Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 14:51:39 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f1s_31424/04_2023/7f1s_31424.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f1s_31424/04_2023/7f1s_31424.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f1s_31424/04_2023/7f1s_31424.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f1s_31424/04_2023/7f1s_31424.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f1s_31424/04_2023/7f1s_31424.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f1s_31424/04_2023/7f1s_31424.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1442 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 4009 2.51 5 N 1055 2.21 5 O 1103 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 76": "OD1" <-> "OD2" Residue "R TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 225": "NH1" <-> "NH2" Residue "R TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 21": "NH1" <-> "NH2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 337": "OD1" <-> "OD2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 303": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 6209 Number of models: 1 Model: "" Number of chains: 4 Chain: "R" Number of atoms: 2051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2051 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 8, 'TRANS': 267} Chain breaks: 1 Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 269 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 6, 'HIS:plan': 2, 'PHE:plan': 5, 'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 127 Chain: "A" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1588 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 2, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 156 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 12, 'ARG:plan': 1, 'TYR:plan': 1, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 91 Chain: "B" Number of atoms: 2338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2338 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 5, 'TRANS': 314} Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 76 Chain: "C" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 232 Classifications: {'peptide': 35} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 30} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Time building chain proxies: 3.65, per 1000 atoms: 0.59 Number of scatterers: 6209 At special positions: 0 Unit cell: (113.905, 112.86, 72.105, 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 42 16.00 O 1103 8.00 N 1055 7.00 C 4009 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 101 " - pdb=" SG CYS R 178 " 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: 2.26 Conformation dependent library (CDL) restraints added in 1.1 seconds 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1598 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 9 sheets defined 45.3% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'R' and resid 33 through 58 removed outlier: 3.790A pdb=" N TYR R 37 " --> pdb=" O LEU R 33 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER R 38 " --> pdb=" O PRO R 34 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE R 41 " --> pdb=" O TYR R 37 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE R 43 " --> pdb=" O LEU R 39 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N PHE R 45 " --> pdb=" O PHE R 41 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N VAL R 46 " --> pdb=" O ILE R 42 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASN R 57 " --> pdb=" O LEU R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 81 removed outlier: 4.062A pdb=" N TYR R 68 " --> pdb=" O MET R 64 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU R 69 " --> pdb=" O THR R 65 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN R 71 " --> pdb=" O ILE R 67 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU R 72 " --> pdb=" O TYR R 68 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU R 77 " --> pdb=" O ALA R 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 87 removed outlier: 4.105A pdb=" N PHE R 85 " --> pdb=" O LEU R 81 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA R 87 " --> pdb=" O VAL R 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 98 through 132 removed outlier: 3.597A pdb=" N GLN R 102 " --> pdb=" O ASN R 98 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY R 115 " --> pdb=" O GLY R 111 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE R 120 " --> pdb=" O ILE R 116 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL R 130 " --> pdb=" O ARG R 126 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS R 132 " --> pdb=" O LEU R 128 " (cutoff:3.500A) Processing helix chain 'R' and resid 132 through 140 removed outlier: 4.061A pdb=" N LYS R 138 " --> pdb=" O VAL R 134 " (cutoff:3.500A) Processing helix chain 'R' and resid 141 through 166 removed outlier: 4.079A pdb=" N VAL R 147 " --> pdb=" O THR R 143 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE R 151 " --> pdb=" O VAL R 147 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR R 152 " --> pdb=" O THR R 148 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA R 156 " --> pdb=" O THR R 152 " (cutoff:3.500A) Proline residue: R 162 - end of helix Processing helix chain 'R' and resid 186 through 201 removed outlier: 3.596A pdb=" N ILE R 200 " --> pdb=" O LEU R 196 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 220 removed outlier: 3.517A pdb=" N TYR R 214 " --> pdb=" O MET R 210 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY R 216 " --> pdb=" O ILE R 212 " (cutoff:3.500A) Processing helix chain 'R' and resid 226 through 248 removed outlier: 4.074A pdb=" N ARG R 232 " --> pdb=" O LYS R 228 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE R 238 " --> pdb=" O VAL R 234 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET R 241 " --> pdb=" O ILE R 237 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR R 244 " --> pdb=" O ILE R 240 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE R 245 " --> pdb=" O MET R 241 " (cutoff:3.500A) Processing helix chain 'R' and resid 248 through 260 removed outlier: 3.947A pdb=" N LEU R 257 " --> pdb=" O ILE R 253 " (cutoff:3.500A) Processing helix chain 'R' and resid 264 through 269 Processing helix chain 'R' and resid 270 through 277 removed outlier: 4.241A pdb=" N ARG R 274 " --> pdb=" O SER R 270 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLN R 277 " --> pdb=" O ASN R 273 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 288 Processing helix chain 'R' and resid 292 through 298 Processing helix chain 'R' and resid 303 through 313 removed outlier: 3.744A pdb=" N TYR R 307 " --> pdb=" O LYS R 303 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL R 310 " --> pdb=" O ASN R 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 33 removed outlier: 3.550A pdb=" N LEU A 23 " --> pdb=" O ILE A 19 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG A 24 " --> pdb=" O ASP A 20 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLU A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 52 Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'A' and resid 242 through 255 removed outlier: 3.568A pdb=" N SER A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.968A pdb=" N GLU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.781A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.658A pdb=" N ALA A 300 " --> pdb=" O TYR A 296 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 352 removed outlier: 3.523A pdb=" N PHE A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'B' and resid 128 through 132 removed outlier: 3.576A pdb=" N GLY B 131 " --> pdb=" O THR B 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'R' and resid 168 through 171 removed outlier: 3.717A pdb=" N GLN R 170 " --> pdb=" O THR R 177 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N THR R 177 " --> pdb=" O GLN R 170 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.841A pdb=" N VAL A 185 " --> pdb=" O ASP A 200 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.982A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.577A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.987A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.609A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.885A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.231A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU B 252 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.541A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU B 308 " --> pdb=" O CYS B 294 " (cutoff:3.500A) 293 hydrogen bonds defined for protein. 828 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.71 Time building geometry restraints manager: 2.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1989 1.35 - 1.46: 1606 1.46 - 1.58: 2690 1.58 - 1.70: 0 1.70 - 1.82: 57 Bond restraints: 6342 Sorted by residual: bond pdb=" N THR B 164 " pdb=" CA THR B 164 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.27e+00 bond pdb=" CA LEU R 33 " pdb=" C LEU R 33 " ideal model delta sigma weight residual 1.525 1.541 -0.016 2.10e-02 2.27e+03 5.99e-01 bond pdb=" C PRO R 34 " pdb=" N PRO R 35 " ideal model delta sigma weight residual 1.336 1.345 -0.009 1.25e-02 6.40e+03 5.21e-01 bond pdb=" CB GLN R 194 " pdb=" CG GLN R 194 " ideal model delta sigma weight residual 1.520 1.541 -0.021 3.00e-02 1.11e+03 5.13e-01 bond pdb=" CA GLU C 47 " pdb=" C GLU C 47 " ideal model delta sigma weight residual 1.526 1.535 -0.010 1.36e-02 5.41e+03 4.97e-01 ... (remaining 6337 not shown) Histogram of bond angle deviations from ideal: 99.32 - 106.28: 113 106.28 - 113.24: 3497 113.24 - 120.19: 2253 120.19 - 127.15: 2725 127.15 - 134.11: 66 Bond angle restraints: 8654 Sorted by residual: angle pdb=" C ASN R 268 " pdb=" N CYS R 269 " pdb=" CA CYS R 269 " ideal model delta sigma weight residual 121.54 126.09 -4.55 1.91e+00 2.74e-01 5.67e+00 angle pdb=" CA LEU R 161 " pdb=" CB LEU R 161 " pdb=" CG LEU R 161 " ideal model delta sigma weight residual 116.30 124.41 -8.11 3.50e+00 8.16e-02 5.37e+00 angle pdb=" C ASP B 195 " pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta sigma weight residual 123.91 127.56 -3.65 1.66e+00 3.63e-01 4.82e+00 angle pdb=" N LEU B 300 " pdb=" CA LEU B 300 " pdb=" C LEU B 300 " ideal model delta sigma weight residual 114.31 111.60 2.71 1.29e+00 6.01e-01 4.40e+00 angle pdb=" C CYS R 224 " pdb=" N ARG R 225 " pdb=" CA ARG R 225 " ideal model delta sigma weight residual 122.08 125.08 -3.00 1.47e+00 4.63e-01 4.17e+00 ... (remaining 8649 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 3465 17.53 - 35.07: 180 35.07 - 52.60: 14 52.60 - 70.14: 6 70.14 - 87.67: 4 Dihedral angle restraints: 3669 sinusoidal: 1207 harmonic: 2462 Sorted by residual: dihedral pdb=" CA ASN R 293 " pdb=" CB ASN R 293 " pdb=" CG ASN R 293 " pdb=" OD1 ASN R 293 " ideal model delta sinusoidal sigma weight residual -90.00 -156.28 66.28 2 2.00e+01 2.50e-03 1.01e+01 dihedral pdb=" CB LYS A 29 " pdb=" CG LYS A 29 " pdb=" CD LYS A 29 " pdb=" CE LYS A 29 " ideal model delta sinusoidal sigma weight residual 60.00 118.28 -58.28 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CA GLN B 220 " pdb=" CB GLN B 220 " pdb=" CG GLN B 220 " pdb=" CD GLN B 220 " ideal model delta sinusoidal sigma weight residual -60.00 -105.58 45.58 3 1.50e+01 4.44e-03 8.19e+00 ... (remaining 3666 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 624 0.030 - 0.061: 309 0.061 - 0.091: 66 0.091 - 0.121: 38 0.121 - 0.152: 5 Chirality restraints: 1042 Sorted by residual: chirality pdb=" CA THR B 196 " pdb=" N THR B 196 " pdb=" C THR B 196 " pdb=" CB THR B 196 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.74e-01 chirality pdb=" CA THR B 164 " pdb=" N THR B 164 " pdb=" C THR B 164 " pdb=" CB THR B 164 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 3.96e-01 chirality pdb=" CA ILE B 232 " pdb=" N ILE B 232 " pdb=" C ILE B 232 " pdb=" CB ILE B 232 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.94e-01 ... (remaining 1039 not shown) Planarity restraints: 1085 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 38 " 0.048 5.00e-02 4.00e+02 7.27e-02 8.46e+00 pdb=" N PRO B 39 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO B 39 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 39 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 33 " -0.037 5.00e-02 4.00e+02 5.51e-02 4.85e+00 pdb=" N PRO R 34 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO R 34 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO R 34 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO B 236 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.022 5.00e-02 4.00e+02 ... (remaining 1082 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1047 2.76 - 3.30: 6289 3.30 - 3.83: 10363 3.83 - 4.37: 12405 4.37 - 4.90: 21056 Nonbonded interactions: 51160 Sorted by model distance: nonbonded pdb=" O ASN R 163 " pdb=" OG1 THR R 167 " model vdw 2.228 2.440 nonbonded pdb=" OH TYR R 108 " pdb=" OE1 GLU R 283 " model vdw 2.252 2.440 nonbonded pdb=" NH1 ARG A 15 " pdb=" O VAL B 90 " model vdw 2.259 2.520 nonbonded pdb=" OD1 ASP A 251 " pdb=" ND2 ASN A 255 " model vdw 2.296 2.520 nonbonded pdb=" NE2 HIS B 225 " pdb=" OG1 THR B 243 " model vdw 2.332 2.520 ... (remaining 51155 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 3.910 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 19.870 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:14.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 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 : 0.002 0.021 6342 Z= 0.125 Angle : 0.552 8.112 8654 Z= 0.289 Chirality : 0.039 0.152 1042 Planarity : 0.004 0.073 1085 Dihedral : 10.910 87.669 2068 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer Outliers : 0.00 % 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: -1.65 (0.27), residues: 833 helix: -2.04 (0.24), residues: 291 sheet: 0.68 (0.41), residues: 155 loop : -0.95 (0.31), residues: 387 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 0.706 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 1.0170 time to fit residues: 163.0101 Evaluate side-chains 98 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.669 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 261 GLN A 294 ASN B 176 GLN B 230 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.064 6342 Z= 0.338 Angle : 0.665 8.332 8654 Z= 0.344 Chirality : 0.044 0.150 1042 Planarity : 0.005 0.056 1085 Dihedral : 3.988 18.254 894 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer Outliers : 3.02 % 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: -0.69 (0.28), residues: 833 helix: -0.56 (0.26), residues: 331 sheet: 0.66 (0.39), residues: 170 loop : -0.79 (0.34), residues: 332 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 109 time to evaluate : 0.739 Fit side-chains outliers start: 18 outliers final: 9 residues processed: 123 average time/residue: 1.1081 time to fit residues: 143.5432 Evaluate side-chains 100 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 91 time to evaluate : 0.776 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 2 average time/residue: 0.1627 time to fit residues: 1.3897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 41 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 20 optimal weight: 0.0010 chunk 75 optimal weight: 0.9990 chunk 81 optimal weight: 0.1980 chunk 67 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 6342 Z= 0.179 Angle : 0.570 8.489 8654 Z= 0.290 Chirality : 0.041 0.139 1042 Planarity : 0.004 0.052 1085 Dihedral : 3.716 17.556 894 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer Outliers : 3.19 % 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 (0.29), residues: 833 helix: 0.17 (0.28), residues: 328 sheet: 0.63 (0.40), residues: 172 loop : -0.68 (0.35), residues: 333 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 105 time to evaluate : 0.766 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 10 residues processed: 119 average time/residue: 1.0453 time to fit residues: 131.4590 Evaluate side-chains 104 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 0.750 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 1 average time/residue: 0.0601 time to fit residues: 1.1002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 3.9990 chunk 56 optimal weight: 0.2980 chunk 39 optimal weight: 0.0370 chunk 8 optimal weight: 0.0030 chunk 36 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 overall best weight: 0.3468 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 6342 Z= 0.159 Angle : 0.556 8.957 8654 Z= 0.285 Chirality : 0.040 0.138 1042 Planarity : 0.004 0.053 1085 Dihedral : 3.627 17.128 894 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer Outliers : 2.85 % 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: 0.02 (0.29), residues: 833 helix: 0.49 (0.28), residues: 330 sheet: 0.52 (0.40), residues: 172 loop : -0.64 (0.35), residues: 331 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 104 time to evaluate : 0.747 Fit side-chains outliers start: 17 outliers final: 11 residues processed: 115 average time/residue: 1.0416 time to fit residues: 126.5760 Evaluate side-chains 105 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 94 time to evaluate : 0.734 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 1.0197 time to fit residues: 3.1120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 45 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 40 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN B 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 6342 Z= 0.237 Angle : 0.585 9.346 8654 Z= 0.301 Chirality : 0.042 0.195 1042 Planarity : 0.004 0.053 1085 Dihedral : 3.694 17.670 894 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer Outliers : 3.02 % 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: 0.02 (0.29), residues: 833 helix: 0.66 (0.29), residues: 333 sheet: 0.31 (0.39), residues: 172 loop : -0.71 (0.34), residues: 328 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 99 time to evaluate : 0.763 Fit side-chains outliers start: 18 outliers final: 11 residues processed: 108 average time/residue: 1.0332 time to fit residues: 117.9452 Evaluate side-chains 102 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 91 time to evaluate : 0.648 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 0.0743 time to fit residues: 1.1664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 72 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 80 optimal weight: 0.4980 chunk 66 optimal weight: 0.2980 chunk 37 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 6342 Z= 0.203 Angle : 0.571 9.492 8654 Z= 0.294 Chirality : 0.041 0.163 1042 Planarity : 0.004 0.054 1085 Dihedral : 3.692 17.760 894 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer Outliers : 3.02 % 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: 0.07 (0.29), residues: 833 helix: 0.75 (0.29), residues: 330 sheet: 0.29 (0.39), residues: 172 loop : -0.71 (0.34), residues: 331 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 97 time to evaluate : 0.750 Fit side-chains outliers start: 18 outliers final: 12 residues processed: 111 average time/residue: 1.0299 time to fit residues: 121.0012 Evaluate side-chains 105 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 0.757 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 2 average time/residue: 0.0983 time to fit residues: 1.3580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 48 optimal weight: 20.0000 chunk 36 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 31 optimal weight: 0.0060 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 293 ASN A 333 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 6342 Z= 0.200 Angle : 0.582 9.338 8654 Z= 0.298 Chirality : 0.041 0.162 1042 Planarity : 0.004 0.053 1085 Dihedral : 3.704 17.795 894 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer Outliers : 3.69 % 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 (0.29), residues: 833 helix: 0.85 (0.29), residues: 330 sheet: 0.26 (0.39), residues: 172 loop : -0.70 (0.34), residues: 331 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 100 time to evaluate : 0.774 Fit side-chains outliers start: 22 outliers final: 12 residues processed: 114 average time/residue: 1.0706 time to fit residues: 129.0763 Evaluate side-chains 108 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 0.684 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 2 average time/residue: 1.1572 time to fit residues: 3.3558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 47 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 39 optimal weight: 0.0970 chunk 7 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 72 optimal weight: 0.0040 chunk 76 optimal weight: 4.9990 chunk 69 optimal weight: 0.0970 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 6342 Z= 0.176 Angle : 0.596 9.989 8654 Z= 0.305 Chirality : 0.041 0.152 1042 Planarity : 0.004 0.054 1085 Dihedral : 3.683 17.421 894 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer Outliers : 3.19 % 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 (0.29), residues: 833 helix: 0.88 (0.29), residues: 331 sheet: 0.17 (0.39), residues: 174 loop : -0.69 (0.34), residues: 328 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 101 time to evaluate : 0.695 Fit side-chains outliers start: 19 outliers final: 12 residues processed: 113 average time/residue: 1.0209 time to fit residues: 122.0287 Evaluate side-chains 107 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 0.662 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 2 average time/residue: 0.0745 time to fit residues: 1.1027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 44 optimal weight: 0.0970 chunk 32 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 48 optimal weight: 20.0000 chunk 78 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.0580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 6342 Z= 0.271 Angle : 0.649 9.813 8654 Z= 0.331 Chirality : 0.042 0.155 1042 Planarity : 0.004 0.053 1085 Dihedral : 3.813 18.062 894 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer Outliers : 3.02 % 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: 0.09 (0.29), residues: 833 helix: 0.86 (0.29), residues: 331 sheet: 0.08 (0.39), residues: 175 loop : -0.67 (0.34), residues: 327 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 97 time to evaluate : 0.697 Fit side-chains outliers start: 18 outliers final: 12 residues processed: 113 average time/residue: 1.0233 time to fit residues: 122.3695 Evaluate side-chains 106 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 94 time to evaluate : 0.731 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 2.0972 time to fit residues: 3.1077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 54 optimal weight: 2.9990 chunk 82 optimal weight: 0.0000 chunk 76 optimal weight: 0.0050 chunk 65 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 6342 Z= 0.192 Angle : 0.630 10.063 8654 Z= 0.320 Chirality : 0.041 0.150 1042 Planarity : 0.004 0.054 1085 Dihedral : 3.756 17.623 894 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer Outliers : 3.02 % 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: 0.06 (0.29), residues: 833 helix: 0.88 (0.29), residues: 330 sheet: 0.01 (0.39), residues: 174 loop : -0.71 (0.34), residues: 329 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 97 time to evaluate : 0.674 Fit side-chains outliers start: 18 outliers final: 14 residues processed: 111 average time/residue: 0.9880 time to fit residues: 116.1791 Evaluate side-chains 109 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 0.718 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 2 average time/residue: 0.1507 time to fit residues: 1.3521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 67 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 57 optimal weight: 0.2980 chunk 3 optimal weight: 0.0570 chunk 47 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.110644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.087033 restraints weight = 13372.201| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.96 r_work: 0.3297 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 6342 Z= 0.196 Angle : 0.638 10.121 8654 Z= 0.321 Chirality : 0.041 0.152 1042 Planarity : 0.004 0.053 1085 Dihedral : 3.748 17.402 894 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer Outliers : 2.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.29), residues: 833 helix: 0.87 (0.29), residues: 332 sheet: 0.02 (0.39), residues: 174 loop : -0.70 (0.34), residues: 327 =============================================================================== Job complete usr+sys time: 2668.24 seconds wall clock time: 48 minutes 0.15 seconds (2880.15 seconds total)