Starting phenix.real_space_refine on Fri Jul 19 13:51:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc3_37429/07_2024/8wc3_37429_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc3_37429/07_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_37429/07_2024/8wc3_37429.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc3_37429/07_2024/8wc3_37429.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc3_37429/07_2024/8wc3_37429_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc3_37429/07_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-5388/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: 4.84, per 1000 atoms: 0.57 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: 3.29 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: 0.98 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: 2.32 Time building geometry restraints manager: 3.62 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 2.520 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 2.440 nonbonded pdb=" N GLN R 52 " pdb=" OE1 GLN R 52 " model vdw 2.246 2.520 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.260 2.440 ... (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 ========== 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: 0.840 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.240 Find NCS groups from input model: 0.130 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:10.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.590 ------------------------------------------------------------------------------- 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 : 0.990 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: 1.0579 time to fit residues: 172.2944 Evaluate side-chains 100 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 95 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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: 10.0000 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 56 optimal weight: 30.0000 chunk 44 optimal weight: 7.9990 chunk 86 optimal weight: 0.0980 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 99 optimal weight: 0.5980 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 ** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** R 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 283 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8608 Z= 0.151 Angle : 0.542 7.990 11718 Z= 0.282 Chirality : 0.042 0.263 1350 Planarity : 0.004 0.052 1484 Dihedral : 4.955 51.596 1224 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.68 % Allowed : 12.57 % Favored : 84.75 % 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: 0.05 (0.26), residues: 1099 helix: 1.85 (0.28), residues: 358 sheet: 0.21 (0.33), residues: 276 loop : -1.57 (0.27), residues: 465 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 0.012 0.001 PHE R 50 TYR 0.030 0.001 TYR S 235 ARG 0.008 0.000 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 128 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 105 time to evaluate : 0.970 Fit side-chains REVERT: B 205 ASP cc_start: 0.7001 (OUTLIER) cc_final: 0.6506 (p0) outliers start: 23 outliers final: 9 residues processed: 119 average time/residue: 0.9877 time to fit residues: 127.1017 Evaluate side-chains 102 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 205 ASP 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 182 SER Chi-restraints excluded: chain S residue 78 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 83 optimal weight: 8.9990 chunk 68 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 108 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 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: B 32 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: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8608 Z= 0.299 Angle : 0.638 7.613 11718 Z= 0.335 Chirality : 0.045 0.271 1350 Planarity : 0.004 0.044 1484 Dihedral : 4.815 46.159 1216 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.49 % Allowed : 15.48 % Favored : 81.02 % 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: 1.77 (0.28), residues: 357 sheet: 0.16 (0.33), residues: 275 loop : -1.68 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 147 HIS 0.005 0.001 HIS B 183 PHE 0.018 0.002 PHE B 151 TYR 0.041 0.002 TYR S 235 ARG 0.014 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 130 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 100 time to evaluate : 0.972 Fit side-chains outliers start: 30 outliers final: 22 residues processed: 119 average time/residue: 1.0541 time to fit residues: 135.0269 Evaluate side-chains 114 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 92 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 292 THR 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 217 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 164 LEU 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 R residue 292 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 10.0000 chunk 75 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 47 optimal weight: 8.9990 chunk 67 optimal weight: 4.9990 chunk 100 optimal weight: 9.9990 chunk 106 optimal weight: 20.0000 chunk 52 optimal weight: 5.9990 chunk 95 optimal weight: 30.0000 chunk 28 optimal weight: 4.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN ** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** R 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.2254 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= 0.318 Angle : 0.636 7.481 11718 Z= 0.335 Chirality : 0.045 0.272 1350 Planarity : 0.004 0.042 1484 Dihedral : 4.889 50.000 1215 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 4.66 % Allowed : 16.41 % Favored : 78.93 % 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: 1.57 (0.28), residues: 363 sheet: 0.23 (0.34), residues: 267 loop : -1.78 (0.26), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 63 HIS 0.004 0.001 HIS S 35 PHE 0.017 0.002 PHE B 151 TYR 0.039 0.002 TYR S 235 ARG 0.013 0.001 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 135 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 95 time to evaluate : 0.995 Fit side-chains REVERT: B 234 PHE cc_start: 0.6975 (OUTLIER) cc_final: 0.6746 (t80) outliers start: 40 outliers final: 25 residues processed: 118 average time/residue: 1.0545 time to fit residues: 133.7572 Evaluate side-chains 114 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 88 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 292 THR 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 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 268 THR Chi-restraints excluded: chain R residue 282 LEU 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: 0.9990 chunk 1 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 54 optimal weight: 1.9990 chunk 95 optimal weight: 40.0000 chunk 26 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN ** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** R 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.2296 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= 0.223 Angle : 0.579 7.553 11718 Z= 0.301 Chirality : 0.043 0.229 1350 Planarity : 0.004 0.050 1484 Dihedral : 4.690 51.685 1215 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 4.07 % Allowed : 19.21 % Favored : 76.72 % 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: -0.05 (0.26), residues: 1099 helix: 1.72 (0.28), residues: 367 sheet: 0.29 (0.34), residues: 266 loop : -1.73 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.019 0.001 PHE B 253 TYR 0.033 0.002 TYR S 235 ARG 0.013 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 128 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 93 time to evaluate : 1.040 Fit side-chains REVERT: A 20 GLU cc_start: 0.7299 (mt-10) cc_final: 0.7080 (mt-10) outliers start: 35 outliers final: 24 residues processed: 118 average time/residue: 0.9850 time to fit residues: 125.4453 Evaluate side-chains 113 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 89 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 292 THR 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 34 THR 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 B residue 322 ASP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain R residue 57 THR 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 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 226 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.9980 chunk 95 optimal weight: 40.0000 chunk 21 optimal weight: 0.6980 chunk 62 optimal weight: 0.3980 chunk 26 optimal weight: 5.9990 chunk 106 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 55 optimal weight: 0.0570 chunk 102 optimal weight: 1.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN ** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8608 Z= 0.135 Angle : 0.523 9.745 11718 Z= 0.265 Chirality : 0.040 0.183 1350 Planarity : 0.004 0.045 1484 Dihedral : 4.258 50.456 1215 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.68 % Allowed : 21.07 % 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: 0.24 (0.26), residues: 1099 helix: 2.04 (0.28), residues: 366 sheet: 0.41 (0.34), residues: 269 loop : -1.62 (0.27), residues: 464 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 0.019 0.001 PHE B 253 TYR 0.024 0.001 TYR S 235 ARG 0.011 0.000 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 116 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 93 time to evaluate : 0.869 Fit side-chains REVERT: B 205 ASP cc_start: 0.7043 (OUTLIER) cc_final: 0.6745 (p0) REVERT: B 234 PHE cc_start: 0.6875 (OUTLIER) cc_final: 0.6634 (t80) REVERT: B 325 MET cc_start: 0.6245 (OUTLIER) cc_final: 0.5905 (mtp) outliers start: 23 outliers final: 11 residues processed: 108 average time/residue: 1.0289 time to fit residues: 119.2981 Evaluate side-chains 101 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 87 time to evaluate : 0.853 ------------------------------------------------------------------------------- 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 34 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain R residue 90 PHE Chi-restraints excluded: chain R residue 100 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.4980 chunk 60 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 59 optimal weight: 0.3980 chunk 106 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 48 optimal weight: 0.0770 chunk 65 optimal weight: 0.9980 chunk 42 optimal weight: 9.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN ** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8608 Z= 0.133 Angle : 0.515 8.912 11718 Z= 0.262 Chirality : 0.040 0.161 1350 Planarity : 0.004 0.063 1484 Dihedral : 4.107 46.930 1215 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.14 % Allowed : 21.19 % 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: 0.45 (0.26), residues: 1099 helix: 2.28 (0.29), residues: 359 sheet: 0.50 (0.33), residues: 275 loop : -1.50 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.023 0.001 PHE B 253 TYR 0.022 0.001 TYR S 235 ARG 0.014 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 119 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 92 time to evaluate : 0.878 Fit side-chains REVERT: A 20 GLU cc_start: 0.7292 (mt-10) cc_final: 0.7033 (mt-10) REVERT: B 205 ASP cc_start: 0.7038 (OUTLIER) cc_final: 0.6739 (p0) REVERT: B 325 MET cc_start: 0.6056 (OUTLIER) cc_final: 0.5739 (mtp) outliers start: 27 outliers final: 15 residues processed: 110 average time/residue: 1.0650 time to fit residues: 125.8619 Evaluate side-chains 105 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 88 time to evaluate : 0.862 ------------------------------------------------------------------------------- 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 34 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 205 ASP 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 90 PHE Chi-restraints excluded: chain R residue 100 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 141 THR Chi-restraints excluded: chain Y residue 38 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.8980 chunk 31 optimal weight: 0.4980 chunk 20 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 9 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 chunk 96 optimal weight: 7.9990 chunk 101 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN ** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8608 Z= 0.140 Angle : 0.521 8.714 11718 Z= 0.266 Chirality : 0.040 0.156 1350 Planarity : 0.004 0.068 1484 Dihedral : 4.076 44.405 1215 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.38 % Allowed : 20.72 % Favored : 75.90 % 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: 0.56 (0.26), residues: 1099 helix: 2.29 (0.29), residues: 360 sheet: 0.80 (0.34), residues: 254 loop : -1.44 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.011 0.001 PHE B 199 TYR 0.021 0.001 TYR S 235 ARG 0.016 0.000 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 120 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 91 time to evaluate : 0.975 Fit side-chains REVERT: B 205 ASP cc_start: 0.7075 (OUTLIER) cc_final: 0.6775 (p0) REVERT: B 234 PHE cc_start: 0.6887 (OUTLIER) cc_final: 0.6635 (t80) REVERT: B 325 MET cc_start: 0.6090 (OUTLIER) cc_final: 0.5783 (mtm) outliers start: 29 outliers final: 14 residues processed: 108 average time/residue: 1.0706 time to fit residues: 124.7279 Evaluate side-chains 105 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 88 time to evaluate : 0.943 ------------------------------------------------------------------------------- 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 34 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain R residue 90 PHE Chi-restraints excluded: chain R residue 100 SER Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 296 LEU Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain Y residue 38 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 43 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN ** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8608 Z= 0.232 Angle : 0.588 8.859 11718 Z= 0.305 Chirality : 0.042 0.181 1350 Planarity : 0.004 0.075 1484 Dihedral : 4.444 45.525 1215 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.91 % Allowed : 21.07 % Favored : 76.02 % 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: 0.32 (0.26), residues: 1099 helix: 2.03 (0.28), residues: 365 sheet: 0.45 (0.33), residues: 274 loop : -1.50 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 147 HIS 0.003 0.001 HIS S 35 PHE 0.014 0.001 PHE A 189 TYR 0.023 0.002 TYR S 235 ARG 0.018 0.001 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 110 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 85 time to evaluate : 0.989 Fit side-chains REVERT: A 20 GLU cc_start: 0.7284 (mt-10) cc_final: 0.7029 (mt-10) REVERT: B 234 PHE cc_start: 0.6961 (OUTLIER) cc_final: 0.6688 (t80) REVERT: Y 25 ILE cc_start: 0.4282 (OUTLIER) cc_final: 0.3909 (pt) outliers start: 25 outliers final: 18 residues processed: 100 average time/residue: 1.2305 time to fit residues: 132.1826 Evaluate side-chains 102 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 82 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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 34 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 57 THR 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 188 VAL Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain Y residue 25 ILE Chi-restraints excluded: chain Y residue 38 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.9990 chunk 72 optimal weight: 8.9990 chunk 109 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 87 optimal weight: 0.4980 chunk 9 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN ** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.2512 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= 0.162 Angle : 0.548 8.571 11718 Z= 0.283 Chirality : 0.041 0.169 1350 Planarity : 0.004 0.075 1484 Dihedral : 4.273 42.677 1215 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.21 % Allowed : 21.54 % 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: 0.45 (0.26), residues: 1099 helix: 2.12 (0.28), residues: 365 sheet: 0.77 (0.34), residues: 254 loop : -1.49 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.012 0.001 PHE A 189 TYR 0.021 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 101 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 82 time to evaluate : 1.007 Fit side-chains REVERT: A 20 GLU cc_start: 0.7273 (mt-10) cc_final: 0.7001 (mt-10) REVERT: B 234 PHE cc_start: 0.6951 (OUTLIER) cc_final: 0.6699 (t80) REVERT: B 256 ARG cc_start: 0.7110 (mtm110) cc_final: 0.6793 (ptt180) REVERT: B 325 MET cc_start: 0.6239 (mmp) cc_final: 0.5884 (mtm) outliers start: 19 outliers final: 15 residues processed: 96 average time/residue: 1.1233 time to fit residues: 115.5061 Evaluate side-chains 94 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 78 time to evaluate : 0.860 ------------------------------------------------------------------------------- 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 34 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 R residue 57 THR Chi-restraints excluded: chain R residue 90 PHE Chi-restraints excluded: chain R residue 100 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 Chi-restraints excluded: chain S residue 226 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 24 optimal weight: 20.0000 chunk 87 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 4 optimal weight: 0.4980 chunk 63 optimal weight: 0.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN ** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.174282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.142711 restraints weight = 10459.827| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.21 r_work: 0.3455 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8608 Z= 0.278 Angle : 0.623 8.920 11718 Z= 0.326 Chirality : 0.044 0.211 1350 Planarity : 0.005 0.076 1484 Dihedral : 4.680 46.170 1215 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.56 % Allowed : 21.65 % Favored : 75.79 % 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: 0.13 (0.26), residues: 1099 helix: 1.80 (0.28), residues: 365 sheet: 0.43 (0.33), residues: 274 loop : -1.60 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP S 47 HIS 0.004 0.001 HIS R 62 PHE 0.016 0.002 PHE A 189 TYR 0.022 0.002 TYR S 235 ARG 0.017 0.001 ARG B 256 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2961.24 seconds wall clock time: 52 minutes 28.02 seconds (3148.02 seconds total)