52e+00 4.33e-01 1.34e+01 angle pdb=" CB MET B 262 " pdb=" CG MET B 262 " pdb=" SD MET B 262 " ideal model delta sigma weight residual 112.70 103.94 8.76 3.00e+00 1.11e-01 8.52e+00 angle pdb=" CA SER R 428 " pdb=" C SER R 428 " pdb=" N CYS R 429 " ideal model delta sigma weight residual 119.58 115.95 3.63 1.39e+00 5.18e-01 6.83e+00 angle pdb=" N GLY S 213 " pdb=" CA GLY S 213 " pdb=" C GLY S 213 " ideal model delta sigma weight residual 110.58 114.06 -3.48 1.35e+00 5.49e-01 6.65e+00 angle pdb=" C GLY B 131 " pdb=" N ASN B 132 " pdb=" CA ASN B 132 " ideal model delta sigma weight residual 121.54 126.35 -4.81 1.91e+00 2.74e-01 6.34e+00 ... (remaining 11854 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 4692 17.55 - 35.09: 362 35.09 - 52.64: 51 52.64 - 70.19: 6 70.19 - 87.73: 7 Dihedral angle restraints: 5118 sinusoidal: 1859 harmonic: 3259 Sorted by residual: dihedral pdb=" CB CYS R 426 " pdb=" SG CYS R 426 " pdb=" SG CYS R 429 " pdb=" CB CYS R 429 " ideal model delta sinusoidal sigma weight residual -86.00 -15.41 -70.59 1 1.00e+01 1.00e-02 6.41e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 159.77 20.23 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA PHE R 84 " pdb=" C PHE R 84 " pdb=" N SER R 85 " pdb=" CA SER R 85 " ideal model delta harmonic sigma weight residual -180.00 -161.84 -18.16 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 5115 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1055 0.046 - 0.091: 265 0.091 - 0.137: 56 0.137 - 0.182: 7 0.182 - 0.228: 2 Chirality restraints: 1385 Sorted by residual: chirality pdb=" CB ILE R 201 " pdb=" CA ILE R 201 " pdb=" CG1 ILE R 201 " pdb=" CG2 ILE R 201 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CB THR B 181 " pdb=" CA THR B 181 " pdb=" OG1 THR B 181 " pdb=" CG2 THR B 181 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB ILE B 157 " pdb=" CA ILE B 157 " pdb=" CG1 ILE B 157 " pdb=" CG2 ILE B 157 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.19e-01 ... (remaining 1382 not shown) Planarity restraints: 1483 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 247 " -0.008 2.00e-02 2.50e+03 1.54e-02 2.38e+00 pdb=" C ASP B 247 " 0.027 2.00e-02 2.50e+03 pdb=" O ASP B 247 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA B 248 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER S 172 " 0.024 5.00e-02 4.00e+02 3.68e-02 2.16e+00 pdb=" N PRO S 173 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO S 173 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO S 173 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 201 " -0.007 2.00e-02 2.50e+03 1.39e-02 1.94e+00 pdb=" C ILE R 201 " 0.024 2.00e-02 2.50e+03 pdb=" O ILE R 201 " -0.009 2.00e-02 2.50e+03 pdb=" N ALA R 202 " -0.008 2.00e-02 2.50e+03 ... (remaining 1480 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 146 2.66 - 3.22: 8107 3.22 - 3.78: 13525 3.78 - 4.34: 18262 4.34 - 4.90: 29704 Nonbonded interactions: 69744 Sorted by model distance: nonbonded pdb=" O ARG S 67 " pdb=" OG1 THR S 84 " model vdw 2.096 2.440 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.151 2.440 nonbonded pdb=" OG SER R 85 " pdb=" OD1 ASP R 112 " model vdw 2.157 2.440 nonbonded pdb=" NH1 ARG B 68 " pdb=" OD1 ASP B 83 " model vdw 2.177 2.520 nonbonded pdb=" OE1 GLN A 304 " pdb=" OG1 THR A 321 " model vdw 2.213 2.440 ... (remaining 69739 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 3.880 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 25.160 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6252 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 : 0.003 0.029 8722 Z= 0.165 Angle : 0.653 8.757 11859 Z= 0.380 Chirality : 0.042 0.228 1385 Planarity : 0.004 0.046 1483 Dihedral : 12.638 87.731 3008 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -2.02 (0.24), residues: 1104 helix: -0.52 (0.27), residues: 386 sheet: -2.17 (0.30), residues: 246 loop : -1.40 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.005 0.001 HIS S 35 PHE 0.024 0.001 PHE B 234 TYR 0.018 0.001 TYR S 103 ARG 0.005 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 0.854 Fit side-chains revert: symmetry clash REVERT: B 61 MET cc_start: 0.6117 (tmm) cc_final: 0.5842 (tmm) REVERT: B 100 VAL cc_start: 0.8258 (p) cc_final: 0.7987 (m) REVERT: B 105 TYR cc_start: 0.7505 (t80) cc_final: 0.7206 (t80) REVERT: B 129 ARG cc_start: 0.6082 (tmt-80) cc_final: 0.5026 (ttt-90) REVERT: B 155 ASN cc_start: 0.7515 (t0) cc_final: 0.7239 (t0) REVERT: B 188 MET cc_start: 0.6510 (mmm) cc_final: 0.5771 (mmm) REVERT: B 308 LEU cc_start: 0.6990 (tt) cc_final: 0.6727 (tt) REVERT: S 79 LEU cc_start: 0.7017 (tp) cc_final: 0.6810 (tp) REVERT: S 162 LEU cc_start: 0.7824 (tt) cc_final: 0.7611 (tp) REVERT: R 42 LEU cc_start: 0.6226 (mt) cc_final: 0.5975 (mt) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.2257 time to fit residues: 51.3646 Evaluate side-chains 155 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.7980 chunk 82 optimal weight: 0.0770 chunk 45 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 55 optimal weight: 0.0970 chunk 44 optimal weight: 0.8980 chunk 85 optimal weight: 0.3980 chunk 33 optimal weight: 0.0970 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 98 optimal weight: 0.5980 overall best weight: 0.2534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN ** R 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 449 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6270 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8722 Z= 0.151 Angle : 0.546 8.483 11859 Z= 0.280 Chirality : 0.041 0.151 1385 Planarity : 0.003 0.035 1483 Dihedral : 4.537 30.120 1205 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.45 % Allowed : 8.94 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.74 (0.25), residues: 1104 helix: -0.09 (0.27), residues: 388 sheet: -1.99 (0.29), residues: 261 loop : -1.42 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 169 HIS 0.003 0.001 HIS S 35 PHE 0.012 0.001 PHE R 128 TYR 0.016 0.001 TYR S 103 ARG 0.004 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 162 time to evaluate : 0.896 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7506 (mtm110) cc_final: 0.7140 (mtm110) REVERT: A 253 ILE cc_start: 0.7917 (tt) cc_final: 0.7524 (pt) REVERT: A 345 LYS cc_start: 0.7551 (mptt) cc_final: 0.7332 (mmtt) REVERT: B 61 MET cc_start: 0.6006 (tmm) cc_final: 0.5768 (tmm) REVERT: B 100 VAL cc_start: 0.8200 (p) cc_final: 0.7968 (m) REVERT: B 105 TYR cc_start: 0.7528 (t80) cc_final: 0.7235 (t80) REVERT: B 129 ARG cc_start: 0.6129 (tmt-80) cc_final: 0.4934 (ttt-90) REVERT: B 155 ASN cc_start: 0.7582 (t0) cc_final: 0.7248 (t0) REVERT: B 188 MET cc_start: 0.6465 (mmm) cc_final: 0.5936 (mmm) REVERT: B 217 MET cc_start: 0.6572 (OUTLIER) cc_final: 0.6349 (ptp) REVERT: B 247 ASP cc_start: 0.6308 (t0) cc_final: 0.6039 (t0) REVERT: B 290 ASP cc_start: 0.6987 (m-30) cc_final: 0.6734 (m-30) REVERT: B 300 LEU cc_start: 0.7119 (mt) cc_final: 0.6907 (mt) REVERT: B 325 MET cc_start: 0.7203 (tpt) cc_final: 0.6955 (tpt) REVERT: C 42 GLU cc_start: 0.6042 (pp20) cc_final: 0.5719 (pp20) REVERT: S 90 ASP cc_start: 0.6745 (m-30) cc_final: 0.6511 (m-30) REVERT: S 128 MET cc_start: 0.7015 (mmm) cc_final: 0.6003 (mmm) REVERT: R 42 LEU cc_start: 0.6250 (mt) cc_final: 0.5995 (mt) REVERT: R 186 PHE cc_start: 0.6211 (p90) cc_final: 0.5958 (p90) outliers start: 13 outliers final: 9 residues processed: 163 average time/residue: 0.2069 time to fit residues: 47.0312 Evaluate side-chains 169 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 159 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 126 ILE Chi-restraints excluded: chain R residue 152 MET Chi-restraints excluded: chain R residue 174 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 0.0980 chunk 30 optimal weight: 2.9990 chunk 82 optimal weight: 0.4980 chunk 67 optimal weight: 4.9990 chunk 27 optimal weight: 0.0970 chunk 99 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 88 optimal weight: 0.0980 chunk 98 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN S 157 ASN R 423 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6279 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8722 Z= 0.150 Angle : 0.520 7.482 11859 Z= 0.265 Chirality : 0.040 0.144 1385 Planarity : 0.003 0.036 1483 Dihedral : 4.377 29.207 1205 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.79 % Allowed : 10.84 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.52 (0.25), residues: 1104 helix: 0.21 (0.27), residues: 386 sheet: -1.97 (0.29), residues: 261 loop : -1.34 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 98 HIS 0.003 0.001 HIS A 213 PHE 0.011 0.001 PHE B 235 TYR 0.014 0.001 TYR S 103 ARG 0.006 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 167 time to evaluate : 0.917 Fit side-chains REVERT: A 210 LYS cc_start: 0.8040 (mmmm) cc_final: 0.7719 (mmmm) REVERT: B 61 MET cc_start: 0.6065 (tmm) cc_final: 0.5826 (tmm) REVERT: B 100 VAL cc_start: 0.8204 (p) cc_final: 0.7948 (m) REVERT: B 105 TYR cc_start: 0.7618 (t80) cc_final: 0.7323 (t80) REVERT: B 129 ARG cc_start: 0.6192 (tmt-80) cc_final: 0.4822 (ttt-90) REVERT: B 155 ASN cc_start: 0.7615 (t0) cc_final: 0.7290 (t0) REVERT: B 217 MET cc_start: 0.6604 (OUTLIER) cc_final: 0.6370 (ptp) REVERT: B 247 ASP cc_start: 0.6475 (t0) cc_final: 0.6120 (t0) REVERT: B 325 MET cc_start: 0.7198 (tpt) cc_final: 0.6936 (tpt) REVERT: S 128 MET cc_start: 0.7017 (mmm) cc_final: 0.6240 (mmm) REVERT: R 42 LEU cc_start: 0.6256 (mt) cc_final: 0.5979 (mt) outliers start: 25 outliers final: 14 residues processed: 173 average time/residue: 0.2104 time to fit residues: 49.5558 Evaluate side-chains 180 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 165 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 126 ILE Chi-restraints excluded: chain R residue 152 MET Chi-restraints excluded: chain R residue 174 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 47 optimal weight: 0.0670 chunk 66 optimal weight: 0.4980 chunk 99 optimal weight: 2.9990 chunk 105 optimal weight: 0.0000 chunk 94 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 overall best weight: 0.4522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6310 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8722 Z= 0.174 Angle : 0.529 7.350 11859 Z= 0.269 Chirality : 0.041 0.144 1385 Planarity : 0.003 0.036 1483 Dihedral : 4.401 30.176 1205 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.91 % Allowed : 14.75 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.36 (0.25), residues: 1104 helix: 0.36 (0.27), residues: 386 sheet: -1.86 (0.29), residues: 264 loop : -1.28 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 98 HIS 0.004 0.001 HIS C 44 PHE 0.015 0.001 PHE B 235 TYR 0.015 0.001 TYR S 60 ARG 0.005 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 165 time to evaluate : 0.971 Fit side-chains REVERT: A 210 LYS cc_start: 0.7991 (mmmm) cc_final: 0.7543 (mmmm) REVERT: A 221 ILE cc_start: 0.7955 (mt) cc_final: 0.7702 (mt) REVERT: B 61 MET cc_start: 0.6234 (tmm) cc_final: 0.5968 (tmm) REVERT: B 100 VAL cc_start: 0.8238 (p) cc_final: 0.7976 (m) REVERT: B 105 TYR cc_start: 0.7716 (t80) cc_final: 0.7515 (t80) REVERT: B 151 PHE cc_start: 0.7935 (OUTLIER) cc_final: 0.7346 (m-80) REVERT: B 247 ASP cc_start: 0.6612 (t0) cc_final: 0.6159 (t0) REVERT: B 314 ARG cc_start: 0.8128 (ttm170) cc_final: 0.7799 (ttm170) REVERT: B 325 MET cc_start: 0.7170 (tpt) cc_final: 0.6884 (tpt) REVERT: S 180 MET cc_start: 0.5060 (OUTLIER) cc_final: 0.4738 (tmm) REVERT: R 42 LEU cc_start: 0.6279 (mt) cc_final: 0.6001 (mt) outliers start: 26 outliers final: 16 residues processed: 170 average time/residue: 0.2451 time to fit residues: 55.7041 Evaluate side-chains 182 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 164 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 126 ILE Chi-restraints excluded: chain R residue 174 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 89 optimal weight: 0.0470 chunk 72 optimal weight: 0.0030 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.5088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6328 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8722 Z= 0.186 Angle : 0.541 8.551 11859 Z= 0.273 Chirality : 0.041 0.138 1385 Planarity : 0.003 0.037 1483 Dihedral : 4.434 30.718 1205 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.02 % Allowed : 16.65 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.23 (0.25), residues: 1104 helix: 0.43 (0.27), residues: 386 sheet: -1.78 (0.29), residues: 277 loop : -1.12 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 98 HIS 0.004 0.001 HIS S 35 PHE 0.016 0.001 PHE B 235 TYR 0.015 0.001 TYR S 60 ARG 0.005 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 173 time to evaluate : 0.912 Fit side-chains REVERT: A 210 LYS cc_start: 0.7943 (mmmm) cc_final: 0.7561 (mmmm) REVERT: B 61 MET cc_start: 0.6297 (tmm) cc_final: 0.6026 (tmm) REVERT: B 100 VAL cc_start: 0.8207 (p) cc_final: 0.7998 (m) REVERT: B 105 TYR cc_start: 0.7728 (t80) cc_final: 0.7506 (t80) REVERT: B 151 PHE cc_start: 0.8028 (OUTLIER) cc_final: 0.7391 (m-80) REVERT: B 247 ASP cc_start: 0.6596 (t0) cc_final: 0.6348 (t0) REVERT: B 314 ARG cc_start: 0.8168 (ttm170) cc_final: 0.7828 (ttm170) REVERT: S 32 PHE cc_start: 0.8206 (m-80) cc_final: 0.7460 (m-80) REVERT: S 180 MET cc_start: 0.4870 (OUTLIER) cc_final: 0.4555 (tmm) REVERT: R 42 LEU cc_start: 0.6367 (mt) cc_final: 0.6081 (mt) REVERT: R 163 LEU cc_start: 0.5189 (OUTLIER) cc_final: 0.4937 (mm) outliers start: 27 outliers final: 19 residues processed: 181 average time/residue: 0.2126 time to fit residues: 52.9472 Evaluate side-chains 195 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 173 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 126 ILE Chi-restraints excluded: chain R residue 152 MET Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 174 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 105 optimal weight: 0.0060 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 55 optimal weight: 0.0030 chunk 101 optimal weight: 4.9990 overall best weight: 0.4606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN S 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6327 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8722 Z= 0.171 Angle : 0.532 7.332 11859 Z= 0.268 Chirality : 0.041 0.141 1385 Planarity : 0.003 0.038 1483 Dihedral : 4.429 31.434 1205 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.91 % Allowed : 16.42 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.13 (0.25), residues: 1104 helix: 0.53 (0.27), residues: 387 sheet: -1.69 (0.29), residues: 277 loop : -1.11 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 98 HIS 0.004 0.001 HIS S 35 PHE 0.014 0.001 PHE B 235 TYR 0.014 0.001 TYR S 60 ARG 0.004 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 172 time to evaluate : 0.891 Fit side-chains REVERT: A 24 ARG cc_start: 0.7487 (mtm110) cc_final: 0.7054 (mtm110) REVERT: A 210 LYS cc_start: 0.7961 (mmmm) cc_final: 0.7624 (mmmm) REVERT: B 14 LEU cc_start: 0.7172 (OUTLIER) cc_final: 0.6892 (mt) REVERT: B 61 MET cc_start: 0.6337 (tmm) cc_final: 0.6033 (tmm) REVERT: B 105 TYR cc_start: 0.7726 (t80) cc_final: 0.7500 (t80) REVERT: B 151 PHE cc_start: 0.7978 (OUTLIER) cc_final: 0.7308 (m-80) REVERT: B 247 ASP cc_start: 0.6562 (t0) cc_final: 0.6326 (t0) REVERT: B 284 LEU cc_start: 0.7463 (mt) cc_final: 0.7260 (mt) REVERT: B 314 ARG cc_start: 0.8166 (ttm170) cc_final: 0.7822 (ttm170) REVERT: S 32 PHE cc_start: 0.8198 (m-80) cc_final: 0.7472 (m-80) REVERT: S 180 MET cc_start: 0.4960 (OUTLIER) cc_final: 0.4656 (tmm) REVERT: R 42 LEU cc_start: 0.6423 (mt) cc_final: 0.6137 (mt) REVERT: R 419 MET cc_start: 0.2424 (tpt) cc_final: 0.1746 (tpt) outliers start: 35 outliers final: 21 residues processed: 188 average time/residue: 0.2110 time to fit residues: 54.3182 Evaluate side-chains 195 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 171 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 126 ILE Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 175 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 chunk 58 optimal weight: 0.1980 chunk 105 optimal weight: 0.9990 chunk 65 optimal weight: 0.0270 chunk 64 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN S 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6332 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8722 Z= 0.178 Angle : 0.538 8.494 11859 Z= 0.272 Chirality : 0.041 0.171 1385 Planarity : 0.003 0.038 1483 Dihedral : 4.417 32.104 1205 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.25 % Allowed : 16.65 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.05 (0.26), residues: 1104 helix: 0.60 (0.28), residues: 385 sheet: -1.64 (0.29), residues: 276 loop : -1.07 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 98 HIS 0.004 0.001 HIS A 213 PHE 0.015 0.001 PHE B 235 TYR 0.014 0.001 TYR S 60 ARG 0.004 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 171 time to evaluate : 0.815 Fit side-chains REVERT: A 24 ARG cc_start: 0.7487 (mtm110) cc_final: 0.7059 (mtm110) REVERT: A 210 LYS cc_start: 0.7974 (mmmm) cc_final: 0.7566 (mmmm) REVERT: A 221 ILE cc_start: 0.7972 (mt) cc_final: 0.7731 (mt) REVERT: B 14 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6882 (mt) REVERT: B 61 MET cc_start: 0.6354 (tmm) cc_final: 0.6045 (tmm) REVERT: B 105 TYR cc_start: 0.7717 (t80) cc_final: 0.7490 (t80) REVERT: B 151 PHE cc_start: 0.7975 (OUTLIER) cc_final: 0.7296 (m-80) REVERT: B 155 ASN cc_start: 0.7442 (t0) cc_final: 0.7052 (t0) REVERT: B 163 ASP cc_start: 0.7920 (OUTLIER) cc_final: 0.7514 (p0) REVERT: B 247 ASP cc_start: 0.6538 (t0) cc_final: 0.6309 (t0) REVERT: S 32 PHE cc_start: 0.8202 (m-80) cc_final: 0.7419 (m-80) REVERT: S 180 MET cc_start: 0.4744 (OUTLIER) cc_final: 0.4374 (tmm) REVERT: R 42 LEU cc_start: 0.6437 (mt) cc_final: 0.6154 (mt) REVERT: R 419 MET cc_start: 0.2551 (tpt) cc_final: 0.1895 (tpt) outliers start: 38 outliers final: 25 residues processed: 190 average time/residue: 0.2023 time to fit residues: 53.0433 Evaluate side-chains 198 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 169 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 126 ILE Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 175 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.0570 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 71 optimal weight: 0.0970 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 82 optimal weight: 9.9990 chunk 95 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.5896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6348 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8722 Z= 0.201 Angle : 0.559 8.112 11859 Z= 0.282 Chirality : 0.041 0.155 1385 Planarity : 0.003 0.038 1483 Dihedral : 4.525 32.068 1205 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.25 % Allowed : 16.76 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.01 (0.26), residues: 1104 helix: 0.60 (0.27), residues: 385 sheet: -1.58 (0.30), residues: 276 loop : -1.05 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 98 HIS 0.005 0.001 HIS B 54 PHE 0.016 0.001 PHE B 235 TYR 0.013 0.001 TYR S 60 ARG 0.005 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 165 time to evaluate : 0.851 Fit side-chains REVERT: A 210 LYS cc_start: 0.7875 (mmmm) cc_final: 0.7444 (mmmm) REVERT: A 221 ILE cc_start: 0.7948 (mt) cc_final: 0.7714 (mt) REVERT: B 14 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6886 (mt) REVERT: B 61 MET cc_start: 0.6374 (tmm) cc_final: 0.6061 (tmm) REVERT: B 105 TYR cc_start: 0.7722 (t80) cc_final: 0.7422 (t80) REVERT: B 151 PHE cc_start: 0.7921 (OUTLIER) cc_final: 0.7005 (m-10) REVERT: B 155 ASN cc_start: 0.7407 (t0) cc_final: 0.7069 (t0) REVERT: B 163 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7540 (p0) REVERT: B 247 ASP cc_start: 0.6545 (t0) cc_final: 0.6320 (t0) REVERT: S 180 MET cc_start: 0.4938 (OUTLIER) cc_final: 0.4529 (tmm) REVERT: R 42 LEU cc_start: 0.6443 (mt) cc_final: 0.6181 (mt) REVERT: R 419 MET cc_start: 0.2581 (tpt) cc_final: 0.1848 (tpt) outliers start: 38 outliers final: 26 residues processed: 183 average time/residue: 0.2018 time to fit residues: 50.6231 Evaluate side-chains 195 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 165 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 221 LEU Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 126 ILE Chi-restraints excluded: chain R residue 152 MET Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 175 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.1980 chunk 100 optimal weight: 1.9990 chunk 58 optimal weight: 0.0670 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 30 optimal weight: 0.4980 chunk 88 optimal weight: 0.3980 chunk 92 optimal weight: 0.3980 chunk 64 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 overall best weight: 0.3118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6309 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8722 Z= 0.143 Angle : 0.539 8.140 11859 Z= 0.269 Chirality : 0.041 0.245 1385 Planarity : 0.003 0.039 1483 Dihedral : 4.337 32.716 1205 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.58 % Allowed : 18.32 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.87 (0.26), residues: 1104 helix: 0.73 (0.28), residues: 387 sheet: -1.54 (0.29), residues: 278 loop : -0.96 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP S 36 HIS 0.004 0.001 HIS A 213 PHE 0.016 0.001 PHE S 27 TYR 0.012 0.001 TYR S 60 ARG 0.006 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 162 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: A 221 ILE cc_start: 0.7862 (mt) cc_final: 0.7619 (mt) REVERT: B 14 LEU cc_start: 0.7128 (OUTLIER) cc_final: 0.6869 (mt) REVERT: B 61 MET cc_start: 0.6311 (tmm) cc_final: 0.6011 (tmm) REVERT: B 151 PHE cc_start: 0.7906 (OUTLIER) cc_final: 0.7033 (m-10) REVERT: B 155 ASN cc_start: 0.7419 (t0) cc_final: 0.7032 (t0) REVERT: B 163 ASP cc_start: 0.7922 (OUTLIER) cc_final: 0.7525 (p0) REVERT: R 42 LEU cc_start: 0.6424 (mt) cc_final: 0.6142 (mt) REVERT: R 216 ILE cc_start: 0.7654 (mm) cc_final: 0.7448 (mm) REVERT: R 419 MET cc_start: 0.2513 (tpt) cc_final: 0.1829 (tpt) outliers start: 32 outliers final: 25 residues processed: 178 average time/residue: 0.2140 time to fit residues: 52.2434 Evaluate side-chains 188 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 160 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 221 LEU Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 152 MET Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 175 VAL Chi-restraints excluded: chain R residue 183 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 chunk 99 optimal weight: 0.2980 chunk 86 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 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 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6356 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8722 Z= 0.223 Angle : 0.576 8.102 11859 Z= 0.294 Chirality : 0.042 0.172 1385 Planarity : 0.004 0.038 1483 Dihedral : 4.582 32.360 1205 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.58 % Allowed : 18.77 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.96 (0.26), residues: 1104 helix: 0.60 (0.27), residues: 390 sheet: -1.61 (0.29), residues: 281 loop : -0.92 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 98 HIS 0.005 0.001 HIS B 54 PHE 0.021 0.001 PHE S 27 TYR 0.014 0.001 TYR S 178 ARG 0.006 0.000 ARG B 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 164 time to evaluate : 0.860 Fit side-chains REVERT: A 210 LYS cc_start: 0.7896 (mmmm) cc_final: 0.7561 (mmmm) REVERT: A 221 ILE cc_start: 0.7984 (mt) cc_final: 0.7755 (mt) REVERT: A 260 THR cc_start: 0.8438 (p) cc_final: 0.8229 (m) REVERT: B 14 LEU cc_start: 0.7189 (OUTLIER) cc_final: 0.6896 (mt) REVERT: B 61 MET cc_start: 0.6422 (tmm) cc_final: 0.6089 (tmm) REVERT: B 105 TYR cc_start: 0.7727 (t80) cc_final: 0.7394 (t80) REVERT: B 118 ASP cc_start: 0.7011 (OUTLIER) cc_final: 0.6689 (p0) REVERT: B 120 ILE cc_start: 0.7272 (mm) cc_final: 0.6881 (mt) REVERT: B 151 PHE cc_start: 0.7894 (OUTLIER) cc_final: 0.7027 (m-10) REVERT: R 42 LEU cc_start: 0.6441 (mt) cc_final: 0.6172 (mt) REVERT: R 419 MET cc_start: 0.2734 (tpt) cc_final: 0.2006 (tpt) outliers start: 32 outliers final: 26 residues processed: 179 average time/residue: 0.2158 time to fit residues: 53.1149 Evaluate side-chains 193 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 164 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 221 LEU Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 175 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 76 optimal weight: 0.4980 chunk 4 optimal weight: 0.8980 chunk 62 optimal weight: 0.0270 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 13 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 = 0.4187 r_free = 0.4187 target = 0.181081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.165304 restraints weight = 12674.990| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 1.80 r_work: 0.3926 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3800 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8722 Z= 0.204 Angle : 0.571 8.316 11859 Z= 0.290 Chirality : 0.042 0.207 1385 Planarity : 0.003 0.039 1483 Dihedral : 4.590 32.994 1205 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.46 % Allowed : 18.77 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.96 (0.26), residues: 1104 helix: 0.61 (0.27), residues: 389 sheet: -1.60 (0.29), residues: 281 loop : -0.94 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 98 HIS 0.005 0.001 HIS B 54 PHE 0.018 0.001 PHE S 27 TYR 0.014 0.001 TYR S 60 ARG 0.006 0.000 ARG B 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2319.89 seconds wall clock time: 43 minutes 13.07 seconds (2593.07 seconds total)