Starting phenix.real_space_refine on Mon Mar 11 17:08:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0z_12684/03_2024/7o0z_12684.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0z_12684/03_2024/7o0z_12684.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0z_12684/03_2024/7o0z_12684.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0z_12684/03_2024/7o0z_12684.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0z_12684/03_2024/7o0z_12684.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0z_12684/03_2024/7o0z_12684.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 5649 2.51 5 N 1516 2.21 5 O 1539 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 146": "OE1" <-> "OE2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 216": "NH1" <-> "NH2" Residue "B ARG 233": "NH1" <-> "NH2" Residue "B ARG 297": "NH1" <-> "NH2" Residue "B ASP 300": "OD1" <-> "OD2" Residue "B ARG 307": "NH1" <-> "NH2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C ARG 124": "NH1" <-> "NH2" Residue "C ARG 148": "NH1" <-> "NH2" Residue "C ASP 153": "OD1" <-> "OD2" Residue "C ASP 160": "OD1" <-> "OD2" Residue "C ARG 173": "NH1" <-> "NH2" Residue "C ARG 216": "NH1" <-> "NH2" Residue "C ARG 224": "NH1" <-> "NH2" Residue "C ARG 226": "NH1" <-> "NH2" Residue "C ARG 233": "NH1" <-> "NH2" Residue "C GLU 252": "OE1" <-> "OE2" Residue "C ARG 269": "NH1" <-> "NH2" Residue "C ARG 297": "NH1" <-> "NH2" Residue "D ARG 145": "NH1" <-> "NH2" Residue "D ASP 219": "OD1" <-> "OD2" Residue "D ARG 222": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "E GLU 132": "OE1" <-> "OE2" Residue "E ASP 219": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8730 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2367 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 12, 'TRANS': 294} Chain: "C" Number of atoms: 2367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2367 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 12, 'TRANS': 294} Chain: "D" Number of atoms: 1999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 1999 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 8, 'TRANS': 255} Chain breaks: 2 Chain: "E" Number of atoms: 1997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 1997 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 255} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 5.01, per 1000 atoms: 0.57 Number of scatterers: 8730 At special positions: 0 Unit cell: (84.132, 103.626, 123.12, 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 26 16.00 O 1539 8.00 N 1516 7.00 C 5649 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.28 Conformation dependent library (CDL) restraints added in 1.7 seconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2050 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 7 sheets defined 59.9% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'B' and resid 39 through 42 removed outlier: 3.903A pdb=" N LYS B 42 " --> pdb=" O GLY B 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 39 through 42' Processing helix chain 'B' and resid 43 through 50 removed outlier: 3.737A pdb=" N LEU B 50 " --> pdb=" O MET B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 74 Processing helix chain 'B' and resid 90 through 103 removed outlier: 3.551A pdb=" N LEU B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG B 100 " --> pdb=" O ARG B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 116 removed outlier: 4.536A pdb=" N ASP B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 143 removed outlier: 3.596A pdb=" N LEU B 137 " --> pdb=" O MET B 133 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA B 142 " --> pdb=" O GLY B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 177 removed outlier: 3.820A pdb=" N GLN B 165 " --> pdb=" O PRO B 161 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP B 166 " --> pdb=" O ILE B 162 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU B 167 " --> pdb=" O ALA B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 219 removed outlier: 3.507A pdb=" N ARG B 216 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 242 removed outlier: 3.699A pdb=" N ARG B 239 " --> pdb=" O SER B 235 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N TRP B 240 " --> pdb=" O TRP B 236 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THR B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 269 Processing helix chain 'B' and resid 286 through 298 removed outlier: 3.522A pdb=" N MET B 295 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU B 296 " --> pdb=" O ARG B 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 50 removed outlier: 3.514A pdb=" N THR C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER C 45 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU C 50 " --> pdb=" O MET C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 103 removed outlier: 3.660A pdb=" N LEU C 95 " --> pdb=" O GLY C 91 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE C 98 " --> pdb=" O THR C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 116 Processing helix chain 'C' and resid 125 through 129 Processing helix chain 'C' and resid 130 through 143 removed outlier: 3.504A pdb=" N ALA C 140 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA C 142 " --> pdb=" O GLY C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 176 removed outlier: 3.513A pdb=" N GLN C 165 " --> pdb=" O PRO C 161 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TYR C 168 " --> pdb=" O THR C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 194 removed outlier: 3.622A pdb=" N ALA C 193 " --> pdb=" O GLY C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 219 Processing helix chain 'C' and resid 232 through 241 removed outlier: 4.039A pdb=" N TRP C 236 " --> pdb=" O GLU C 232 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG C 239 " --> pdb=" O SER C 235 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 274 removed outlier: 3.764A pdb=" N LEU C 271 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY C 273 " --> pdb=" O ARG C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 299 removed outlier: 4.065A pdb=" N ALA C 298 " --> pdb=" O TYR C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 307 removed outlier: 4.256A pdb=" N GLY C 306 " --> pdb=" O ALA C 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 16 removed outlier: 3.757A pdb=" N LYS D 10 " --> pdb=" O ASN D 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 43 removed outlier: 3.619A pdb=" N ALA D 23 " --> pdb=" O ARG D 19 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU D 26 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER D 43 " --> pdb=" O GLY D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 75 removed outlier: 3.775A pdb=" N ILE D 55 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER D 60 " --> pdb=" O ALA D 56 " (cutoff:3.500A) Proline residue: D 67 - end of helix removed outlier: 3.527A pdb=" N ALA D 70 " --> pdb=" O MET D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 83 Processing helix chain 'D' and resid 85 through 91 removed outlier: 3.598A pdb=" N LEU D 89 " --> pdb=" O GLY D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 131 removed outlier: 3.959A pdb=" N ILE D 111 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE D 118 " --> pdb=" O LEU D 114 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY D 121 " --> pdb=" O LEU D 117 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N CYS D 122 " --> pdb=" O ILE D 118 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA D 123 " --> pdb=" O GLY D 119 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE D 127 " --> pdb=" O ALA D 123 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA D 128 " --> pdb=" O ALA D 124 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU D 129 " --> pdb=" O LEU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 143 removed outlier: 3.754A pdb=" N LEU D 139 " --> pdb=" O GLU D 135 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE D 140 " --> pdb=" O LEU D 136 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TRP D 141 " --> pdb=" O GLY D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 168 removed outlier: 3.875A pdb=" N ILE D 148 " --> pdb=" O GLY D 144 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER D 149 " --> pdb=" O ARG D 145 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR D 151 " --> pdb=" O MET D 147 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LEU D 152 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL D 156 " --> pdb=" O LEU D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 188 removed outlier: 3.537A pdb=" N GLY D 180 " --> pdb=" O GLY D 176 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL D 186 " --> pdb=" O TRP D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 199 Processing helix chain 'D' and resid 209 through 214 removed outlier: 4.010A pdb=" N LEU D 213 " --> pdb=" O PRO D 210 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU D 214 " --> pdb=" O TRP D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 226 removed outlier: 3.819A pdb=" N ILE D 220 " --> pdb=" O ASN D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 273 removed outlier: 3.967A pdb=" N LEU D 254 " --> pdb=" O ALA D 250 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU D 256 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER D 263 " --> pdb=" O TRP D 259 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU D 265 " --> pdb=" O GLY D 261 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG D 273 " --> pdb=" O ALA D 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 17 removed outlier: 4.049A pdb=" N LYS E 10 " --> pdb=" O ASN E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 41 removed outlier: 3.526A pdb=" N LEU E 22 " --> pdb=" O ASN E 18 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU E 38 " --> pdb=" O GLY E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 75 removed outlier: 4.213A pdb=" N ALA E 56 " --> pdb=" O PRO E 52 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N SER E 57 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA E 62 " --> pdb=" O LEU E 58 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE E 64 " --> pdb=" O SER E 60 " (cutoff:3.500A) Proline residue: E 67 - end of helix Processing helix chain 'E' and resid 78 through 85 removed outlier: 3.705A pdb=" N GLY E 84 " --> pdb=" O GLY E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 93 removed outlier: 3.755A pdb=" N THR E 92 " --> pdb=" O MET E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 132 removed outlier: 3.511A pdb=" N LEU E 101 " --> pdb=" O ARG E 97 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE E 111 " --> pdb=" O GLY E 107 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU E 112 " --> pdb=" O HIS E 108 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLY E 121 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N CYS E 122 " --> pdb=" O ILE E 118 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA E 123 " --> pdb=" O GLY E 119 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU E 125 " --> pdb=" O GLY E 121 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU E 132 " --> pdb=" O ALA E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 138 Processing helix chain 'E' and resid 139 through 168 removed outlier: 4.022A pdb=" N ARG E 145 " --> pdb=" O TRP E 141 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE E 148 " --> pdb=" O GLY E 144 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N SER E 149 " --> pdb=" O ARG E 145 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL E 156 " --> pdb=" O LEU E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 188 removed outlier: 3.562A pdb=" N GLY E 176 " --> pdb=" O SER E 172 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL E 186 " --> pdb=" O TRP E 182 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 200 removed outlier: 3.758A pdb=" N ALA E 195 " --> pdb=" O LEU E 191 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL E 198 " --> pdb=" O LEU E 194 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER E 200 " --> pdb=" O LEU E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 213 removed outlier: 3.865A pdb=" N LEU E 212 " --> pdb=" O LEU E 209 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU E 213 " --> pdb=" O PRO E 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 209 through 213' Processing helix chain 'E' and resid 216 through 225 removed outlier: 3.512A pdb=" N ASN E 225 " --> pdb=" O TYR E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 245 removed outlier: 3.659A pdb=" N SER E 240 " --> pdb=" O GLY E 237 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU E 241 " --> pdb=" O VAL E 238 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY E 242 " --> pdb=" O LEU E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 272 removed outlier: 3.508A pdb=" N LEU E 254 " --> pdb=" O ALA E 250 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU E 256 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE E 260 " --> pdb=" O LEU E 256 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY E 261 " --> pdb=" O LEU E 257 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER E 263 " --> pdb=" O TRP E 259 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 25 through 26 removed outlier: 3.771A pdb=" N VAL B 4 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLN B 59 " --> pdb=" O GLN B 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 9 through 12 removed outlier: 5.380A pdb=" N VAL B 9 " --> pdb=" O ASP B 21 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 76 through 79 removed outlier: 6.174A pdb=" N LEU B 150 " --> pdb=" O ILE B 182 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N CYS B 184 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU B 152 " --> pdb=" O CYS B 184 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU B 32 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLY B 33 " --> pdb=" O ALA B 199 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU B 201 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N PHE B 35 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ALA B 202 " --> pdb=" O LEU B 206 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N LEU B 206 " --> pdb=" O ALA B 202 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 246 through 250 removed outlier: 3.576A pdb=" N LEU B 250 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 22 through 26 removed outlier: 5.468A pdb=" N LEU C 22 " --> pdb=" O GLY C 8 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL C 4 " --> pdb=" O LEU C 26 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN C 59 " --> pdb=" O GLN C 7 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 149 through 153 removed outlier: 6.468A pdb=" N LEU C 32 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL C 31 " --> pdb=" O ARG C 197 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ALA C 199 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLY C 33 " --> pdb=" O ALA C 199 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LEU C 201 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N PHE C 35 " --> pdb=" O LEU C 201 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ALA C 202 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LEU C 206 " --> pdb=" O ALA C 202 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 248 through 251 removed outlier: 3.550A pdb=" N ARG C 248 " --> pdb=" O GLU C 256 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N SER C 254 " --> pdb=" O LEU C 250 " (cutoff:3.500A) 432 hydrogen bonds defined for protein. 1254 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.29 Time building geometry restraints manager: 3.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2832 1.34 - 1.46: 1611 1.46 - 1.57: 4401 1.57 - 1.69: 0 1.69 - 1.80: 44 Bond restraints: 8888 Sorted by residual: bond pdb=" C LEU D 209 " pdb=" N PRO D 210 " ideal model delta sigma weight residual 1.337 1.363 -0.026 1.11e-02 8.12e+03 5.66e+00 bond pdb=" CB ASN C 38 " pdb=" CG ASN C 38 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.50e-02 1.60e+03 3.87e+00 bond pdb=" C ILE E 51 " pdb=" N PRO E 52 " ideal model delta sigma weight residual 1.337 1.355 -0.019 1.06e-02 8.90e+03 3.17e+00 bond pdb=" CG LEU C 151 " pdb=" CD2 LEU C 151 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 3.03e+00 bond pdb=" CA LEU D 209 " pdb=" C LEU D 209 " ideal model delta sigma weight residual 1.522 1.544 -0.022 1.26e-02 6.30e+03 2.97e+00 ... (remaining 8883 not shown) Histogram of bond angle deviations from ideal: 99.03 - 106.30: 200 106.30 - 113.57: 5041 113.57 - 120.84: 4289 120.84 - 128.11: 2438 128.11 - 135.38: 93 Bond angle restraints: 12061 Sorted by residual: angle pdb=" C SER B 231 " pdb=" N GLU B 232 " pdb=" CA GLU B 232 " ideal model delta sigma weight residual 121.54 133.07 -11.53 1.91e+00 2.74e-01 3.65e+01 angle pdb=" C GLU B 81 " pdb=" N ASN B 82 " pdb=" CA ASN B 82 " ideal model delta sigma weight residual 121.54 132.26 -10.72 1.91e+00 2.74e-01 3.15e+01 angle pdb=" CA LEU C 188 " pdb=" CB LEU C 188 " pdb=" CG LEU C 188 " ideal model delta sigma weight residual 116.30 131.71 -15.41 3.50e+00 8.16e-02 1.94e+01 angle pdb=" C VAL C 260 " pdb=" N ASN C 261 " pdb=" CA ASN C 261 " ideal model delta sigma weight residual 124.31 131.61 -7.30 1.67e+00 3.59e-01 1.91e+01 angle pdb=" C GLN C 304 " pdb=" N GLU C 305 " pdb=" CA GLU C 305 " ideal model delta sigma weight residual 121.54 129.86 -8.32 1.91e+00 2.74e-01 1.90e+01 ... (remaining 12056 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.57: 4490 15.57 - 31.13: 576 31.13 - 46.70: 157 46.70 - 62.26: 26 62.26 - 77.83: 8 Dihedral angle restraints: 5257 sinusoidal: 2047 harmonic: 3210 Sorted by residual: dihedral pdb=" CA GLU B 232 " pdb=" C GLU B 232 " pdb=" N ARG B 233 " pdb=" CA ARG B 233 " ideal model delta harmonic sigma weight residual 180.00 146.88 33.12 0 5.00e+00 4.00e-02 4.39e+01 dihedral pdb=" CA GLU B 305 " pdb=" C GLU B 305 " pdb=" N GLY B 306 " pdb=" CA GLY B 306 " ideal model delta harmonic sigma weight residual 180.00 156.39 23.61 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA MET E 66 " pdb=" C MET E 66 " pdb=" N PRO E 67 " pdb=" CA PRO E 67 " ideal model delta harmonic sigma weight residual 180.00 156.89 23.11 0 5.00e+00 4.00e-02 2.14e+01 ... (remaining 5254 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 1327 0.106 - 0.212: 84 0.212 - 0.317: 12 0.317 - 0.423: 1 0.423 - 0.529: 1 Chirality restraints: 1425 Sorted by residual: chirality pdb=" CB ILE E 51 " pdb=" CA ILE E 51 " pdb=" CG1 ILE E 51 " pdb=" CG2 ILE E 51 " both_signs ideal model delta sigma weight residual False 2.64 2.12 0.53 2.00e-01 2.50e+01 6.99e+00 chirality pdb=" CB VAL C 260 " pdb=" CA VAL C 260 " pdb=" CG1 VAL C 260 " pdb=" CG2 VAL C 260 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CB ILE B 200 " pdb=" CA ILE B 200 " pdb=" CG1 ILE B 200 " pdb=" CG2 ILE B 200 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 1422 not shown) Planarity restraints: 1520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET E 66 " 0.052 5.00e-02 4.00e+02 7.84e-02 9.83e+00 pdb=" N PRO E 67 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO E 67 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO E 67 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET D 66 " -0.049 5.00e-02 4.00e+02 7.26e-02 8.44e+00 pdb=" N PRO D 67 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO D 67 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 67 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 51 " -0.043 5.00e-02 4.00e+02 6.41e-02 6.57e+00 pdb=" N PRO D 52 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO D 52 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 52 " -0.036 5.00e-02 4.00e+02 ... (remaining 1517 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 2934 2.84 - 3.35: 7686 3.35 - 3.87: 15151 3.87 - 4.38: 16958 4.38 - 4.90: 27991 Nonbonded interactions: 70720 Sorted by model distance: nonbonded pdb=" O ILE D 51 " pdb=" OG1 THR D 54 " model vdw 2.319 2.440 nonbonded pdb=" O TRP E 259 " pdb=" OG SER E 263 " model vdw 2.324 2.440 nonbonded pdb=" O ALA D 59 " pdb=" OG1 THR D 63 " model vdw 2.341 2.440 nonbonded pdb=" O SER B 90 " pdb=" OG1 THR B 94 " model vdw 2.342 2.440 nonbonded pdb=" OE1 GLU D 81 " pdb=" OG1 THR D 86 " model vdw 2.342 2.440 ... (remaining 70715 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 2 through 42 or (resid 43 and (name N or name CA or name C \ or name O or name CB )) or resid 50 through 231 or resid 236 through 274)) selection = (chain 'E' and (resid 2 through 43 or resid 50 through 274)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.140 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 25.990 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 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 : 0.007 0.073 8888 Z= 0.478 Angle : 1.083 15.411 12061 Z= 0.564 Chirality : 0.062 0.529 1425 Planarity : 0.007 0.078 1520 Dihedral : 15.074 77.831 3207 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 0.44 % Allowed : 13.92 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.96 (0.16), residues: 1126 helix: -4.61 (0.08), residues: 633 sheet: -2.85 (0.39), residues: 114 loop : -2.56 (0.27), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 240 HIS 0.009 0.002 HIS C 97 PHE 0.019 0.002 PHE E 143 TYR 0.019 0.002 TYR C 86 ARG 0.006 0.001 ARG B 307 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 137 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 42 LYS cc_start: 0.7798 (pttp) cc_final: 0.6941 (ptpp) REVERT: B 47 LYS cc_start: 0.9761 (mttm) cc_final: 0.9474 (mttp) REVERT: B 111 GLU cc_start: 0.9282 (mt-10) cc_final: 0.9078 (pt0) REVERT: C 42 LYS cc_start: 0.9462 (ttpt) cc_final: 0.8466 (ttmm) REVERT: C 46 MET cc_start: 0.9000 (ttp) cc_final: 0.8780 (ttp) REVERT: C 47 LYS cc_start: 0.9808 (mttt) cc_final: 0.9423 (mtmm) REVERT: C 89 LEU cc_start: 0.9567 (mt) cc_final: 0.9103 (tp) REVERT: C 141 GLN cc_start: 0.9609 (pp30) cc_final: 0.9370 (pp30) REVERT: C 200 ILE cc_start: 0.9928 (mt) cc_final: 0.9549 (tt) REVERT: D 147 MET cc_start: 0.9313 (mmt) cc_final: 0.8927 (mmm) REVERT: D 171 LYS cc_start: 0.9116 (ttpt) cc_final: 0.8836 (tttm) REVERT: E 76 ASP cc_start: 0.8812 (p0) cc_final: 0.8548 (p0) REVERT: E 88 MET cc_start: 0.9159 (tpp) cc_final: 0.8780 (tpp) REVERT: E 97 ARG cc_start: 0.9122 (mtt180) cc_final: 0.7786 (mmm-85) REVERT: E 147 MET cc_start: 0.9314 (mtt) cc_final: 0.8743 (mmt) REVERT: E 170 GLU cc_start: 0.8909 (pm20) cc_final: 0.8050 (pm20) REVERT: E 222 ARG cc_start: 0.9452 (mtm180) cc_final: 0.9225 (mtt-85) outliers start: 4 outliers final: 2 residues processed: 141 average time/residue: 0.2342 time to fit residues: 44.3516 Evaluate side-chains 91 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 89 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 187 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 2 ASN C 176 GLN C 270 GLN D 6 ASN D 225 ASN E 99 GLN E 225 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8888 Z= 0.164 Angle : 0.642 9.065 12061 Z= 0.325 Chirality : 0.041 0.211 1425 Planarity : 0.005 0.038 1520 Dihedral : 5.332 33.328 1234 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.66 % Allowed : 20.00 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.83 (0.20), residues: 1126 helix: -2.43 (0.16), residues: 649 sheet: -2.40 (0.43), residues: 104 loop : -2.37 (0.29), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP E 259 HIS 0.002 0.001 HIS C 97 PHE 0.009 0.001 PHE D 157 TYR 0.014 0.001 TYR B 86 ARG 0.005 0.000 ARG B 248 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 110 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 42 LYS cc_start: 0.7774 (pttp) cc_final: 0.7397 (pttm) REVERT: B 47 LYS cc_start: 0.9748 (mttm) cc_final: 0.9468 (mttp) REVERT: B 89 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8819 (tt) REVERT: B 111 GLU cc_start: 0.9192 (mt-10) cc_final: 0.8939 (pt0) REVERT: C 16 MET cc_start: 0.9056 (mtp) cc_final: 0.8852 (mtt) REVERT: C 42 LYS cc_start: 0.9429 (ttpt) cc_final: 0.8460 (ttmm) REVERT: C 47 LYS cc_start: 0.9801 (mttt) cc_final: 0.9496 (mtmm) REVERT: C 48 LEU cc_start: 0.9707 (OUTLIER) cc_final: 0.9481 (mm) REVERT: C 89 LEU cc_start: 0.9588 (mt) cc_final: 0.9064 (tp) REVERT: C 295 MET cc_start: 0.9481 (mmm) cc_final: 0.9132 (mmm) REVERT: D 11 GLU cc_start: 0.9453 (mm-30) cc_final: 0.9015 (mm-30) REVERT: D 81 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8212 (mm-30) REVERT: D 146 PHE cc_start: 0.9096 (m-80) cc_final: 0.8635 (t80) REVERT: D 147 MET cc_start: 0.9196 (mmt) cc_final: 0.8843 (mmp) REVERT: D 221 TYR cc_start: 0.8935 (t80) cc_final: 0.8320 (t80) REVERT: E 83 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8834 (mt-10) REVERT: E 88 MET cc_start: 0.9167 (tpp) cc_final: 0.8847 (tpp) REVERT: E 170 GLU cc_start: 0.8433 (pm20) cc_final: 0.7801 (pm20) REVERT: E 222 ARG cc_start: 0.9357 (mtm180) cc_final: 0.9094 (mtt-85) outliers start: 15 outliers final: 7 residues processed: 122 average time/residue: 0.1965 time to fit residues: 34.0618 Evaluate side-chains 94 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 100 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 30.0000 chunk 31 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 101 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 90 optimal weight: 20.0000 chunk 34 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 GLN B 194 HIS B 263 HIS ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 HIS C 207 GLN C 214 GLN ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8888 Z= 0.238 Angle : 0.650 9.239 12061 Z= 0.326 Chirality : 0.041 0.197 1425 Planarity : 0.004 0.037 1520 Dihedral : 4.806 31.517 1234 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.87 % Allowed : 21.88 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.24), residues: 1126 helix: -0.61 (0.20), residues: 648 sheet: -2.13 (0.43), residues: 114 loop : -2.04 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 259 HIS 0.003 0.001 HIS C 194 PHE 0.016 0.001 PHE D 157 TYR 0.015 0.001 TYR B 293 ARG 0.003 0.000 ARG B 248 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 93 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 LYS cc_start: 0.7690 (pttp) cc_final: 0.6834 (ptpp) REVERT: B 47 LYS cc_start: 0.9783 (mttm) cc_final: 0.9515 (mttp) REVERT: B 89 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8777 (tt) REVERT: C 42 LYS cc_start: 0.9483 (ttpt) cc_final: 0.8482 (ttmt) REVERT: C 47 LYS cc_start: 0.9820 (mttt) cc_final: 0.9462 (mtmm) REVERT: C 89 LEU cc_start: 0.9482 (mt) cc_final: 0.9203 (tp) REVERT: C 133 MET cc_start: 0.9336 (mtm) cc_final: 0.8642 (ptp) REVERT: D 58 LEU cc_start: 0.9698 (OUTLIER) cc_final: 0.9494 (mm) REVERT: D 81 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8114 (mm-30) REVERT: D 146 PHE cc_start: 0.8990 (m-80) cc_final: 0.8601 (t80) REVERT: D 147 MET cc_start: 0.9322 (mmt) cc_final: 0.9058 (mmp) REVERT: D 221 TYR cc_start: 0.9024 (t80) cc_final: 0.8420 (t80) REVERT: E 11 GLU cc_start: 0.9399 (mm-30) cc_final: 0.8638 (tp30) REVERT: E 145 ARG cc_start: 0.6822 (OUTLIER) cc_final: 0.5915 (mtm-85) REVERT: E 147 MET cc_start: 0.9407 (mtt) cc_final: 0.9011 (mtp) REVERT: E 223 LEU cc_start: 0.9655 (OUTLIER) cc_final: 0.9389 (mm) outliers start: 35 outliers final: 22 residues processed: 123 average time/residue: 0.1854 time to fit residues: 33.1214 Evaluate side-chains 107 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 81 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 TYR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 145 ARG Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 266 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 9.9990 chunk 52 optimal weight: 20.0000 chunk 11 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 108 optimal weight: 20.0000 chunk 53 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 chunk 90 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 ASN C 38 ASN ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8888 Z= 0.206 Angle : 0.623 9.337 12061 Z= 0.306 Chirality : 0.041 0.195 1425 Planarity : 0.003 0.043 1520 Dihedral : 4.653 31.225 1234 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 4.31 % Allowed : 23.20 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.25), residues: 1126 helix: 0.07 (0.21), residues: 649 sheet: -1.94 (0.44), residues: 114 loop : -1.80 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 259 HIS 0.004 0.001 HIS C 194 PHE 0.013 0.001 PHE D 157 TYR 0.012 0.001 TYR E 93 ARG 0.003 0.000 ARG E 222 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 95 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 LYS cc_start: 0.7628 (pttp) cc_final: 0.6771 (ptpp) REVERT: B 47 LYS cc_start: 0.9774 (mttm) cc_final: 0.9492 (mttp) REVERT: B 89 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8659 (tt) REVERT: B 133 MET cc_start: 0.9427 (mtm) cc_final: 0.9112 (mtm) REVERT: C 38 ASN cc_start: 0.7955 (OUTLIER) cc_final: 0.7693 (p0) REVERT: C 42 LYS cc_start: 0.9447 (ttpt) cc_final: 0.8909 (ttmt) REVERT: C 89 LEU cc_start: 0.9416 (mt) cc_final: 0.9149 (tp) REVERT: C 133 MET cc_start: 0.9312 (mtm) cc_final: 0.8552 (ptp) REVERT: C 295 MET cc_start: 0.9310 (mmm) cc_final: 0.9023 (mmm) REVERT: D 11 GLU cc_start: 0.9459 (mm-30) cc_final: 0.9048 (mm-30) REVERT: D 81 GLU cc_start: 0.8648 (mm-30) cc_final: 0.7962 (mm-30) REVERT: D 83 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8446 (mt-10) REVERT: D 146 PHE cc_start: 0.8933 (OUTLIER) cc_final: 0.8641 (t80) REVERT: D 147 MET cc_start: 0.9319 (mmt) cc_final: 0.9063 (mmp) REVERT: D 221 TYR cc_start: 0.9027 (t80) cc_final: 0.8217 (t80) REVERT: E 11 GLU cc_start: 0.9277 (mm-30) cc_final: 0.8490 (tp30) REVERT: E 147 MET cc_start: 0.9374 (mtt) cc_final: 0.8987 (mtp) REVERT: E 223 LEU cc_start: 0.9626 (OUTLIER) cc_final: 0.9342 (mm) outliers start: 39 outliers final: 23 residues processed: 126 average time/residue: 0.1747 time to fit residues: 32.4287 Evaluate side-chains 106 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 79 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 146 PHE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 145 ARG Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 266 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 80 optimal weight: 0.0970 chunk 44 optimal weight: 0.9980 chunk 92 optimal weight: 8.9990 chunk 74 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 55 optimal weight: 30.0000 chunk 97 optimal weight: 0.9980 chunk 27 optimal weight: 0.1980 chunk 36 optimal weight: 10.0000 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8888 Z= 0.143 Angle : 0.603 11.467 12061 Z= 0.287 Chirality : 0.041 0.186 1425 Planarity : 0.003 0.041 1520 Dihedral : 4.464 30.547 1234 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.20 % Allowed : 24.42 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.26), residues: 1126 helix: 0.36 (0.21), residues: 649 sheet: -1.68 (0.45), residues: 114 loop : -1.73 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 259 HIS 0.008 0.001 HIS C 37 PHE 0.009 0.001 PHE D 157 TYR 0.022 0.001 TYR E 93 ARG 0.002 0.000 ARG C 136 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 92 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 LYS cc_start: 0.7642 (pttp) cc_final: 0.6791 (ptpp) REVERT: B 89 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8657 (tt) REVERT: C 42 LYS cc_start: 0.9593 (ttpt) cc_final: 0.9161 (tttt) REVERT: C 48 LEU cc_start: 0.9717 (OUTLIER) cc_final: 0.9389 (mm) REVERT: C 89 LEU cc_start: 0.9432 (mt) cc_final: 0.9164 (tp) REVERT: C 131 LYS cc_start: 0.9372 (tppt) cc_final: 0.9130 (tppt) REVERT: C 133 MET cc_start: 0.9326 (mtm) cc_final: 0.8686 (ptp) REVERT: C 295 MET cc_start: 0.9296 (mmm) cc_final: 0.8992 (mmm) REVERT: D 11 GLU cc_start: 0.9389 (mm-30) cc_final: 0.9012 (mm-30) REVERT: D 58 LEU cc_start: 0.9680 (OUTLIER) cc_final: 0.9365 (mm) REVERT: D 65 LEU cc_start: 0.9483 (mt) cc_final: 0.9179 (tt) REVERT: D 81 GLU cc_start: 0.8568 (mm-30) cc_final: 0.7866 (mm-30) REVERT: D 83 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8461 (mt-10) REVERT: D 146 PHE cc_start: 0.8854 (m-80) cc_final: 0.8294 (t80) REVERT: D 147 MET cc_start: 0.9262 (mmt) cc_final: 0.8978 (mmp) REVERT: D 221 TYR cc_start: 0.8903 (t80) cc_final: 0.8305 (t80) REVERT: E 88 MET cc_start: 0.8829 (tpp) cc_final: 0.8566 (tpp) REVERT: E 147 MET cc_start: 0.9340 (mtt) cc_final: 0.9005 (mtp) outliers start: 29 outliers final: 16 residues processed: 113 average time/residue: 0.1749 time to fit residues: 29.3677 Evaluate side-chains 104 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 85 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 152 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 108 optimal weight: 30.0000 chunk 89 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 9 optimal weight: 0.6980 chunk 35 optimal weight: 0.0060 chunk 56 optimal weight: 0.7980 chunk 104 optimal weight: 5.9990 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8888 Z= 0.147 Angle : 0.605 9.795 12061 Z= 0.286 Chirality : 0.040 0.141 1425 Planarity : 0.003 0.039 1520 Dihedral : 4.326 30.289 1234 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.20 % Allowed : 25.41 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.26), residues: 1126 helix: 0.58 (0.21), residues: 652 sheet: -1.53 (0.47), residues: 112 loop : -1.59 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 259 HIS 0.003 0.000 HIS C 194 PHE 0.009 0.001 PHE D 157 TYR 0.019 0.001 TYR E 93 ARG 0.001 0.000 ARG C 173 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 93 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 LYS cc_start: 0.7617 (pttp) cc_final: 0.6775 (ptpp) REVERT: B 89 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8665 (tt) REVERT: B 133 MET cc_start: 0.9412 (mtm) cc_final: 0.8615 (ptp) REVERT: B 182 ILE cc_start: 0.9464 (mt) cc_final: 0.9239 (mm) REVERT: C 42 LYS cc_start: 0.9657 (ttpt) cc_final: 0.8885 (ttmm) REVERT: C 48 LEU cc_start: 0.9681 (OUTLIER) cc_final: 0.9260 (mm) REVERT: C 131 LYS cc_start: 0.9389 (tppt) cc_final: 0.9140 (tppt) REVERT: C 133 MET cc_start: 0.9323 (mtm) cc_final: 0.8655 (ptp) REVERT: D 65 LEU cc_start: 0.9481 (mt) cc_final: 0.9179 (tt) REVERT: D 81 GLU cc_start: 0.8561 (mm-30) cc_final: 0.7872 (mm-30) REVERT: D 83 GLU cc_start: 0.8880 (mm-30) cc_final: 0.8454 (mt-10) REVERT: D 146 PHE cc_start: 0.8771 (m-80) cc_final: 0.8494 (t80) REVERT: D 147 MET cc_start: 0.9280 (mmt) cc_final: 0.9038 (mmp) REVERT: D 148 ILE cc_start: 0.9078 (mt) cc_final: 0.8831 (mm) REVERT: D 221 TYR cc_start: 0.8953 (t80) cc_final: 0.8625 (t80) REVERT: E 11 GLU cc_start: 0.9294 (mm-30) cc_final: 0.8764 (tp30) REVERT: E 147 MET cc_start: 0.9337 (mtt) cc_final: 0.9061 (mtp) outliers start: 29 outliers final: 17 residues processed: 115 average time/residue: 0.1855 time to fit residues: 30.8578 Evaluate side-chains 106 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 87 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 266 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 79 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 67 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 66 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8888 Z= 0.260 Angle : 0.679 9.577 12061 Z= 0.326 Chirality : 0.041 0.147 1425 Planarity : 0.003 0.042 1520 Dihedral : 4.422 29.781 1234 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 3.43 % Allowed : 25.64 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.26), residues: 1126 helix: 0.82 (0.21), residues: 649 sheet: -1.53 (0.46), residues: 112 loop : -1.50 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 259 HIS 0.004 0.001 HIS C 194 PHE 0.014 0.001 PHE D 157 TYR 0.023 0.002 TYR B 86 ARG 0.002 0.000 ARG E 145 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 83 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 42 LYS cc_start: 0.7633 (pttp) cc_final: 0.7321 (pttm) REVERT: B 86 TYR cc_start: 0.8612 (m-10) cc_final: 0.8156 (m-10) REVERT: B 89 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8616 (tt) REVERT: C 42 LYS cc_start: 0.9607 (ttpt) cc_final: 0.8922 (ttmm) REVERT: C 48 LEU cc_start: 0.9715 (OUTLIER) cc_final: 0.9426 (mm) REVERT: C 131 LYS cc_start: 0.9458 (tppt) cc_final: 0.9224 (tppt) REVERT: D 81 GLU cc_start: 0.8686 (mm-30) cc_final: 0.7971 (mm-30) REVERT: D 83 GLU cc_start: 0.8948 (mm-30) cc_final: 0.8522 (mt-10) REVERT: D 146 PHE cc_start: 0.8813 (OUTLIER) cc_final: 0.8523 (t80) REVERT: D 147 MET cc_start: 0.9386 (mmt) cc_final: 0.9150 (mmp) REVERT: E 11 GLU cc_start: 0.9352 (mm-30) cc_final: 0.9047 (tp30) REVERT: E 81 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8493 (mm-30) REVERT: E 88 MET cc_start: 0.9027 (tpp) cc_final: 0.8762 (tpp) REVERT: E 147 MET cc_start: 0.9357 (mtt) cc_final: 0.9055 (mtp) outliers start: 31 outliers final: 24 residues processed: 106 average time/residue: 0.1882 time to fit residues: 28.8079 Evaluate side-chains 107 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 80 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 146 PHE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 266 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 53 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 84 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 103 optimal weight: 0.0370 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8888 Z= 0.167 Angle : 0.637 10.016 12061 Z= 0.297 Chirality : 0.041 0.140 1425 Planarity : 0.003 0.038 1520 Dihedral : 4.364 29.931 1234 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.98 % Allowed : 26.41 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.26), residues: 1126 helix: 0.92 (0.21), residues: 649 sheet: -1.54 (0.46), residues: 112 loop : -1.50 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 259 HIS 0.003 0.001 HIS C 194 PHE 0.010 0.001 PHE D 157 TYR 0.021 0.001 TYR B 86 ARG 0.001 0.000 ARG C 307 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 88 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 LYS cc_start: 0.7643 (pttp) cc_final: 0.6793 (ptpp) REVERT: B 86 TYR cc_start: 0.8481 (m-10) cc_final: 0.7950 (m-10) REVERT: B 89 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8548 (tt) REVERT: B 133 MET cc_start: 0.9402 (mtm) cc_final: 0.8679 (ptp) REVERT: C 42 LYS cc_start: 0.9589 (ttpt) cc_final: 0.8901 (ttmm) REVERT: C 48 LEU cc_start: 0.9698 (OUTLIER) cc_final: 0.9366 (mm) REVERT: C 131 LYS cc_start: 0.9451 (tppt) cc_final: 0.9233 (tppt) REVERT: C 133 MET cc_start: 0.9393 (mtm) cc_final: 0.8681 (ptp) REVERT: D 11 GLU cc_start: 0.9442 (mm-30) cc_final: 0.8960 (mm-30) REVERT: D 81 GLU cc_start: 0.8611 (mm-30) cc_final: 0.7932 (mm-30) REVERT: D 83 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8506 (mt-10) REVERT: D 146 PHE cc_start: 0.8744 (m-80) cc_final: 0.8369 (t80) REVERT: D 147 MET cc_start: 0.9321 (mmt) cc_final: 0.9083 (mmp) REVERT: D 221 TYR cc_start: 0.9028 (t80) cc_final: 0.8463 (t80) REVERT: E 11 GLU cc_start: 0.9328 (mm-30) cc_final: 0.8701 (mm-30) REVERT: E 81 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8184 (mm-30) REVERT: E 147 MET cc_start: 0.9339 (mtt) cc_final: 0.9050 (mtp) outliers start: 27 outliers final: 23 residues processed: 109 average time/residue: 0.1806 time to fit residues: 28.9193 Evaluate side-chains 109 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 84 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 266 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 78 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8888 Z= 0.247 Angle : 0.678 9.690 12061 Z= 0.321 Chirality : 0.041 0.142 1425 Planarity : 0.003 0.040 1520 Dihedral : 4.394 29.411 1234 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 3.31 % Allowed : 25.86 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.26), residues: 1126 helix: 0.91 (0.21), residues: 652 sheet: -1.57 (0.46), residues: 112 loop : -1.41 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 259 HIS 0.004 0.001 HIS C 37 PHE 0.012 0.001 PHE D 157 TYR 0.023 0.002 TYR B 86 ARG 0.002 0.000 ARG C 307 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 81 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 LYS cc_start: 0.7604 (pttp) cc_final: 0.7275 (pttm) REVERT: B 86 TYR cc_start: 0.8676 (m-10) cc_final: 0.8153 (m-10) REVERT: B 89 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8551 (tt) REVERT: B 133 MET cc_start: 0.9392 (mtm) cc_final: 0.8881 (ptp) REVERT: C 42 LYS cc_start: 0.9560 (ttpt) cc_final: 0.8863 (ttmm) REVERT: C 48 LEU cc_start: 0.9721 (OUTLIER) cc_final: 0.9431 (mm) REVERT: C 131 LYS cc_start: 0.9468 (tppt) cc_final: 0.9252 (tppt) REVERT: C 133 MET cc_start: 0.9431 (mtm) cc_final: 0.8720 (ptp) REVERT: D 11 GLU cc_start: 0.9428 (mm-30) cc_final: 0.8943 (mm-30) REVERT: D 81 GLU cc_start: 0.8620 (mm-30) cc_final: 0.7910 (mm-30) REVERT: D 147 MET cc_start: 0.9419 (mmt) cc_final: 0.9211 (mmp) REVERT: D 221 TYR cc_start: 0.9034 (t80) cc_final: 0.8446 (t80) REVERT: E 11 GLU cc_start: 0.9325 (mm-30) cc_final: 0.8481 (mm-30) REVERT: E 81 GLU cc_start: 0.8994 (mm-30) cc_final: 0.8262 (mm-30) REVERT: E 88 MET cc_start: 0.8881 (tpp) cc_final: 0.8549 (tpp) REVERT: E 147 MET cc_start: 0.9365 (mtt) cc_final: 0.9047 (mtp) outliers start: 30 outliers final: 25 residues processed: 105 average time/residue: 0.1781 time to fit residues: 27.3458 Evaluate side-chains 106 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 79 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 TYR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 266 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 88 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 chunk 68 optimal weight: 7.9990 chunk 54 optimal weight: 20.0000 chunk 70 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8888 Z= 0.190 Angle : 0.659 10.124 12061 Z= 0.306 Chirality : 0.041 0.139 1425 Planarity : 0.003 0.038 1520 Dihedral : 4.367 29.671 1234 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.65 % Allowed : 26.85 % Favored : 70.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.26), residues: 1126 helix: 1.03 (0.21), residues: 646 sheet: -1.56 (0.46), residues: 114 loop : -1.42 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 259 HIS 0.004 0.001 HIS C 194 PHE 0.011 0.001 PHE D 157 TYR 0.021 0.001 TYR B 86 ARG 0.002 0.000 ARG C 307 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 83 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 LYS cc_start: 0.7623 (pttp) cc_final: 0.7302 (pttm) REVERT: B 86 TYR cc_start: 0.8567 (m-10) cc_final: 0.8146 (m-10) REVERT: B 89 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8501 (tt) REVERT: B 133 MET cc_start: 0.9349 (mtm) cc_final: 0.8853 (ptp) REVERT: C 42 LYS cc_start: 0.9592 (ttpt) cc_final: 0.8952 (ttmm) REVERT: C 48 LEU cc_start: 0.9717 (mm) cc_final: 0.9408 (mm) REVERT: C 131 LYS cc_start: 0.9461 (tppt) cc_final: 0.9250 (tppt) REVERT: C 133 MET cc_start: 0.9394 (mtm) cc_final: 0.8762 (ptp) REVERT: D 11 GLU cc_start: 0.9386 (mm-30) cc_final: 0.8899 (mm-30) REVERT: D 81 GLU cc_start: 0.8597 (mm-30) cc_final: 0.7931 (mm-30) REVERT: D 147 MET cc_start: 0.9494 (mmt) cc_final: 0.9259 (mmp) REVERT: D 221 TYR cc_start: 0.8968 (t80) cc_final: 0.8680 (t80) REVERT: E 11 GLU cc_start: 0.9319 (mm-30) cc_final: 0.8728 (mm-30) REVERT: E 81 GLU cc_start: 0.8951 (mm-30) cc_final: 0.8242 (mm-30) REVERT: E 88 MET cc_start: 0.8857 (tpp) cc_final: 0.8518 (tpp) REVERT: E 147 MET cc_start: 0.9356 (mtt) cc_final: 0.9035 (mtp) outliers start: 24 outliers final: 22 residues processed: 102 average time/residue: 0.1820 time to fit residues: 27.7340 Evaluate side-chains 106 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 83 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 266 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 0.4980 chunk 88 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 263 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.054149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.042763 restraints weight = 46810.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.044239 restraints weight = 25354.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.045249 restraints weight = 16686.374| |-----------------------------------------------------------------------------| r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8888 Z= 0.194 Angle : 0.654 9.949 12061 Z= 0.305 Chirality : 0.041 0.139 1425 Planarity : 0.003 0.038 1520 Dihedral : 4.317 29.666 1234 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 3.09 % Allowed : 26.41 % Favored : 70.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.26), residues: 1126 helix: 1.11 (0.21), residues: 649 sheet: -1.66 (0.46), residues: 108 loop : -1.42 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 259 HIS 0.004 0.001 HIS C 37 PHE 0.011 0.001 PHE D 157 TYR 0.021 0.001 TYR B 86 ARG 0.002 0.000 ARG C 307 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1587.37 seconds wall clock time: 29 minutes 50.02 seconds (1790.02 seconds total)