Starting phenix.real_space_refine on Wed Sep 25 11:23:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v69_31739/09_2024/7v69_31739.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v69_31739/09_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_31739/09_2024/7v69_31739.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v69_31739/09_2024/7v69_31739.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v69_31739/09_2024/7v69_31739.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v69_31739/09_2024/7v69_31739.cif" } 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. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 5.34, per 1000 atoms: 0.63 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 - 3.00 Amino acid : True - 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: 2.13 Conformation dependent library (CDL) restraints added in 1.0 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: 1.00 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: 2.39 Time building geometry restraints manager: 2.49 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: 0.00 - 1.75: 11580 1.75 - 3.50: 241 3.50 - 5.25: 28 5.25 - 7.01: 9 7.01 - 8.76: 1 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 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.151 3.040 nonbonded pdb=" OG SER R 85 " pdb=" OD1 ASP R 112 " model vdw 2.157 3.040 nonbonded pdb=" NH1 ARG B 68 " pdb=" OD1 ASP B 83 " model vdw 2.177 3.120 nonbonded pdb=" OE1 GLN A 304 " pdb=" OG1 THR A 321 " model vdw 2.213 3.040 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 22.230 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.160 ------------------------------------------------------------------------------- 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 : 0.878 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: 0.2268 time to fit residues: 51.6243 Evaluate side-chains 155 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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: 1.9990 chunk 82 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 98 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 110 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN S 39 GLN ** R 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6351 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8722 Z= 0.250 Angle : 0.618 8.825 11859 Z= 0.322 Chirality : 0.044 0.147 1385 Planarity : 0.004 0.037 1483 Dihedral : 4.949 29.012 1205 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.56 % Allowed : 9.72 % Favored : 88.72 % 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: -1.93 (0.24), residues: 1104 helix: -0.28 (0.26), residues: 384 sheet: -2.18 (0.28), residues: 265 loop : -1.41 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 98 HIS 0.006 0.001 HIS C 44 PHE 0.021 0.002 PHE B 235 TYR 0.018 0.002 TYR B 264 ARG 0.004 0.001 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 189 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 175 time to evaluate : 0.923 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7523 (mtm110) cc_final: 0.7135 (mtm110) REVERT: A 210 LYS cc_start: 0.8160 (mmmm) cc_final: 0.7949 (mmmm) REVERT: A 253 ILE cc_start: 0.7956 (tt) cc_final: 0.7580 (pt) REVERT: B 61 MET cc_start: 0.6224 (tmm) cc_final: 0.5811 (tmm) REVERT: B 100 VAL cc_start: 0.8268 (p) cc_final: 0.8033 (m) REVERT: B 105 TYR cc_start: 0.7607 (t80) cc_final: 0.7272 (t80) REVERT: B 217 MET cc_start: 0.6560 (OUTLIER) cc_final: 0.6346 (ptp) REVERT: B 247 ASP cc_start: 0.6481 (t0) cc_final: 0.6186 (t0) REVERT: B 255 LEU cc_start: 0.7676 (mt) cc_final: 0.7461 (mt) REVERT: B 271 CYS cc_start: 0.6654 (p) cc_final: 0.6339 (p) REVERT: B 300 LEU cc_start: 0.7170 (mt) cc_final: 0.6878 (mt) REVERT: B 325 MET cc_start: 0.7216 (tpt) cc_final: 0.6992 (tpt) REVERT: C 42 GLU cc_start: 0.6069 (pp20) cc_final: 0.5857 (pp20) REVERT: S 67 ARG cc_start: 0.4706 (ptt180) cc_final: 0.4341 (ttp-170) REVERT: R 42 LEU cc_start: 0.6272 (mt) cc_final: 0.6013 (mt) outliers start: 14 outliers final: 10 residues processed: 177 average time/residue: 0.2041 time to fit residues: 49.4635 Evaluate side-chains 172 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 161 time to evaluate : 0.913 ------------------------------------------------------------------------------- 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 81 LEU Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 115 THR 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: 0.0670 chunk 30 optimal weight: 2.9990 chunk 82 optimal weight: 0.0970 chunk 67 optimal weight: 0.6980 chunk 27 optimal weight: 0.2980 chunk 99 optimal weight: 1.9990 chunk 107 optimal weight: 0.4980 chunk 88 optimal weight: 0.2980 chunk 98 optimal weight: 0.3980 chunk 33 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 overall best weight: 0.2316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN R 423 ASN R 449 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6291 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8722 Z= 0.147 Angle : 0.540 8.133 11859 Z= 0.276 Chirality : 0.041 0.149 1385 Planarity : 0.003 0.037 1483 Dihedral : 4.551 30.117 1205 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.35 % Allowed : 13.07 % Favored : 84.58 % 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: -1.66 (0.25), residues: 1104 helix: 0.07 (0.27), residues: 386 sheet: -2.09 (0.28), residues: 258 loop : -1.36 (0.28), residues: 460 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 0.010 0.001 PHE R 186 TYR 0.015 0.001 TYR S 163 ARG 0.002 0.000 ARG B 219 *********************** 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 193 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 172 time to evaluate : 0.859 Fit side-chains revert: symmetry clash REVERT: A 210 LYS cc_start: 0.8177 (mmmm) cc_final: 0.7960 (mmmm) REVERT: B 61 MET cc_start: 0.6153 (tmm) cc_final: 0.5859 (tmm) REVERT: B 79 LEU cc_start: 0.8045 (tt) cc_final: 0.7821 (tp) REVERT: B 100 VAL cc_start: 0.8183 (p) cc_final: 0.7942 (t) REVERT: B 105 TYR cc_start: 0.7612 (t80) cc_final: 0.7330 (t80) REVERT: B 118 ASP cc_start: 0.7033 (p0) cc_final: 0.6637 (p0) REVERT: B 129 ARG cc_start: 0.6323 (tmt-80) cc_final: 0.4981 (ttt-90) REVERT: B 246 ASP cc_start: 0.6402 (m-30) cc_final: 0.6084 (m-30) REVERT: B 247 ASP cc_start: 0.6344 (t0) cc_final: 0.6028 (t0) REVERT: B 271 CYS cc_start: 0.6654 (p) cc_final: 0.6450 (p) REVERT: B 290 ASP cc_start: 0.6977 (m-30) cc_final: 0.6728 (m-30) REVERT: B 325 MET cc_start: 0.7172 (tpt) cc_final: 0.6908 (tpt) REVERT: R 42 LEU cc_start: 0.6285 (mt) cc_final: 0.6074 (mt) REVERT: R 186 PHE cc_start: 0.6253 (p90) cc_final: 0.5725 (p90) outliers start: 21 outliers final: 14 residues processed: 178 average time/residue: 0.2078 time to fit residues: 50.2990 Evaluate side-chains 182 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 168 time to evaluate : 0.833 ------------------------------------------------------------------------------- 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 133 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 157 ASN Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain R residue 112 ASP Chi-restraints excluded: chain R residue 123 LEU 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: 0.9980 chunk 74 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 99 optimal weight: 0.0020 chunk 105 optimal weight: 0.0030 chunk 94 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS B 237 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6324 moved from start: 0.1996 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= 0.179 Angle : 0.543 7.240 11859 Z= 0.278 Chirality : 0.041 0.138 1385 Planarity : 0.003 0.037 1483 Dihedral : 4.516 30.978 1205 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.24 % Allowed : 14.75 % Favored : 82.01 % 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: -1.44 (0.25), residues: 1104 helix: 0.26 (0.27), residues: 386 sheet: -1.96 (0.29), residues: 264 loop : -1.24 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.015 0.001 PHE B 235 TYR 0.015 0.001 TYR S 60 ARG 0.005 0.000 ARG B 219 *********************** 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 197 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 168 time to evaluate : 0.884 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7502 (mtm110) cc_final: 0.7251 (mtm110) REVERT: A 210 LYS cc_start: 0.8179 (mmmm) cc_final: 0.7942 (mmmm) REVERT: B 61 MET cc_start: 0.6336 (tmm) cc_final: 0.5966 (tmm) REVERT: B 79 LEU cc_start: 0.8073 (tt) cc_final: 0.7863 (tp) REVERT: B 100 VAL cc_start: 0.8238 (p) cc_final: 0.8014 (m) REVERT: B 118 ASP cc_start: 0.6986 (p0) cc_final: 0.6634 (p0) REVERT: B 151 PHE cc_start: 0.8080 (OUTLIER) cc_final: 0.7539 (m-80) REVERT: B 161 SER cc_start: 0.7799 (m) cc_final: 0.7520 (p) REVERT: B 246 ASP cc_start: 0.6535 (m-30) cc_final: 0.6216 (m-30) REVERT: B 247 ASP cc_start: 0.6481 (t0) cc_final: 0.6055 (t0) REVERT: S 78 THR cc_start: 0.7634 (p) cc_final: 0.7264 (m) REVERT: S 128 MET cc_start: 0.6929 (mmm) cc_final: 0.6417 (mmm) REVERT: S 180 MET cc_start: 0.4929 (OUTLIER) cc_final: 0.4557 (tmm) REVERT: R 42 LEU cc_start: 0.6315 (mt) cc_final: 0.6098 (mt) REVERT: R 186 PHE cc_start: 0.6290 (p90) cc_final: 0.5884 (p90) outliers start: 29 outliers final: 19 residues processed: 178 average time/residue: 0.2090 time to fit residues: 50.4875 Evaluate side-chains 191 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 170 time to evaluate : 0.868 ------------------------------------------------------------------------------- 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 B residue 133 VAL 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 S residue 81 LEU Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 157 ASN 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 112 ASP Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 126 ILE Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 175 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN S 39 GLN ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6399 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8722 Z= 0.307 Angle : 0.624 8.374 11859 Z= 0.322 Chirality : 0.044 0.144 1385 Planarity : 0.004 0.043 1483 Dihedral : 4.966 31.170 1205 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.80 % Allowed : 15.75 % Favored : 80.45 % 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: -1.53 (0.25), residues: 1104 helix: 0.17 (0.27), residues: 385 sheet: -2.04 (0.28), residues: 279 loop : -1.19 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 82 HIS 0.010 0.002 HIS B 225 PHE 0.025 0.002 PHE B 235 TYR 0.017 0.002 TYR S 178 ARG 0.003 0.000 ARG B 219 *********************** 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 202 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 168 time to evaluate : 0.828 Fit side-chains revert: symmetry clash REVERT: A 210 LYS cc_start: 0.8090 (mmmm) cc_final: 0.7707 (mmmm) REVERT: B 61 MET cc_start: 0.6485 (tmm) cc_final: 0.6164 (tmm) REVERT: B 100 VAL cc_start: 0.8299 (p) cc_final: 0.8067 (m) REVERT: B 118 ASP cc_start: 0.7014 (p0) cc_final: 0.6731 (p0) REVERT: B 151 PHE cc_start: 0.8046 (OUTLIER) cc_final: 0.7490 (m-80) REVERT: B 247 ASP cc_start: 0.6577 (t0) cc_final: 0.6375 (t0) REVERT: B 271 CYS cc_start: 0.6593 (p) cc_final: 0.6346 (p) REVERT: S 32 PHE cc_start: 0.8105 (m-80) cc_final: 0.7146 (m-80) REVERT: S 180 MET cc_start: 0.5470 (OUTLIER) cc_final: 0.5018 (tmm) REVERT: R 42 LEU cc_start: 0.6347 (mt) cc_final: 0.6066 (mt) REVERT: R 71 LEU cc_start: 0.6224 (tt) cc_final: 0.5916 (tt) outliers start: 34 outliers final: 22 residues processed: 183 average time/residue: 0.1836 time to fit residues: 47.0431 Evaluate side-chains 194 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 170 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain B residue 133 VAL 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 318 LEU Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 157 ASN 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 112 ASP 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 175 VAL Chi-restraints excluded: chain R residue 442 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 105 optimal weight: 0.0170 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 0.4980 chunk 55 optimal weight: 0.9980 chunk 101 optimal weight: 0.0980 overall best weight: 0.4818 ------------------------------------------------------------------------------- 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** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6353 moved from start: 0.2437 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= 0.186 Angle : 0.570 7.724 11859 Z= 0.288 Chirality : 0.042 0.148 1385 Planarity : 0.003 0.038 1483 Dihedral : 4.696 31.893 1205 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.58 % Allowed : 16.87 % Favored : 79.55 % 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: -1.34 (0.25), residues: 1104 helix: 0.37 (0.27), residues: 386 sheet: -1.98 (0.28), residues: 276 loop : -1.12 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 98 HIS 0.004 0.001 HIS B 54 PHE 0.013 0.001 PHE B 235 TYR 0.016 0.001 TYR S 60 ARG 0.006 0.000 ARG B 219 *********************** 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 211 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 179 time to evaluate : 0.755 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7492 (mtm110) cc_final: 0.7279 (mtm110) REVERT: A 210 LYS cc_start: 0.8102 (mmmm) cc_final: 0.7731 (mmmm) REVERT: B 61 MET cc_start: 0.6386 (tmm) cc_final: 0.6079 (tmm) REVERT: B 100 VAL cc_start: 0.8192 (p) cc_final: 0.7966 (t) REVERT: B 118 ASP cc_start: 0.6975 (p0) cc_final: 0.6657 (p0) REVERT: B 151 PHE cc_start: 0.8020 (OUTLIER) cc_final: 0.7415 (m-80) REVERT: B 155 ASN cc_start: 0.7351 (t0) cc_final: 0.7035 (t0) REVERT: B 161 SER cc_start: 0.7702 (m) cc_final: 0.7446 (p) REVERT: B 247 ASP cc_start: 0.6411 (t0) cc_final: 0.6202 (t0) REVERT: S 32 PHE cc_start: 0.8110 (m-80) cc_final: 0.7106 (m-80) REVERT: R 42 LEU cc_start: 0.6317 (mt) cc_final: 0.6058 (mt) REVERT: R 186 PHE cc_start: 0.6505 (p90) cc_final: 0.6178 (p90) REVERT: R 419 MET cc_start: 0.2652 (tpt) cc_final: 0.1928 (tpt) outliers start: 32 outliers final: 22 residues processed: 193 average time/residue: 0.2109 time to fit residues: 55.3965 Evaluate side-chains 195 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 172 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 B residue 133 VAL 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 318 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 157 ASN Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 221 LEU Chi-restraints excluded: chain R residue 112 ASP 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 Chi-restraints excluded: chain R residue 190 LEU 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: 3.9990 chunk 77 optimal weight: 0.0370 chunk 59 optimal weight: 0.6980 chunk 88 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 65 optimal weight: 0.0040 chunk 64 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 overall best weight: 0.3870 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6335 moved from start: 0.2544 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= 0.170 Angle : 0.569 8.085 11859 Z= 0.286 Chirality : 0.042 0.221 1385 Planarity : 0.003 0.039 1483 Dihedral : 4.547 32.883 1205 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.02 % Allowed : 17.65 % Favored : 78.32 % 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: -1.20 (0.25), residues: 1104 helix: 0.52 (0.27), residues: 387 sheet: -1.89 (0.28), residues: 276 loop : -1.08 (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 0.011 0.001 PHE B 235 TYR 0.014 0.001 TYR S 103 ARG 0.005 0.000 ARG B 49 *********************** 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 204 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 168 time to evaluate : 1.150 Fit side-chains revert: symmetry clash REVERT: A 210 LYS cc_start: 0.8140 (mmmm) cc_final: 0.7744 (mmmm) REVERT: B 61 MET cc_start: 0.6444 (tmm) cc_final: 0.6174 (tmm) REVERT: B 79 LEU cc_start: 0.7981 (tt) cc_final: 0.7761 (tp) REVERT: B 100 VAL cc_start: 0.8186 (p) cc_final: 0.7956 (t) REVERT: B 151 PHE cc_start: 0.8024 (OUTLIER) cc_final: 0.7420 (m-80) REVERT: B 155 ASN cc_start: 0.7339 (t0) cc_final: 0.6989 (t0) REVERT: B 247 ASP cc_start: 0.6288 (t0) cc_final: 0.6060 (t0) REVERT: B 276 VAL cc_start: 0.7746 (OUTLIER) cc_final: 0.7513 (t) REVERT: S 32 PHE cc_start: 0.8085 (m-80) cc_final: 0.7094 (m-80) REVERT: S 157 ASN cc_start: 0.7333 (OUTLIER) cc_final: 0.7020 (p0) REVERT: R 42 LEU cc_start: 0.6361 (mt) cc_final: 0.6131 (mt) REVERT: R 186 PHE cc_start: 0.6438 (p90) cc_final: 0.6196 (p90) REVERT: R 419 MET cc_start: 0.2598 (tpt) cc_final: 0.1877 (tpt) outliers start: 36 outliers final: 25 residues processed: 185 average time/residue: 0.2025 time to fit residues: 52.1629 Evaluate side-chains 192 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 164 time to evaluate : 0.862 ------------------------------------------------------------------------------- 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 B residue 133 VAL 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 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 157 ASN 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 112 ASP 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 190 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 66 optimal weight: 0.0470 chunk 71 optimal weight: 0.2980 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 100 optimal weight: 0.2980 chunk 91 optimal weight: 0.8980 overall best weight: 0.4478 ------------------------------------------------------------------------------- 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** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN ** B 239 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: 0.6339 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8722 Z= 0.180 Angle : 0.577 10.565 11859 Z= 0.288 Chirality : 0.042 0.213 1385 Planarity : 0.003 0.042 1483 Dihedral : 4.530 32.616 1205 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.58 % Allowed : 18.55 % Favored : 77.88 % 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 (0.26), residues: 1104 helix: 0.57 (0.27), residues: 387 sheet: -1.86 (0.29), residues: 274 loop : -1.04 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.011 0.001 PHE B 235 TYR 0.015 0.001 TYR S 60 ARG 0.004 0.000 ARG B 49 *********************** 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 199 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 167 time to evaluate : 0.943 Fit side-chains revert: symmetry clash REVERT: A 210 LYS cc_start: 0.8120 (mmmm) cc_final: 0.7729 (mmmm) REVERT: B 61 MET cc_start: 0.6525 (tmm) cc_final: 0.6243 (tmm) REVERT: B 100 VAL cc_start: 0.8189 (p) cc_final: 0.7958 (t) REVERT: B 151 PHE cc_start: 0.7988 (OUTLIER) cc_final: 0.7432 (m-80) REVERT: B 155 ASN cc_start: 0.7327 (t0) cc_final: 0.6995 (t0) REVERT: B 276 VAL cc_start: 0.7856 (OUTLIER) cc_final: 0.7622 (t) REVERT: S 32 PHE cc_start: 0.8099 (m-80) cc_final: 0.7101 (m-80) REVERT: R 42 LEU cc_start: 0.6415 (mt) cc_final: 0.6146 (mt) REVERT: R 419 MET cc_start: 0.2624 (tpt) cc_final: 0.1947 (tpt) outliers start: 32 outliers final: 28 residues processed: 184 average time/residue: 0.2001 time to fit residues: 51.5107 Evaluate side-chains 197 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 167 time to evaluate : 0.863 ------------------------------------------------------------------------------- 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 B residue 71 VAL Chi-restraints excluded: chain B residue 133 VAL 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 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL 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 51 ILE Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 157 ASN 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 112 ASP 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 Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 442 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 chunk 58 optimal weight: 0.0980 chunk 42 optimal weight: 0.1980 chunk 76 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 92 optimal weight: 0.0980 chunk 64 optimal weight: 0.3980 chunk 103 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 overall best weight: 0.2980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** 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: 0.6311 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8722 Z= 0.149 Angle : 0.559 7.986 11859 Z= 0.279 Chirality : 0.041 0.190 1385 Planarity : 0.003 0.042 1483 Dihedral : 4.374 33.235 1205 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.35 % Allowed : 19.11 % Favored : 77.54 % 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: -0.97 (0.26), residues: 1104 helix: 0.66 (0.28), residues: 389 sheet: -1.73 (0.29), residues: 273 loop : -0.95 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.019 0.001 PHE R 186 TYR 0.015 0.001 TYR S 103 ARG 0.004 0.000 ARG B 49 *********************** 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 196 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 166 time to evaluate : 0.877 Fit side-chains revert: symmetry clash REVERT: A 210 LYS cc_start: 0.8138 (mmmm) cc_final: 0.7802 (mmmm) REVERT: B 61 MET cc_start: 0.6472 (tmm) cc_final: 0.6181 (tmm) REVERT: B 83 ASP cc_start: 0.7679 (t0) cc_final: 0.6520 (m-30) REVERT: B 100 VAL cc_start: 0.8116 (p) cc_final: 0.7907 (t) REVERT: B 151 PHE cc_start: 0.7985 (OUTLIER) cc_final: 0.7334 (m-80) REVERT: B 155 ASN cc_start: 0.7315 (t0) cc_final: 0.6972 (t0) REVERT: B 161 SER cc_start: 0.7773 (m) cc_final: 0.7505 (p) REVERT: B 276 VAL cc_start: 0.7786 (OUTLIER) cc_final: 0.7549 (t) REVERT: S 32 PHE cc_start: 0.8071 (m-80) cc_final: 0.7072 (m-80) REVERT: R 42 LEU cc_start: 0.6427 (mt) cc_final: 0.6144 (mt) REVERT: R 419 MET cc_start: 0.2549 (tpt) cc_final: 0.1823 (tpt) outliers start: 30 outliers final: 27 residues processed: 180 average time/residue: 0.1920 time to fit residues: 48.1804 Evaluate side-chains 195 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 166 time to evaluate : 0.845 ------------------------------------------------------------------------------- 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 B residue 133 VAL 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 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL 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 45 LEU Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 157 ASN 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 112 ASP 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 190 LEU Chi-restraints excluded: chain R residue 442 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 108 optimal weight: 0.0170 chunk 99 optimal weight: 0.4980 chunk 86 optimal weight: 0.9990 chunk 8 optimal weight: 0.0980 chunk 66 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 overall best weight: 0.5222 ------------------------------------------------------------------------------- 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** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 13 GLN ** 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: 0.6343 moved from start: 0.2898 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= 0.196 Angle : 0.576 7.912 11859 Z= 0.292 Chirality : 0.042 0.184 1385 Planarity : 0.004 0.047 1483 Dihedral : 4.540 32.944 1205 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.24 % Allowed : 19.55 % Favored : 77.21 % 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: -1.03 (0.26), residues: 1104 helix: 0.62 (0.27), residues: 389 sheet: -1.81 (0.29), residues: 277 loop : -0.94 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS B 54 PHE 0.024 0.001 PHE R 186 TYR 0.017 0.001 TYR S 103 ARG 0.004 0.000 ARG B 68 ********************** 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 194 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 165 time to evaluate : 0.890 Fit side-chains revert: symmetry clash REVERT: A 210 LYS cc_start: 0.8104 (mmmm) cc_final: 0.7765 (mmmm) REVERT: B 100 VAL cc_start: 0.8147 (p) cc_final: 0.7918 (t) REVERT: B 151 PHE cc_start: 0.8012 (OUTLIER) cc_final: 0.7455 (m-80) REVERT: B 155 ASN cc_start: 0.7320 (t0) cc_final: 0.7017 (t0) REVERT: B 246 ASP cc_start: 0.6421 (m-30) cc_final: 0.6048 (m-30) REVERT: S 32 PHE cc_start: 0.8117 (m-80) cc_final: 0.7123 (m-80) REVERT: R 42 LEU cc_start: 0.6434 (mt) cc_final: 0.6149 (mt) REVERT: R 419 MET cc_start: 0.2629 (tpt) cc_final: 0.1994 (tpt) outliers start: 29 outliers final: 25 residues processed: 179 average time/residue: 0.2005 time to fit residues: 49.6304 Evaluate side-chains 192 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 166 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 133 VAL 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 229 ILE Chi-restraints excluded: chain B residue 234 PHE 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 45 LEU Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 157 ASN 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 112 ASP 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 175 VAL Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 442 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 0.0020 chunk 86 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- 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** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 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 = 0.4179 r_free = 0.4179 target = 0.179108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.162767 restraints weight = 12636.071| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 1.86 r_work: 0.3909 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3779 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8722 Z= 0.227 Angle : 0.603 8.181 11859 Z= 0.305 Chirality : 0.043 0.178 1385 Planarity : 0.004 0.047 1483 Dihedral : 4.691 32.547 1205 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.02 % Allowed : 20.45 % Favored : 76.54 % 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: -1.07 (0.26), residues: 1104 helix: 0.48 (0.27), residues: 396 sheet: -1.73 (0.29), residues: 277 loop : -0.94 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.005 0.001 HIS B 54 PHE 0.026 0.001 PHE R 186 TYR 0.018 0.001 TYR S 103 ARG 0.004 0.000 ARG B 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2213.43 seconds wall clock time: 40 minutes 14.84 seconds (2414.84 seconds total)