Starting phenix.real_space_refine on Sat Aug 3 12:24:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc3_37429/08_2024/8wc3_37429_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc3_37429/08_2024/8wc3_37429.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc3_37429/08_2024/8wc3_37429.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc3_37429/08_2024/8wc3_37429.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc3_37429/08_2024/8wc3_37429_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc3_37429/08_2024/8wc3_37429_neut.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 59 5.16 5 C 5376 2.51 5 N 1427 2.21 5 O 1556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 14": "OE1" <-> "OE2" Residue "A ARG 232": "NH1" <-> "NH2" Residue "A GLU 337": "OE1" <-> "OE2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 309": "NH1" <-> "NH2" Residue "S TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8418 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1835 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 2 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 4, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 62 Chain: "B" Number of atoms: 2491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2491 Classifications: {'peptide': 332} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 326} Chain breaks: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 51 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "R" Number of atoms: 1970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 1970 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 12, 'TRANS': 252} Chain breaks: 1 Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 185 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 3, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 83 Chain: "S" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1734 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 40 Chain: "Y" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 376 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "R" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'UJL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.24, per 1000 atoms: 0.62 Number of scatterers: 8418 At special positions: 0 Unit cell: (117.3, 96.05, 129.2, 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 59 16.00 O 1556 8.00 N 1427 7.00 C 5376 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 181 " distance=2.05 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.37 Conformation dependent library (CDL) restraints added in 1.7 seconds 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2094 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 14 sheets defined 36.2% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.925A pdb=" N ALA A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.595A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 216 removed outlier: 4.040A pdb=" N GLN A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N CYS A 214 " --> pdb=" O TRP A 211 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 245 Processing helix chain 'A' and resid 260 through 269 removed outlier: 3.659A pdb=" N LEU A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 269 " --> pdb=" O ALA A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 285 removed outlier: 3.832A pdb=" N ALA A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 318 removed outlier: 4.107A pdb=" N THR A 302 " --> pdb=" O ASP A 298 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ARG A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA A 304 " --> pdb=" O ARG A 300 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N SER A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR A 317 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'B' and resid 9 through 24 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.881A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 50 removed outlier: 4.033A pdb=" N VAL R 43 " --> pdb=" O GLY R 39 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE R 44 " --> pdb=" O ASN R 40 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE R 50 " --> pdb=" O SER R 46 " (cutoff:3.500A) Processing helix chain 'R' and resid 55 through 74 removed outlier: 3.511A pdb=" N TRP R 59 " --> pdb=" O THR R 55 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU R 60 " --> pdb=" O PRO R 56 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU R 61 " --> pdb=" O THR R 57 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY R 72 " --> pdb=" O ASP R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 85 removed outlier: 3.528A pdb=" N CYS R 78 " --> pdb=" O LEU R 74 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG R 82 " --> pdb=" O CYS R 78 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR R 83 " --> pdb=" O SER R 79 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU R 85 " --> pdb=" O VAL R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 126 removed outlier: 3.755A pdb=" N CYS R 95 " --> pdb=" O GLY R 91 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS R 96 " --> pdb=" O GLU R 92 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL R 97 " --> pdb=" O ILE R 93 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER R 100 " --> pdb=" O LYS R 96 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU R 105 " --> pdb=" O THR R 101 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER R 106 " --> pdb=" O ASP R 102 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 134 Processing helix chain 'R' and resid 135 through 160 Proline residue: R 150 - end of helix Processing helix chain 'R' and resid 167 through 174 removed outlier: 3.565A pdb=" N GLN R 174 " --> pdb=" O LEU R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 221 removed outlier: 3.798A pdb=" N LEU R 192 " --> pdb=" O VAL R 188 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ILE R 200 " --> pdb=" O THR R 196 " (cutoff:3.500A) Proline residue: R 201 - end of helix removed outlier: 3.619A pdb=" N PHE R 214 " --> pdb=" O TYR R 210 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG R 221 " --> pdb=" O LYS R 217 " (cutoff:3.500A) Processing helix chain 'R' and resid 248 through 275 Proline residue: R 263 - end of helix Proline residue: R 272 - end of helix Processing helix chain 'R' and resid 279 through 301 removed outlier: 4.938A pdb=" N ASN R 293 " --> pdb=" O PHE R 289 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N SER R 294 " --> pdb=" O GLY R 290 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA R 295 " --> pdb=" O TYR R 291 " (cutoff:3.500A) Proline residue: R 298 - end of helix removed outlier: 3.556A pdb=" N TYR R 301 " --> pdb=" O ASN R 297 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 220 through 224 removed outlier: 4.186A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 24 removed outlier: 3.509A pdb=" N VAL Y 16 " --> pdb=" O ALA Y 12 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU Y 17 " --> pdb=" O ARG Y 13 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASN Y 24 " --> pdb=" O LYS Y 20 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 44 removed outlier: 3.919A pdb=" N ALA Y 35 " --> pdb=" O SER Y 31 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP Y 36 " --> pdb=" O LYS Y 32 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU Y 37 " --> pdb=" O ALA Y 33 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N MET Y 38 " --> pdb=" O ALA Y 34 " (cutoff:3.500A) Processing helix chain 'Y' and resid 45 through 48 removed outlier: 3.755A pdb=" N ASP Y 48 " --> pdb=" O ALA Y 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 45 through 48' Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 3.534A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N VAL A 254 " --> pdb=" O TYR A 327 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.519A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.907A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.965A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.645A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.699A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET B 217 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.648A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 Processing sheet with id=AB2, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.648A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 142 Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.791A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 194 through 195 369 hydrogen bonds defined for protein. 1047 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: 2.12 Time building geometry restraints manager: 3.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1367 1.31 - 1.44: 2457 1.44 - 1.57: 4698 1.57 - 1.70: 1 1.70 - 1.84: 85 Bond restraints: 8608 Sorted by residual: bond pdb=" C LEU R 74 " pdb=" O LEU R 74 " ideal model delta sigma weight residual 1.234 1.188 0.046 8.30e-03 1.45e+04 3.05e+01 bond pdb=" N ILE R 103 " pdb=" CA ILE R 103 " ideal model delta sigma weight residual 1.460 1.395 0.065 1.32e-02 5.74e+03 2.42e+01 bond pdb=" CA LEU Y 15 " pdb=" C LEU Y 15 " ideal model delta sigma weight residual 1.522 1.457 0.065 1.36e-02 5.41e+03 2.29e+01 bond pdb=" CA ILE R 75 " pdb=" CB ILE R 75 " ideal model delta sigma weight residual 1.540 1.480 0.059 1.29e-02 6.01e+03 2.10e+01 bond pdb=" CA GLN A 24 " pdb=" C GLN A 24 " ideal model delta sigma weight residual 1.524 1.466 0.058 1.29e-02 6.01e+03 2.00e+01 ... (remaining 8603 not shown) Histogram of bond angle deviations from ideal: 100.28 - 107.37: 306 107.37 - 114.45: 4890 114.45 - 121.53: 4371 121.53 - 128.62: 2076 128.62 - 135.70: 75 Bond angle restraints: 11718 Sorted by residual: angle pdb=" N LYS Y 14 " pdb=" CA LYS Y 14 " pdb=" C LYS Y 14 " ideal model delta sigma weight residual 111.36 123.27 -11.91 1.09e+00 8.42e-01 1.19e+02 angle pdb=" N ILE R 75 " pdb=" CA ILE R 75 " pdb=" C ILE R 75 " ideal model delta sigma weight residual 110.72 120.96 -10.24 1.01e+00 9.80e-01 1.03e+02 angle pdb=" N ALA Y 10 " pdb=" CA ALA Y 10 " pdb=" C ALA Y 10 " ideal model delta sigma weight residual 112.12 124.44 -12.32 1.34e+00 5.57e-01 8.46e+01 angle pdb=" N ALA Y 12 " pdb=" CA ALA Y 12 " pdb=" C ALA Y 12 " ideal model delta sigma weight residual 111.71 102.47 9.24 1.15e+00 7.56e-01 6.45e+01 angle pdb=" N THR S 238 " pdb=" CA THR S 238 " pdb=" C THR S 238 " ideal model delta sigma weight residual 109.96 120.60 -10.64 1.50e+00 4.44e-01 5.03e+01 ... (remaining 11713 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.03: 4491 16.03 - 32.05: 414 32.05 - 48.08: 104 48.08 - 64.10: 23 64.10 - 80.13: 9 Dihedral angle restraints: 5041 sinusoidal: 1795 harmonic: 3246 Sorted by residual: dihedral pdb=" C TYR S 235 " pdb=" N TYR S 235 " pdb=" CA TYR S 235 " pdb=" CB TYR S 235 " ideal model delta harmonic sigma weight residual -122.60 -150.56 27.96 0 2.50e+00 1.60e-01 1.25e+02 dihedral pdb=" N TYR S 235 " pdb=" C TYR S 235 " pdb=" CA TYR S 235 " pdb=" CB TYR S 235 " ideal model delta harmonic sigma weight residual 122.80 149.53 -26.73 0 2.50e+00 1.60e-01 1.14e+02 dihedral pdb=" CB CYS S 22 " pdb=" SG CYS S 22 " pdb=" SG CYS S 96 " pdb=" CB CYS S 96 " ideal model delta sinusoidal sigma weight residual 93.00 43.24 49.76 1 1.00e+01 1.00e-02 3.40e+01 ... (remaining 5038 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.231: 1333 0.231 - 0.461: 16 0.461 - 0.692: 0 0.692 - 0.922: 0 0.922 - 1.153: 1 Chirality restraints: 1350 Sorted by residual: chirality pdb=" CA TYR S 235 " pdb=" N TYR S 235 " pdb=" C TYR S 235 " pdb=" CB TYR S 235 " both_signs ideal model delta sigma weight residual False 2.51 1.36 1.15 2.00e-01 2.50e+01 3.32e+01 chirality pdb=" CA ILE R 75 " pdb=" N ILE R 75 " pdb=" C ILE R 75 " pdb=" CB ILE R 75 " both_signs ideal model delta sigma weight residual False 2.43 2.00 0.43 2.00e-01 2.50e+01 4.69e+00 chirality pdb=" CA ALA Y 10 " pdb=" N ALA Y 10 " pdb=" C ALA Y 10 " pdb=" CB ALA Y 10 " both_signs ideal model delta sigma weight residual False 2.48 2.09 0.40 2.00e-01 2.50e+01 3.93e+00 ... (remaining 1347 not shown) Planarity restraints: 1484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 75 " 0.021 2.00e-02 2.50e+03 4.16e-02 1.73e+01 pdb=" C ILE R 75 " -0.072 2.00e-02 2.50e+03 pdb=" O ILE R 75 " 0.027 2.00e-02 2.50e+03 pdb=" N MET R 76 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS R 217 " 0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C LYS R 217 " -0.056 2.00e-02 2.50e+03 pdb=" O LYS R 217 " 0.022 2.00e-02 2.50e+03 pdb=" N GLY R 218 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 285 " 0.015 2.00e-02 2.50e+03 3.00e-02 9.03e+00 pdb=" C TYR A 285 " -0.052 2.00e-02 2.50e+03 pdb=" O TYR A 285 " 0.019 2.00e-02 2.50e+03 pdb=" N THR A 286 " 0.017 2.00e-02 2.50e+03 ... (remaining 1481 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.06: 2 2.06 - 2.77: 1615 2.77 - 3.48: 11105 3.48 - 4.19: 18842 4.19 - 4.90: 33918 Nonbonded interactions: 65482 Sorted by model distance: nonbonded pdb=" NH1 ARG A 352 " pdb=" O ILE R 223 " model vdw 1.356 3.120 nonbonded pdb=" OG SER R 100 " pdb=" CG2 ILE R 158 " model vdw 1.809 3.460 nonbonded pdb=" OG SER B 281 " pdb=" O HIS Y 44 " model vdw 2.232 3.040 nonbonded pdb=" N GLN R 52 " pdb=" OE1 GLN R 52 " model vdw 2.246 3.120 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.260 3.040 ... (remaining 65477 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: 0.850 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: 0.000 Extract box with map and model: 0.420 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 25.940 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 8608 Z= 0.425 Angle : 0.955 12.323 11718 Z= 0.637 Chirality : 0.071 1.153 1350 Planarity : 0.005 0.049 1484 Dihedral : 13.967 80.127 2938 Min Nonbonded Distance : 1.356 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.40 % Allowed : 2.68 % Favored : 95.93 % Cbeta Deviations : 0.19 % 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: -1.08 (0.25), residues: 1099 helix: 0.21 (0.28), residues: 348 sheet: 0.08 (0.33), residues: 276 loop : -1.91 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP R 261 HIS 0.003 0.001 HIS B 183 PHE 0.017 0.001 PHE R 289 TYR 0.026 0.001 TYR S 235 ARG 0.007 0.000 ARG R 309 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 144 time to evaluate : 0.958 Fit side-chains REVERT: S 235 TYR cc_start: 0.6621 (OUTLIER) cc_final: 0.5976 (t80) outliers start: 12 outliers final: 4 residues processed: 152 average time/residue: 1.0779 time to fit residues: 175.5809 Evaluate side-chains 100 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 95 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 167 VAL Chi-restraints excluded: chain R residue 309 ARG Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 56 optimal weight: 30.0000 chunk 44 optimal weight: 9.9990 chunk 86 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 99 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 261 GLN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8608 Z= 0.229 Angle : 0.608 8.040 11718 Z= 0.320 Chirality : 0.044 0.275 1350 Planarity : 0.004 0.049 1484 Dihedral : 5.179 49.038 1224 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.26 % Allowed : 13.39 % Favored : 83.35 % 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: -0.06 (0.26), residues: 1099 helix: 1.75 (0.28), residues: 352 sheet: 0.14 (0.33), residues: 276 loop : -1.58 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.006 0.001 HIS S 35 PHE 0.014 0.002 PHE B 151 TYR 0.034 0.002 TYR S 235 ARG 0.008 0.001 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 99 time to evaluate : 0.848 Fit side-chains REVERT: R 294 SER cc_start: 0.7334 (t) cc_final: 0.6859 (m) outliers start: 28 outliers final: 17 residues processed: 117 average time/residue: 1.0252 time to fit residues: 129.1743 Evaluate side-chains 104 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 90 PHE Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 153 TYR Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 268 THR Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 226 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8608 Z= 0.299 Angle : 0.636 7.613 11718 Z= 0.336 Chirality : 0.045 0.280 1350 Planarity : 0.004 0.046 1484 Dihedral : 4.848 47.161 1216 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.38 % Allowed : 16.53 % Favored : 80.09 % 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: -0.10 (0.26), residues: 1099 helix: 1.78 (0.28), residues: 351 sheet: 0.06 (0.32), residues: 278 loop : -1.62 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 63 HIS 0.005 0.001 HIS B 183 PHE 0.017 0.002 PHE B 151 TYR 0.036 0.002 TYR S 235 ARG 0.013 0.001 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 96 time to evaluate : 1.004 Fit side-chains REVERT: S 235 TYR cc_start: 0.6585 (OUTLIER) cc_final: 0.5664 (t80) outliers start: 29 outliers final: 21 residues processed: 115 average time/residue: 1.0615 time to fit residues: 131.4618 Evaluate side-chains 109 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 87 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 153 TYR Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 268 THR Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 0.0870 chunk 106 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 95 optimal weight: 40.0000 chunk 28 optimal weight: 3.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8608 Z= 0.197 Angle : 0.563 6.663 11718 Z= 0.296 Chirality : 0.042 0.239 1350 Planarity : 0.004 0.049 1484 Dihedral : 4.573 48.077 1215 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.07 % Allowed : 17.93 % Favored : 78.00 % 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: 0.08 (0.26), residues: 1099 helix: 1.99 (0.28), residues: 351 sheet: 0.25 (0.33), residues: 269 loop : -1.61 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.013 0.001 PHE B 199 TYR 0.032 0.001 TYR S 235 ARG 0.014 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 95 time to evaluate : 0.861 Fit side-chains outliers start: 35 outliers final: 22 residues processed: 119 average time/residue: 1.0161 time to fit residues: 130.0490 Evaluate side-chains 112 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 90 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 90 PHE Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 153 TYR Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 226 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 1 optimal weight: 0.6980 chunk 79 optimal weight: 0.0770 chunk 43 optimal weight: 8.9990 chunk 90 optimal weight: 0.8980 chunk 73 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 95 optimal weight: 40.0000 chunk 26 optimal weight: 6.9990 overall best weight: 1.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8608 Z= 0.195 Angle : 0.565 10.367 11718 Z= 0.292 Chirality : 0.042 0.209 1350 Planarity : 0.004 0.050 1484 Dihedral : 4.466 48.793 1215 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 4.31 % Allowed : 18.74 % Favored : 76.95 % 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: 1099 helix: 2.10 (0.28), residues: 351 sheet: 0.34 (0.34), residues: 264 loop : -1.60 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.013 0.001 PHE R 50 TYR 0.029 0.001 TYR S 235 ARG 0.014 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 94 time to evaluate : 0.950 Fit side-chains REVERT: B 234 PHE cc_start: 0.6888 (OUTLIER) cc_final: 0.6640 (t80) outliers start: 37 outliers final: 26 residues processed: 119 average time/residue: 1.0272 time to fit residues: 131.6013 Evaluate side-chains 117 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 90 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 90 PHE Chi-restraints excluded: chain R residue 100 SER Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 153 TYR Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 226 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 6.9990 chunk 95 optimal weight: 30.0000 chunk 21 optimal weight: 3.9990 chunk 62 optimal weight: 30.0000 chunk 26 optimal weight: 5.9990 chunk 106 optimal weight: 20.0000 chunk 88 optimal weight: 0.9990 chunk 49 optimal weight: 0.1980 chunk 8 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8608 Z= 0.258 Angle : 0.616 9.411 11718 Z= 0.321 Chirality : 0.043 0.226 1350 Planarity : 0.004 0.060 1484 Dihedral : 4.651 49.633 1215 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 4.66 % Allowed : 19.09 % Favored : 76.25 % 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: 0.08 (0.26), residues: 1099 helix: 1.95 (0.28), residues: 353 sheet: 0.27 (0.33), residues: 266 loop : -1.60 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 82 HIS 0.004 0.001 HIS S 167 PHE 0.015 0.002 PHE B 151 TYR 0.030 0.002 TYR S 235 ARG 0.015 0.001 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 99 time to evaluate : 0.987 Fit side-chains REVERT: B 234 PHE cc_start: 0.6952 (OUTLIER) cc_final: 0.6700 (t80) outliers start: 40 outliers final: 26 residues processed: 123 average time/residue: 1.0230 time to fit residues: 135.3349 Evaluate side-chains 120 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 93 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 90 PHE Chi-restraints excluded: chain R residue 100 SER Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 153 TYR Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 226 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 65 optimal weight: 0.8980 chunk 42 optimal weight: 8.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8608 Z= 0.155 Angle : 0.548 8.593 11718 Z= 0.281 Chirality : 0.041 0.177 1350 Planarity : 0.004 0.064 1484 Dihedral : 4.330 48.052 1215 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.33 % Allowed : 22.00 % Favored : 75.67 % 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: 0.37 (0.26), residues: 1099 helix: 2.26 (0.29), residues: 352 sheet: 0.56 (0.35), residues: 250 loop : -1.49 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.012 0.001 PHE B 199 TYR 0.024 0.001 TYR S 235 ARG 0.016 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 95 time to evaluate : 0.968 Fit side-chains REVERT: A 20 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6903 (mt-10) REVERT: B 234 PHE cc_start: 0.6890 (OUTLIER) cc_final: 0.6634 (t80) REVERT: B 325 MET cc_start: 0.6240 (mmp) cc_final: 0.5960 (mtp) REVERT: R 294 SER cc_start: 0.7311 (t) cc_final: 0.7048 (t) outliers start: 20 outliers final: 12 residues processed: 108 average time/residue: 1.0798 time to fit residues: 125.6966 Evaluate side-chains 101 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 88 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 90 PHE Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 208 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8608 Z= 0.256 Angle : 0.615 8.540 11718 Z= 0.322 Chirality : 0.043 0.213 1350 Planarity : 0.004 0.070 1484 Dihedral : 4.601 47.872 1215 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.38 % Allowed : 21.07 % Favored : 75.55 % 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: 1099 helix: 2.09 (0.28), residues: 353 sheet: 0.34 (0.34), residues: 264 loop : -1.54 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 63 HIS 0.004 0.001 HIS S 167 PHE 0.015 0.002 PHE B 151 TYR 0.025 0.002 TYR S 235 ARG 0.017 0.001 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 93 time to evaluate : 0.975 Fit side-chains REVERT: A 20 GLU cc_start: 0.7271 (mt-10) cc_final: 0.7030 (mt-10) REVERT: B 234 PHE cc_start: 0.6950 (OUTLIER) cc_final: 0.6667 (t80) outliers start: 29 outliers final: 22 residues processed: 113 average time/residue: 1.1083 time to fit residues: 134.4570 Evaluate side-chains 113 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 90 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 76 MET Chi-restraints excluded: chain R residue 90 PHE Chi-restraints excluded: chain R residue 100 SER Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 153 TYR Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 226 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 101 optimal weight: 0.0040 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 chunk 93 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 63 optimal weight: 0.0270 overall best weight: 1.2056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8608 Z= 0.168 Angle : 0.560 7.983 11718 Z= 0.291 Chirality : 0.041 0.161 1350 Planarity : 0.004 0.072 1484 Dihedral : 4.373 46.986 1215 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.98 % Allowed : 22.70 % Favored : 75.32 % 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: 0.38 (0.26), residues: 1099 helix: 2.24 (0.28), residues: 353 sheet: 0.61 (0.35), residues: 249 loop : -1.50 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.012 0.001 PHE B 199 TYR 0.021 0.001 TYR S 235 ARG 0.019 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 90 time to evaluate : 1.046 Fit side-chains revert: symmetry clash REVERT: A 20 GLU cc_start: 0.7269 (mt-10) cc_final: 0.7012 (mt-10) REVERT: B 234 PHE cc_start: 0.6862 (OUTLIER) cc_final: 0.6564 (t80) REVERT: R 294 SER cc_start: 0.7371 (t) cc_final: 0.7123 (t) outliers start: 17 outliers final: 13 residues processed: 100 average time/residue: 1.1379 time to fit residues: 122.1562 Evaluate side-chains 101 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 87 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 90 PHE Chi-restraints excluded: chain R residue 100 SER Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 208 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 2.9990 chunk 72 optimal weight: 0.0670 chunk 109 optimal weight: 0.0170 chunk 100 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 92 optimal weight: 0.0670 chunk 26 optimal weight: 5.9990 overall best weight: 0.7896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8608 Z= 0.150 Angle : 0.541 8.029 11718 Z= 0.280 Chirality : 0.041 0.149 1350 Planarity : 0.004 0.077 1484 Dihedral : 4.138 43.591 1215 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.86 % Allowed : 22.47 % Favored : 75.67 % 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: 0.55 (0.26), residues: 1099 helix: 2.34 (0.28), residues: 352 sheet: 0.60 (0.34), residues: 258 loop : -1.32 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.011 0.001 PHE B 199 TYR 0.022 0.001 TYR S 235 ARG 0.018 0.000 ARG B 256 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 94 time to evaluate : 0.939 Fit side-chains REVERT: A 20 GLU cc_start: 0.7253 (mt-10) cc_final: 0.6958 (mt-10) REVERT: R 294 SER cc_start: 0.7270 (t) cc_final: 0.7041 (t) outliers start: 16 outliers final: 13 residues processed: 105 average time/residue: 1.0747 time to fit residues: 121.0879 Evaluate side-chains 102 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 89 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 90 PHE Chi-restraints excluded: chain R residue 100 SER Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain S residue 141 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 20.0000 chunk 87 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.177592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.146293 restraints weight = 10318.313| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 1.99 r_work: 0.3490 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8608 Z= 0.188 Angle : 0.570 7.819 11718 Z= 0.297 Chirality : 0.042 0.166 1350 Planarity : 0.004 0.076 1484 Dihedral : 4.260 43.066 1215 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.33 % Allowed : 22.47 % Favored : 75.20 % 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: 0.45 (0.26), residues: 1099 helix: 2.20 (0.28), residues: 351 sheet: 0.58 (0.34), residues: 259 loop : -1.35 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.030 0.001 PHE B 253 TYR 0.024 0.001 TYR S 235 ARG 0.019 0.000 ARG B 256 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3064.27 seconds wall clock time: 54 minutes 17.85 seconds (3257.85 seconds total)