Starting phenix.real_space_refine on Wed Mar 4 02:40:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v69_31739/03_2026/7v69_31739.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v69_31739/03_2026/7v69_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/cci-nas-00/data/ceres_data/7v69_31739/03_2026/7v69_31739.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v69_31739/03_2026/7v69_31739.map" model { file = "/net/cci-nas-00/data/ceres_data/7v69_31739/03_2026/7v69_31739.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v69_31739/03_2026/7v69_31739.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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, 'ASP:plan': 7, 'ARG:plan': 1, 'ASN:plan1': 1} 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: {'GLU:plan': 4, 'ASP:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 4, 'ARG:plan': 1} 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: {'ARG:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 19 Time building chain proxies: 2.17, per 1000 atoms: 0.25 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: 0.68 Conformation dependent library (CDL) restraints added in 350.6 milliseconds 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: 0.37 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: 1.37 Time building geometry restraints manager: 0.97 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: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.680 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.210 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.720 ------------------------------------------------------------------------------- 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 8724 Z= 0.138 Angle : 0.654 8.757 11863 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 : 13.05 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.005 0.001 ARG B 68 TYR 0.018 0.001 TYR S 103 PHE 0.024 0.001 PHE B 234 TRP 0.013 0.001 TRP B 169 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 8722) covalent geometry : angle 0.65331 (11859) SS BOND : bond 0.00239 ( 2) SS BOND : angle 1.45880 ( 4) hydrogen bonds : bond 0.19353 ( 363) hydrogen bonds : angle 7.30817 ( 1017) *********************** 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 to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: B 61 MET cc_start: 0.6117 (tmm) cc_final: 0.5843 (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: 0.1069 time to fit residues: 24.4354 Evaluate side-chains 155 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.0010 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.179209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.163031 restraints weight = 12979.673| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 1.86 r_work: 0.3916 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3792 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8724 Z= 0.169 Angle : 0.611 8.629 11863 Z= 0.318 Chirality : 0.044 0.146 1385 Planarity : 0.004 0.036 1483 Dihedral : 4.906 28.915 1205 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.56 % Allowed : 9.61 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.24), residues: 1104 helix: -0.28 (0.27), residues: 384 sheet: -2.18 (0.28), residues: 265 loop : -1.40 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 219 TYR 0.016 0.002 TYR B 264 PHE 0.020 0.002 PHE B 235 TRP 0.010 0.001 TRP R 98 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 8722) covalent geometry : angle 0.61001 (11859) SS BOND : bond 0.00327 ( 2) SS BOND : angle 1.66076 ( 4) hydrogen bonds : bond 0.03920 ( 363) hydrogen bonds : angle 5.27329 ( 1017) *********************** 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 to be fit. rotamer outliers: 14 poor density : 175 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7926 (mtm110) cc_final: 0.7523 (mtm110) REVERT: A 210 LYS cc_start: 0.8495 (mmmm) cc_final: 0.8281 (mmmm) REVERT: A 253 ILE cc_start: 0.8147 (tt) cc_final: 0.7790 (pt) REVERT: B 61 MET cc_start: 0.6879 (tmm) cc_final: 0.6400 (tmm) REVERT: B 105 TYR cc_start: 0.7849 (t80) cc_final: 0.7474 (t80) REVERT: B 188 MET cc_start: 0.7230 (mmm) cc_final: 0.6987 (mmm) REVERT: B 233 CYS cc_start: 0.7775 (t) cc_final: 0.7435 (p) REVERT: B 247 ASP cc_start: 0.6759 (t0) cc_final: 0.6490 (t0) REVERT: B 255 LEU cc_start: 0.7755 (mt) cc_final: 0.7526 (mt) REVERT: B 271 CYS cc_start: 0.7320 (p) cc_final: 0.7035 (p) REVERT: B 300 LEU cc_start: 0.7693 (mt) cc_final: 0.7432 (mt) REVERT: B 325 MET cc_start: 0.8019 (tpt) cc_final: 0.7814 (tpt) REVERT: C 42 GLU cc_start: 0.6688 (pp20) cc_final: 0.6331 (pp20) REVERT: S 67 ARG cc_start: 0.5002 (ptt180) cc_final: 0.4721 (ttp-170) REVERT: S 79 LEU cc_start: 0.7279 (tp) cc_final: 0.7009 (tp) REVERT: R 42 LEU cc_start: 0.6326 (mt) cc_final: 0.6072 (mt) outliers start: 14 outliers final: 11 residues processed: 177 average time/residue: 0.0930 time to fit residues: 22.7744 Evaluate side-chains 173 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 162 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU 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 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 31 optimal weight: 0.0570 chunk 19 optimal weight: 0.0870 chunk 27 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 47 optimal weight: 0.0010 chunk 75 optimal weight: 0.0570 chunk 11 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 overall best weight: 0.2000 ------------------------------------------------------------------------------- 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 S 39 GLN R 423 ASN R 449 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.181473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.165249 restraints weight = 12971.664| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 1.88 r_work: 0.3951 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3825 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8724 Z= 0.100 Angle : 0.538 8.208 11863 Z= 0.274 Chirality : 0.041 0.152 1385 Planarity : 0.003 0.037 1483 Dihedral : 4.510 29.799 1205 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.57 % Allowed : 12.29 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.25), residues: 1104 helix: 0.08 (0.27), residues: 386 sheet: -2.11 (0.28), residues: 255 loop : -1.30 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 219 TYR 0.015 0.001 TYR S 163 PHE 0.010 0.001 PHE R 186 TRP 0.009 0.001 TRP R 98 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 8722) covalent geometry : angle 0.53738 (11859) SS BOND : bond 0.00357 ( 2) SS BOND : angle 1.21879 ( 4) hydrogen bonds : bond 0.03072 ( 363) hydrogen bonds : angle 4.73671 ( 1017) *********************** 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 194 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 171 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7867 (mtm110) cc_final: 0.7456 (mtm110) REVERT: B 61 MET cc_start: 0.6791 (tmm) cc_final: 0.6571 (tmm) REVERT: B 105 TYR cc_start: 0.7830 (t80) cc_final: 0.7516 (t80) REVERT: B 118 ASP cc_start: 0.7357 (p0) cc_final: 0.6981 (p0) REVERT: B 129 ARG cc_start: 0.6534 (tmt-80) cc_final: 0.5182 (ttt-90) REVERT: B 246 ASP cc_start: 0.7025 (m-30) cc_final: 0.6800 (m-30) REVERT: B 247 ASP cc_start: 0.6725 (t0) cc_final: 0.6374 (t0) REVERT: B 290 ASP cc_start: 0.7448 (m-30) cc_final: 0.7150 (m-30) REVERT: B 325 MET cc_start: 0.8005 (tpt) cc_final: 0.7773 (tpt) REVERT: S 79 LEU cc_start: 0.7128 (tp) cc_final: 0.6878 (tp) REVERT: R 186 PHE cc_start: 0.6636 (p90) cc_final: 0.6065 (p90) outliers start: 23 outliers final: 14 residues processed: 176 average time/residue: 0.1008 time to fit residues: 24.2882 Evaluate side-chains 182 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 168 time to evaluate : 0.302 ------------------------------------------------------------------------------- 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 157 ASN Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain R residue 74 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 174 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 13 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 12 optimal weight: 0.0170 chunk 79 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.7420 ------------------------------------------------------------------------------- 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 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.178938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.162598 restraints weight = 12885.978| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 1.88 r_work: 0.3903 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3773 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6707 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8724 Z= 0.174 Angle : 0.592 7.249 11863 Z= 0.305 Chirality : 0.043 0.141 1385 Planarity : 0.004 0.038 1483 Dihedral : 4.795 30.626 1205 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.24 % Allowed : 14.30 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.25), residues: 1104 helix: 0.16 (0.27), residues: 385 sheet: -2.10 (0.27), residues: 278 loop : -1.14 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 219 TYR 0.015 0.002 TYR S 178 PHE 0.024 0.001 PHE B 235 TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 8722) covalent geometry : angle 0.59124 (11859) SS BOND : bond 0.00194 ( 2) SS BOND : angle 1.34272 ( 4) hydrogen bonds : bond 0.03341 ( 363) hydrogen bonds : angle 4.76858 ( 1017) *********************** 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 202 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 210 LYS cc_start: 0.8494 (mmmm) cc_final: 0.8228 (mtpp) REVERT: B 61 MET cc_start: 0.7050 (tmm) cc_final: 0.6659 (tmm) REVERT: B 118 ASP cc_start: 0.7360 (p0) cc_final: 0.7060 (p0) REVERT: B 151 PHE cc_start: 0.8269 (OUTLIER) cc_final: 0.7658 (m-80) REVERT: B 161 SER cc_start: 0.7925 (m) cc_final: 0.7665 (p) REVERT: B 233 CYS cc_start: 0.7869 (t) cc_final: 0.7447 (p) REVERT: B 246 ASP cc_start: 0.7256 (m-30) cc_final: 0.6992 (m-30) REVERT: B 247 ASP cc_start: 0.7009 (t0) cc_final: 0.6727 (t0) REVERT: B 271 CYS cc_start: 0.7339 (p) cc_final: 0.7115 (p) REVERT: S 32 PHE cc_start: 0.8294 (m-80) cc_final: 0.7704 (m-80) REVERT: S 79 LEU cc_start: 0.7208 (tp) cc_final: 0.6997 (tp) REVERT: S 128 MET cc_start: 0.7446 (mmm) cc_final: 0.6926 (mmm) REVERT: S 180 MET cc_start: 0.5654 (OUTLIER) cc_final: 0.5263 (tmm) REVERT: S 191 PHE cc_start: 0.7537 (m-80) cc_final: 0.7285 (m-80) outliers start: 29 outliers final: 18 residues processed: 183 average time/residue: 0.0879 time to fit residues: 22.3117 Evaluate side-chains 190 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 0.241 ------------------------------------------------------------------------------- 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 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 S residue 221 LEU Chi-restraints excluded: chain R residue 107 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 101 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 52 optimal weight: 0.3980 chunk 45 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 85 optimal weight: 0.0770 chunk 88 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 0.0570 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.180092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.163771 restraints weight = 12924.589| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 1.89 r_work: 0.3925 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3797 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8724 Z= 0.122 Angle : 0.560 7.721 11863 Z= 0.284 Chirality : 0.041 0.137 1385 Planarity : 0.003 0.038 1483 Dihedral : 4.597 32.097 1205 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.02 % Allowed : 16.09 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.25), residues: 1104 helix: 0.35 (0.27), residues: 386 sheet: -2.06 (0.28), residues: 273 loop : -1.15 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 314 TYR 0.014 0.001 TYR S 163 PHE 0.013 0.001 PHE B 235 TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 8722) covalent geometry : angle 0.56010 (11859) SS BOND : bond 0.00270 ( 2) SS BOND : angle 1.18812 ( 4) hydrogen bonds : bond 0.02961 ( 363) hydrogen bonds : angle 4.62640 ( 1017) *********************** 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 197 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 170 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7897 (mtm110) cc_final: 0.7631 (mtm110) REVERT: B 61 MET cc_start: 0.7066 (tmm) cc_final: 0.6656 (tmm) REVERT: B 118 ASP cc_start: 0.7370 (p0) cc_final: 0.7050 (p0) REVERT: B 151 PHE cc_start: 0.8198 (OUTLIER) cc_final: 0.7543 (m-80) REVERT: B 155 ASN cc_start: 0.7872 (t0) cc_final: 0.7517 (t0) REVERT: B 161 SER cc_start: 0.7814 (m) cc_final: 0.7599 (p) REVERT: B 233 CYS cc_start: 0.7887 (t) cc_final: 0.7440 (p) REVERT: B 247 ASP cc_start: 0.6859 (t0) cc_final: 0.6603 (t0) REVERT: S 32 PHE cc_start: 0.8239 (m-80) cc_final: 0.7634 (m-80) REVERT: S 128 MET cc_start: 0.7429 (mmm) cc_final: 0.6904 (mmm) REVERT: S 180 MET cc_start: 0.5481 (OUTLIER) cc_final: 0.5123 (tmm) REVERT: S 191 PHE cc_start: 0.7533 (m-80) cc_final: 0.7289 (m-80) REVERT: R 163 LEU cc_start: 0.5636 (OUTLIER) cc_final: 0.5343 (mm) outliers start: 27 outliers final: 18 residues processed: 181 average time/residue: 0.0806 time to fit residues: 20.8218 Evaluate side-chains 189 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 0.210 ------------------------------------------------------------------------------- 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 95 LEU 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 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 163 LEU Chi-restraints excluded: chain R residue 175 VAL Chi-restraints excluded: chain R residue 190 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 23 optimal weight: 0.0970 chunk 48 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 HIS ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.177994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.161675 restraints weight = 12747.157| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 1.85 r_work: 0.3905 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3775 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8724 Z= 0.169 Angle : 0.596 7.517 11863 Z= 0.304 Chirality : 0.043 0.185 1385 Planarity : 0.004 0.043 1483 Dihedral : 4.780 31.513 1205 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.36 % Allowed : 15.98 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.25), residues: 1104 helix: 0.28 (0.27), residues: 392 sheet: -1.90 (0.28), residues: 275 loop : -1.16 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 72 TYR 0.014 0.002 TYR S 178 PHE 0.019 0.001 PHE B 235 TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 8722) covalent geometry : angle 0.59570 (11859) SS BOND : bond 0.00191 ( 2) SS BOND : angle 1.29466 ( 4) hydrogen bonds : bond 0.03207 ( 363) hydrogen bonds : angle 4.67904 ( 1017) *********************** 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 208 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 169 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: B 61 MET cc_start: 0.7068 (tmm) cc_final: 0.6708 (tmm) REVERT: B 118 ASP cc_start: 0.7337 (p0) cc_final: 0.7055 (p0) REVERT: B 151 PHE cc_start: 0.8186 (OUTLIER) cc_final: 0.7576 (m-80) REVERT: B 155 ASN cc_start: 0.7731 (t0) cc_final: 0.7407 (t0) REVERT: B 163 ASP cc_start: 0.7970 (OUTLIER) cc_final: 0.7474 (p0) REVERT: B 213 VAL cc_start: 0.8087 (t) cc_final: 0.7886 (m) REVERT: B 233 CYS cc_start: 0.7800 (t) cc_final: 0.7385 (p) REVERT: B 247 ASP cc_start: 0.6957 (t0) cc_final: 0.6727 (t0) REVERT: S 32 PHE cc_start: 0.8319 (m-80) cc_final: 0.7703 (m-80) REVERT: S 180 MET cc_start: 0.5715 (OUTLIER) cc_final: 0.5319 (tmm) REVERT: R 71 LEU cc_start: 0.6417 (tt) cc_final: 0.6088 (tt) outliers start: 39 outliers final: 26 residues processed: 191 average time/residue: 0.0836 time to fit residues: 22.1884 Evaluate side-chains 198 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 0.304 ------------------------------------------------------------------------------- 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 95 LEU Chi-restraints excluded: chain B residue 133 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 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 54 VAL 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 152 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 102 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 88 optimal weight: 0.2980 chunk 82 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 chunk 33 optimal weight: 0.0170 chunk 1 optimal weight: 0.7980 overall best weight: 0.5218 ------------------------------------------------------------------------------- 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 ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN ** S 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.178185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.161742 restraints weight = 12968.158| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 1.89 r_work: 0.3917 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3782 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8724 Z= 0.137 Angle : 0.588 8.106 11863 Z= 0.296 Chirality : 0.042 0.222 1385 Planarity : 0.003 0.041 1483 Dihedral : 4.680 32.464 1205 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.58 % Allowed : 17.43 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.25), residues: 1104 helix: 0.44 (0.27), residues: 386 sheet: -1.92 (0.28), residues: 280 loop : -1.05 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 219 TYR 0.014 0.001 TYR S 103 PHE 0.018 0.001 PHE R 186 TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 8722) covalent geometry : angle 0.58760 (11859) SS BOND : bond 0.00227 ( 2) SS BOND : angle 1.22479 ( 4) hydrogen bonds : bond 0.02998 ( 363) hydrogen bonds : angle 4.61664 ( 1017) *********************** 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 202 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 170 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7883 (mtm110) cc_final: 0.7647 (mtm110) REVERT: A 210 LYS cc_start: 0.8450 (mmmm) cc_final: 0.8215 (mtmm) REVERT: B 61 MET cc_start: 0.7095 (tmm) cc_final: 0.6732 (tmm) REVERT: B 118 ASP cc_start: 0.7330 (p0) cc_final: 0.7040 (p0) REVERT: B 151 PHE cc_start: 0.8156 (OUTLIER) cc_final: 0.7556 (m-80) REVERT: B 155 ASN cc_start: 0.7769 (t0) cc_final: 0.7398 (t0) REVERT: B 163 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7711 (p0) REVERT: B 233 CYS cc_start: 0.7857 (t) cc_final: 0.7488 (p) REVERT: B 247 ASP cc_start: 0.6855 (t0) cc_final: 0.6615 (t0) REVERT: B 278 PHE cc_start: 0.8371 (OUTLIER) cc_final: 0.7993 (m-80) REVERT: S 32 PHE cc_start: 0.8317 (m-80) cc_final: 0.7707 (m-80) REVERT: S 180 MET cc_start: 0.5538 (OUTLIER) cc_final: 0.5144 (tmm) REVERT: S 191 PHE cc_start: 0.7521 (m-80) cc_final: 0.7305 (m-80) REVERT: R 71 LEU cc_start: 0.6450 (tt) cc_final: 0.6109 (tt) REVERT: R 419 MET cc_start: 0.3440 (tpt) cc_final: 0.2549 (tpt) outliers start: 32 outliers final: 24 residues processed: 187 average time/residue: 0.0946 time to fit residues: 24.7628 Evaluate side-chains 195 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 167 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 71 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 54 VAL 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 152 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 100 optimal weight: 0.4980 chunk 39 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 11 optimal weight: 0.0170 chunk 5 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 chunk 86 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.179967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.163581 restraints weight = 12801.715| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 1.92 r_work: 0.3923 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3792 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8724 Z= 0.126 Angle : 0.579 8.615 11863 Z= 0.288 Chirality : 0.042 0.202 1385 Planarity : 0.003 0.041 1483 Dihedral : 4.592 32.552 1205 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.35 % Allowed : 18.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.26), residues: 1104 helix: 0.50 (0.27), residues: 389 sheet: -1.82 (0.29), residues: 269 loop : -1.06 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 219 TYR 0.016 0.001 TYR S 103 PHE 0.011 0.001 PHE B 235 TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 8722) covalent geometry : angle 0.57833 (11859) SS BOND : bond 0.00200 ( 2) SS BOND : angle 1.26512 ( 4) hydrogen bonds : bond 0.02923 ( 363) hydrogen bonds : angle 4.51634 ( 1017) *********************** 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 201 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7895 (mtm110) cc_final: 0.7692 (mtm110) REVERT: A 210 LYS cc_start: 0.8462 (mmmm) cc_final: 0.8248 (mtmm) REVERT: B 61 MET cc_start: 0.7134 (tmm) cc_final: 0.6791 (tmm) REVERT: B 151 PHE cc_start: 0.8137 (OUTLIER) cc_final: 0.7528 (m-80) REVERT: B 155 ASN cc_start: 0.7753 (t0) cc_final: 0.7462 (t0) REVERT: B 163 ASP cc_start: 0.8067 (OUTLIER) cc_final: 0.7747 (p0) REVERT: B 233 CYS cc_start: 0.7845 (t) cc_final: 0.7474 (p) REVERT: B 247 ASP cc_start: 0.6785 (t0) cc_final: 0.6532 (t0) REVERT: B 278 PHE cc_start: 0.8263 (OUTLIER) cc_final: 0.7877 (m-80) REVERT: S 32 PHE cc_start: 0.8344 (m-80) cc_final: 0.7697 (m-80) REVERT: S 180 MET cc_start: 0.5464 (OUTLIER) cc_final: 0.5061 (tmm) REVERT: R 419 MET cc_start: 0.3333 (tpt) cc_final: 0.2512 (tpt) outliers start: 30 outliers final: 25 residues processed: 186 average time/residue: 0.0942 time to fit residues: 24.2819 Evaluate side-chains 199 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 71 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 163 ASP 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 278 PHE 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 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 212 VAL 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 66 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 98 optimal weight: 0.0270 chunk 9 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 90 optimal weight: 0.1980 chunk 2 optimal weight: 0.6980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.178879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.162721 restraints weight = 12803.980| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 1.86 r_work: 0.3927 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3797 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8724 Z= 0.126 Angle : 0.585 9.434 11863 Z= 0.290 Chirality : 0.042 0.270 1385 Planarity : 0.003 0.043 1483 Dihedral : 4.574 32.981 1205 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.58 % Allowed : 18.88 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.26), residues: 1104 helix: 0.56 (0.27), residues: 389 sheet: -1.81 (0.29), residues: 270 loop : -0.97 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 219 TYR 0.019 0.001 TYR S 103 PHE 0.012 0.001 PHE B 235 TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8722) covalent geometry : angle 0.58500 (11859) SS BOND : bond 0.00212 ( 2) SS BOND : angle 1.21960 ( 4) hydrogen bonds : bond 0.02852 ( 363) hydrogen bonds : angle 4.50844 ( 1017) *********************** 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 203 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 171 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7920 (mtm110) cc_final: 0.7715 (mtm110) REVERT: B 61 MET cc_start: 0.7105 (tmm) cc_final: 0.6777 (tmm) REVERT: B 151 PHE cc_start: 0.8111 (OUTLIER) cc_final: 0.7498 (m-80) REVERT: B 155 ASN cc_start: 0.7726 (t0) cc_final: 0.7450 (t0) REVERT: B 163 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7775 (p0) REVERT: B 233 CYS cc_start: 0.7822 (t) cc_final: 0.7511 (p) REVERT: B 247 ASP cc_start: 0.6706 (t0) cc_final: 0.6425 (t0) REVERT: B 278 PHE cc_start: 0.8238 (OUTLIER) cc_final: 0.7840 (m-80) REVERT: S 32 PHE cc_start: 0.8316 (m-80) cc_final: 0.7655 (m-80) REVERT: S 180 MET cc_start: 0.5392 (OUTLIER) cc_final: 0.5001 (tmm) REVERT: R 419 MET cc_start: 0.3379 (tpt) cc_final: 0.2560 (tpt) outliers start: 32 outliers final: 24 residues processed: 187 average time/residue: 0.0919 time to fit residues: 23.9523 Evaluate side-chains 195 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 167 time to evaluate : 0.311 ------------------------------------------------------------------------------- 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 151 PHE Chi-restraints excluded: chain B residue 163 ASP 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 278 PHE 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 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 212 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 3 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 82 optimal weight: 4.9990 chunk 42 optimal weight: 0.0770 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 48 optimal weight: 0.0770 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.177721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.161614 restraints weight = 12768.794| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 1.87 r_work: 0.3913 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3783 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8724 Z= 0.167 Angle : 0.624 10.543 11863 Z= 0.311 Chirality : 0.044 0.248 1385 Planarity : 0.004 0.047 1483 Dihedral : 4.781 32.594 1205 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.35 % Allowed : 19.55 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.26), residues: 1104 helix: 0.38 (0.27), residues: 395 sheet: -1.82 (0.29), residues: 269 loop : -0.99 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 68 TYR 0.021 0.002 TYR S 103 PHE 0.018 0.001 PHE S 27 TRP 0.016 0.001 TRP B 82 HIS 0.006 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 8722) covalent geometry : angle 0.62346 (11859) SS BOND : bond 0.00216 ( 2) SS BOND : angle 1.38555 ( 4) hydrogen bonds : bond 0.03079 ( 363) hydrogen bonds : angle 4.59892 ( 1017) ********************** 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 203 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 173 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: B 61 MET cc_start: 0.7117 (tmm) cc_final: 0.6750 (tmm) REVERT: B 151 PHE cc_start: 0.8108 (OUTLIER) cc_final: 0.7408 (m-10) REVERT: B 155 ASN cc_start: 0.7700 (t0) cc_final: 0.7461 (t0) REVERT: B 198 LEU cc_start: 0.8456 (mm) cc_final: 0.8235 (mp) REVERT: B 233 CYS cc_start: 0.7804 (t) cc_final: 0.7457 (p) REVERT: B 247 ASP cc_start: 0.6871 (t0) cc_final: 0.6568 (t0) REVERT: B 278 PHE cc_start: 0.8279 (OUTLIER) cc_final: 0.7878 (m-80) REVERT: S 32 PHE cc_start: 0.8280 (m-80) cc_final: 0.7551 (m-80) REVERT: S 180 MET cc_start: 0.5646 (OUTLIER) cc_final: 0.5239 (tmm) REVERT: R 70 PHE cc_start: 0.7149 (m-80) cc_final: 0.6860 (m-80) REVERT: R 419 MET cc_start: 0.3480 (tpt) cc_final: 0.2630 (tpt) outliers start: 30 outliers final: 25 residues processed: 188 average time/residue: 0.0879 time to fit residues: 23.3847 Evaluate side-chains 201 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 173 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 151 PHE 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 278 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 54 VAL 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 212 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 58 optimal weight: 0.0000 chunk 68 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 86 optimal weight: 0.4980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4187 r_free = 0.4187 target = 0.179919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.163677 restraints weight = 12731.835| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 1.90 r_work: 0.3919 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3788 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8724 Z= 0.138 Angle : 0.609 9.925 11863 Z= 0.301 Chirality : 0.043 0.235 1385 Planarity : 0.003 0.043 1483 Dihedral : 4.710 32.581 1205 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.46 % Allowed : 19.78 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.26), residues: 1104 helix: 0.51 (0.27), residues: 389 sheet: -1.78 (0.29), residues: 268 loop : -0.99 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 68 TYR 0.020 0.001 TYR S 103 PHE 0.020 0.001 PHE S 27 TRP 0.018 0.001 TRP B 82 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 8722) covalent geometry : angle 0.60828 (11859) SS BOND : bond 0.00204 ( 2) SS BOND : angle 1.33557 ( 4) hydrogen bonds : bond 0.02940 ( 363) hydrogen bonds : angle 4.53314 ( 1017) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2259.80 seconds wall clock time: 39 minutes 31.35 seconds (2371.35 seconds total)