Starting phenix.real_space_refine on Tue Sep 24 16:08:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xav_33100/09_2024/7xav_33100.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xav_33100/09_2024/7xav_33100.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xav_33100/09_2024/7xav_33100.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xav_33100/09_2024/7xav_33100.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xav_33100/09_2024/7xav_33100.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xav_33100/09_2024/7xav_33100.cif" } resolution = 2.87 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= 0.004 sd= 0.128 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 54 5.16 5 C 5319 2.51 5 N 1436 2.21 5 O 1601 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8410 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 1896 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 11, 'TRANS': 268} Chain breaks: 1 Unresolved non-hydrogen bonds: 353 Unresolved non-hydrogen angles: 441 Unresolved non-hydrogen dihedrals: 327 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 5, 'HIS:plan': 1, 'PHE:plan': 11, 'GLU:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 184 Chain: "B" Number of atoms: 1602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1602 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 2, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 238 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 6, 'TYR:plan': 4, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 9, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 115 Chain: "C" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "D" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "E" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1791 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "F" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain: "F" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 36 Classifications: {'peptide': 4} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 3} Time building chain proxies: 5.04, per 1000 atoms: 0.60 Number of scatterers: 8410 At special positions: 0 Unit cell: (87.74, 121.98, 127.33, 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 54 16.00 O 1601 8.00 N 1436 7.00 C 5319 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 115 " - pdb=" SG CYS A 193 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 149 " distance=2.05 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.05 Simple disulfide: pdb=" SG CYS F 2 " - pdb=" SG CYS F 7 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied TRANS " DTR F 4 " - " TYR F 3 " Time building additional restraints: 1.96 Conformation dependent library (CDL) restraints added in 1.1 seconds 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTR F 4 " Number of C-beta restraints generated: 2132 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 14 sheets defined 30.2% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 43 through 61 removed outlier: 4.025A pdb=" N THR A 47 " --> pdb=" O ASN A 43 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N PHE A 48 " --> pdb=" O ALA A 44 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N PHE A 51 " --> pdb=" O THR A 47 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 55 " --> pdb=" O PHE A 51 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ILE A 56 " --> pdb=" O VAL A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 66 Processing helix chain 'A' and resid 77 through 92 removed outlier: 3.654A pdb=" N TYR A 81 " --> pdb=" O ILE A 77 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU A 83 " --> pdb=" O ASN A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 101 removed outlier: 3.819A pdb=" N MET A 101 " --> pdb=" O PRO A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 104 No H-bonds generated for 'chain 'A' and resid 102 through 104' Processing helix chain 'A' and resid 113 through 125 removed outlier: 4.776A pdb=" N MET A 119 " --> pdb=" O CYS A 115 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N THR A 120 " --> pdb=" O ARG A 116 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY A 123 " --> pdb=" O MET A 119 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 124 " --> pdb=" O THR A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 145 removed outlier: 3.518A pdb=" N TYR A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 170 removed outlier: 3.622A pdb=" N SER A 170 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 180 removed outlier: 3.657A pdb=" N ILE A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 214 Processing helix chain 'A' and resid 219 through 236 removed outlier: 4.626A pdb=" N ILE A 231 " --> pdb=" O CYS A 227 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS A 234 " --> pdb=" O PHE A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 249 removed outlier: 4.061A pdb=" N LYS A 249 " --> pdb=" O LYS A 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 246 through 249' Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 259 through 281 removed outlier: 3.626A pdb=" N PHE A 265 " --> pdb=" O VAL A 261 " (cutoff:3.500A) Proline residue: A 271 - end of helix removed outlier: 3.639A pdb=" N SER A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 294 Processing helix chain 'A' and resid 294 through 299 removed outlier: 3.703A pdb=" N VAL A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 312 Proline residue: A 309 - end of helix Processing helix chain 'A' and resid 316 through 326 Processing helix chain 'B' and resid 8 through 26 removed outlier: 3.758A pdb=" N MET B 18 " --> pdb=" O GLU B 14 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN B 22 " --> pdb=" O MET B 18 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU B 25 " --> pdb=" O ARG B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 53 removed outlier: 3.641A pdb=" N LYS B 51 " --> pdb=" O ASN B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 216 removed outlier: 4.595A pdb=" N ILE B 212 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N HIS B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N CYS B 214 " --> pdb=" O TRP B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 230 removed outlier: 3.533A pdb=" N TYR B 230 " --> pdb=" O LEU B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 255 removed outlier: 3.626A pdb=" N ASN B 255 " --> pdb=" O ASP B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 279 removed outlier: 3.644A pdb=" N PHE B 274 " --> pdb=" O LYS B 270 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU B 275 " --> pdb=" O LYS B 271 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 301 Processing helix chain 'B' and resid 302 through 309 Processing helix chain 'B' and resid 332 through 351 removed outlier: 3.514A pdb=" N ASP B 341 " --> pdb=" O ASP B 337 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL B 342 " --> pdb=" O ALA B 338 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS B 349 " --> pdb=" O LYS B 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 25 removed outlier: 3.642A pdb=" N GLU C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS C 15 " --> pdb=" O ALA C 11 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN C 17 " --> pdb=" O GLN C 13 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 removed outlier: 3.814A pdb=" N ILE C 33 " --> pdb=" O THR C 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 22 removed outlier: 3.804A pdb=" N ALA D 12 " --> pdb=" O SER D 8 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU D 15 " --> pdb=" O GLN D 11 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL D 16 " --> pdb=" O ALA D 12 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU D 17 " --> pdb=" O ARG D 13 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN D 18 " --> pdb=" O LYS D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 34 Processing helix chain 'D' and resid 34 through 42 removed outlier: 3.694A pdb=" N CYS D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'A' and resid 183 through 184 Processing sheet with id=AA2, first strand: chain 'B' and resid 185 through 188 removed outlier: 6.194A pdb=" N VAL B 34 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N PHE B 199 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU B 36 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N ALA B 220 " --> pdb=" O GLU B 33 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LYS B 35 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ILE B 222 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU B 37 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N CYS B 224 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N LEU B 39 " --> pdb=" O CYS B 224 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ILE B 221 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N PHE B 267 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N PHE B 223 " --> pdb=" O PHE B 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 46 through 52 removed outlier: 6.048A pdb=" N THR C 47 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ASN C 340 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS C 337 " --> pdb=" O THR C 329 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.594A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105 removed outlier: 3.964A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.887A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 192 removed outlier: 7.041A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE C 199 " --> pdb=" O TRP C 211 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.264A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 275 through 277 removed outlier: 3.504A pdb=" N CYS C 294 " --> pdb=" O LEU C 308 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 6 removed outlier: 3.561A pdb=" N THR E 78 " --> pdb=" O ASP E 73 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 58 through 60 removed outlier: 3.654A pdb=" N TYR E 59 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.933A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR E 243 " --> pdb=" O TYR E 227 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 155 through 160 removed outlier: 3.751A pdb=" N ALA E 211 " --> pdb=" O SER E 208 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 189 through 190 289 hydrogen bonds defined for protein. 795 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: 2.35 Time building geometry restraints manager: 2.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2544 1.33 - 1.46: 2293 1.46 - 1.59: 3655 1.59 - 1.72: 0 1.72 - 1.85: 75 Bond restraints: 8567 Sorted by residual: bond pdb=" CB VAL C 112 " pdb=" CG2 VAL C 112 " ideal model delta sigma weight residual 1.521 1.434 0.087 3.30e-02 9.18e+02 7.02e+00 bond pdb=" CG1 ILE C 338 " pdb=" CD1 ILE C 338 " ideal model delta sigma weight residual 1.513 1.415 0.098 3.90e-02 6.57e+02 6.35e+00 bond pdb=" CG1 ILE C 58 " pdb=" CD1 ILE C 58 " ideal model delta sigma weight residual 1.513 1.422 0.091 3.90e-02 6.57e+02 5.46e+00 bond pdb=" CA SER B 16 " pdb=" CB SER B 16 " ideal model delta sigma weight residual 1.529 1.490 0.039 1.74e-02 3.30e+03 5.10e+00 bond pdb=" CB CYS C 317 " pdb=" SG CYS C 317 " ideal model delta sigma weight residual 1.808 1.737 0.071 3.30e-02 9.18e+02 4.65e+00 ... (remaining 8562 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.53: 11490 3.53 - 7.07: 150 7.07 - 10.60: 19 10.60 - 14.14: 0 14.14 - 17.67: 1 Bond angle restraints: 11660 Sorted by residual: angle pdb=" C THR B 190 " pdb=" N PHE B 191 " pdb=" CA PHE B 191 " ideal model delta sigma weight residual 122.58 114.37 8.21 2.07e+00 2.33e-01 1.57e+01 angle pdb=" C ASP C 246 " pdb=" N ASP C 247 " pdb=" CA ASP C 247 " ideal model delta sigma weight residual 121.52 130.50 -8.98 2.34e+00 1.83e-01 1.47e+01 angle pdb=" C ASP C 291 " pdb=" N PHE C 292 " pdb=" CA PHE C 292 " ideal model delta sigma weight residual 125.66 132.54 -6.88 1.85e+00 2.92e-01 1.38e+01 angle pdb=" C ASN C 88 " pdb=" CA ASN C 88 " pdb=" CB ASN C 88 " ideal model delta sigma weight residual 109.38 115.72 -6.34 1.80e+00 3.09e-01 1.24e+01 angle pdb=" C ASP C 333 " pdb=" N SER C 334 " pdb=" CA SER C 334 " ideal model delta sigma weight residual 121.54 128.02 -6.48 1.91e+00 2.74e-01 1.15e+01 ... (remaining 11655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.39: 4441 15.39 - 30.77: 480 30.77 - 46.15: 118 46.15 - 61.54: 24 61.54 - 76.92: 7 Dihedral angle restraints: 5070 sinusoidal: 1769 harmonic: 3301 Sorted by residual: dihedral pdb=" CB CYS C 121 " pdb=" SG CYS C 121 " pdb=" SG CYS C 149 " pdb=" CB CYS C 149 " ideal model delta sinusoidal sigma weight residual 93.00 161.80 -68.80 1 1.00e+01 1.00e-02 6.13e+01 dihedral pdb=" CB CYS F 2 " pdb=" SG CYS F 2 " pdb=" SG CYS F 7 " pdb=" CB CYS F 7 " ideal model delta sinusoidal sigma weight residual -86.00 -31.70 -54.30 1 1.00e+01 1.00e-02 4.00e+01 dihedral pdb=" CB CYS A 115 " pdb=" SG CYS A 115 " pdb=" SG CYS A 193 " pdb=" CB CYS A 193 " ideal model delta sinusoidal sigma weight residual -86.00 -33.81 -52.19 1 1.00e+01 1.00e-02 3.72e+01 ... (remaining 5067 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 911 0.054 - 0.108: 342 0.108 - 0.162: 90 0.162 - 0.216: 24 0.216 - 0.270: 9 Chirality restraints: 1376 Sorted by residual: chirality pdb=" CB VAL B 218 " pdb=" CA VAL B 218 " pdb=" CG1 VAL B 218 " pdb=" CG2 VAL B 218 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA CYS F 2 " pdb=" N CYS F 2 " pdb=" C CYS F 2 " pdb=" CB CYS F 2 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CB VAL A 145 " pdb=" CA VAL A 145 " pdb=" CG1 VAL A 145 " pdb=" CG2 VAL A 145 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 1373 not shown) Planarity restraints: 1490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 175 " -0.052 5.00e-02 4.00e+02 7.86e-02 9.87e+00 pdb=" N PRO A 176 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 176 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 176 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 319 " -0.014 2.00e-02 2.50e+03 2.88e-02 8.29e+00 pdb=" C ILE B 319 " 0.050 2.00e-02 2.50e+03 pdb=" O ILE B 319 " -0.019 2.00e-02 2.50e+03 pdb=" N TYR B 320 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 151 " -0.029 2.00e-02 2.50e+03 1.99e-02 6.92e+00 pdb=" CG PHE C 151 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE C 151 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE C 151 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE C 151 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE C 151 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE C 151 " -0.007 2.00e-02 2.50e+03 ... (remaining 1487 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.18: 1 2.18 - 2.86: 3112 2.86 - 3.54: 10857 3.54 - 4.22: 20826 4.22 - 4.90: 35098 Nonbonded interactions: 69894 Sorted by model distance: nonbonded pdb=" CG2 THR A 212 " pdb=" CZ3 DTR F 4 " model vdw 1.494 3.760 nonbonded pdb=" OG SER C 331 " pdb=" OD1 ASP C 333 " model vdw 2.181 3.040 nonbonded pdb=" O ILE C 58 " pdb=" OG SER C 316 " model vdw 2.240 3.040 nonbonded pdb=" O ASP E 223 " pdb=" OH TYR E 227 " model vdw 2.240 3.040 nonbonded pdb=" OG1 THR C 274 " pdb=" O GLY C 288 " model vdw 2.252 3.040 ... (remaining 69889 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.500 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 21.660 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 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 : 0.009 0.098 8567 Z= 0.614 Angle : 1.051 17.673 11660 Z= 0.567 Chirality : 0.064 0.270 1376 Planarity : 0.007 0.079 1489 Dihedral : 14.144 76.924 2920 Min Nonbonded Distance : 1.494 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 0.71 % Allowed : 10.12 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -4.66 (0.20), residues: 1120 helix: -4.55 (0.13), residues: 343 sheet: -1.92 (0.30), residues: 257 loop : -2.53 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP C 99 HIS 0.008 0.002 HIS C 91 PHE 0.042 0.004 PHE C 151 TYR 0.035 0.003 TYR C 105 ARG 0.006 0.001 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 183 time to evaluate : 0.853 Fit side-chains REVERT: A 122 ASP cc_start: 0.6663 (m-30) cc_final: 0.6403 (m-30) REVERT: A 173 VAL cc_start: 0.8208 (t) cc_final: 0.7973 (p) REVERT: A 180 TYR cc_start: 0.7658 (m-80) cc_final: 0.7038 (m-80) REVERT: A 196 ASN cc_start: 0.7340 (m110) cc_final: 0.7107 (m110) REVERT: B 24 ARG cc_start: 0.7468 (ttp-110) cc_final: 0.7040 (ttp-110) REVERT: B 262 THR cc_start: 0.8514 (p) cc_final: 0.8314 (p) REVERT: B 333 GLN cc_start: 0.8052 (tp40) cc_final: 0.7360 (tp40) REVERT: C 154 ASP cc_start: 0.7530 (m-30) cc_final: 0.7283 (m-30) REVERT: C 175 GLN cc_start: 0.7974 (pt0) cc_final: 0.7555 (pp30) REVERT: C 215 GLU cc_start: 0.7278 (tp30) cc_final: 0.6693 (tp30) REVERT: E 19 LYS cc_start: 0.8430 (tttp) cc_final: 0.8096 (tppp) REVERT: E 38 ARG cc_start: 0.8021 (ptt180) cc_final: 0.7772 (ptp-170) outliers start: 6 outliers final: 2 residues processed: 187 average time/residue: 1.0580 time to fit residues: 211.2780 Evaluate side-chains 154 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 152 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 47 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 47 optimal weight: 8.9990 chunk 28 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 87 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN B 188 HIS B 346 ASN B 347 ASN C 62 HIS C 239 ASN E 39 GLN E 113 GLN E 142 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8567 Z= 0.276 Angle : 0.684 12.382 11660 Z= 0.358 Chirality : 0.045 0.236 1376 Planarity : 0.005 0.057 1489 Dihedral : 6.330 37.657 1219 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.53 % Allowed : 16.59 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -3.78 (0.22), residues: 1120 helix: -3.37 (0.19), residues: 365 sheet: -1.75 (0.29), residues: 280 loop : -2.04 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 99 HIS 0.005 0.001 HIS C 91 PHE 0.019 0.002 PHE C 151 TYR 0.019 0.002 TYR C 59 ARG 0.006 0.001 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 177 time to evaluate : 0.995 Fit side-chains REVERT: A 93 MET cc_start: 0.6683 (mmm) cc_final: 0.6450 (tpt) REVERT: A 122 ASP cc_start: 0.6702 (m-30) cc_final: 0.6253 (t0) REVERT: A 196 ASN cc_start: 0.7344 (m110) cc_final: 0.7087 (m110) REVERT: A 209 ILE cc_start: 0.7600 (pt) cc_final: 0.7359 (mp) REVERT: A 302 TYR cc_start: 0.8187 (m-80) cc_final: 0.7870 (m-80) REVERT: B 24 ARG cc_start: 0.7525 (ttp-110) cc_final: 0.7040 (ttp-110) REVERT: C 154 ASP cc_start: 0.7663 (m-30) cc_final: 0.7307 (m-30) REVERT: C 175 GLN cc_start: 0.7841 (pt0) cc_final: 0.7489 (pp30) REVERT: E 19 LYS cc_start: 0.8496 (tttp) cc_final: 0.8121 (tppp) REVERT: E 234 GLU cc_start: 0.7373 (pt0) cc_final: 0.6967 (pt0) outliers start: 30 outliers final: 12 residues processed: 195 average time/residue: 1.0104 time to fit residues: 211.6851 Evaluate side-chains 166 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 154 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 210 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.3980 chunk 31 optimal weight: 0.9990 chunk 84 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 34 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8567 Z= 0.210 Angle : 0.619 12.536 11660 Z= 0.321 Chirality : 0.044 0.163 1376 Planarity : 0.004 0.055 1489 Dihedral : 5.815 41.072 1219 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 5.06 % Allowed : 19.29 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -3.09 (0.23), residues: 1120 helix: -2.53 (0.23), residues: 363 sheet: -1.44 (0.28), residues: 283 loop : -1.84 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.004 0.001 HIS C 91 PHE 0.017 0.002 PHE C 241 TYR 0.016 0.002 TYR A 180 ARG 0.004 0.000 ARG A 154 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 165 time to evaluate : 0.968 Fit side-chains REVERT: A 122 ASP cc_start: 0.6172 (m-30) cc_final: 0.5853 (t0) REVERT: A 196 ASN cc_start: 0.7357 (m110) cc_final: 0.7133 (m110) REVERT: A 302 TYR cc_start: 0.8196 (m-80) cc_final: 0.7919 (m-80) REVERT: B 9 ASP cc_start: 0.7726 (m-30) cc_final: 0.7359 (m-30) REVERT: B 24 ARG cc_start: 0.7629 (ttp-110) cc_final: 0.7188 (ttp-110) REVERT: B 274 PHE cc_start: 0.5936 (OUTLIER) cc_final: 0.5369 (p90) REVERT: C 154 ASP cc_start: 0.7625 (m-30) cc_final: 0.7256 (m-30) REVERT: C 175 GLN cc_start: 0.7743 (pt0) cc_final: 0.7489 (pp30) REVERT: C 275 SER cc_start: 0.7768 (OUTLIER) cc_final: 0.7566 (m) REVERT: C 325 MET cc_start: 0.7230 (tpp) cc_final: 0.6798 (mmt) REVERT: E 13 GLN cc_start: 0.7222 (pp30) cc_final: 0.6986 (pp30) REVERT: E 19 LYS cc_start: 0.8478 (tttp) cc_final: 0.8055 (tppp) REVERT: E 234 GLU cc_start: 0.7308 (pt0) cc_final: 0.6985 (pt0) outliers start: 43 outliers final: 20 residues processed: 193 average time/residue: 1.0341 time to fit residues: 214.0146 Evaluate side-chains 168 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 146 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 215 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.7980 chunk 52 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 96 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 0.0000 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN C 75 GLN C 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8567 Z= 0.176 Angle : 0.594 12.339 11660 Z= 0.305 Chirality : 0.043 0.184 1376 Planarity : 0.004 0.052 1489 Dihedral : 5.405 43.994 1219 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 4.59 % Allowed : 21.06 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -2.69 (0.24), residues: 1120 helix: -2.01 (0.25), residues: 364 sheet: -1.29 (0.28), residues: 283 loop : -1.72 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.003 0.001 HIS C 91 PHE 0.011 0.001 PHE B 334 TYR 0.011 0.001 TYR C 59 ARG 0.009 0.000 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 163 time to evaluate : 0.999 Fit side-chains REVERT: A 122 ASP cc_start: 0.6076 (m-30) cc_final: 0.5782 (t70) REVERT: A 180 TYR cc_start: 0.7123 (m-80) cc_final: 0.6528 (m-10) REVERT: A 302 TYR cc_start: 0.8117 (m-80) cc_final: 0.7889 (m-80) REVERT: B 9 ASP cc_start: 0.7810 (m-30) cc_final: 0.7398 (m-30) REVERT: B 21 ARG cc_start: 0.7612 (ptp90) cc_final: 0.7217 (mtm110) REVERT: B 24 ARG cc_start: 0.7625 (ttp-110) cc_final: 0.7204 (ttp-110) REVERT: B 274 PHE cc_start: 0.6027 (OUTLIER) cc_final: 0.5549 (p90) REVERT: C 325 MET cc_start: 0.7259 (tpp) cc_final: 0.6917 (mmt) REVERT: E 19 LYS cc_start: 0.8449 (tttp) cc_final: 0.8028 (tppp) REVERT: E 189 ILE cc_start: 0.7945 (OUTLIER) cc_final: 0.7622 (mp) REVERT: E 234 GLU cc_start: 0.7370 (pt0) cc_final: 0.7113 (pt0) outliers start: 39 outliers final: 18 residues processed: 186 average time/residue: 0.9972 time to fit residues: 199.0790 Evaluate side-chains 165 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 145 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 189 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 55 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN C 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8567 Z= 0.343 Angle : 0.673 11.908 11660 Z= 0.350 Chirality : 0.046 0.189 1376 Planarity : 0.004 0.057 1489 Dihedral : 5.686 50.108 1219 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 5.29 % Allowed : 22.12 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -2.58 (0.24), residues: 1120 helix: -1.75 (0.25), residues: 365 sheet: -1.44 (0.28), residues: 286 loop : -1.65 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 99 HIS 0.005 0.001 HIS C 91 PHE 0.031 0.002 PHE B 189 TYR 0.016 0.002 TYR E 103 ARG 0.007 0.001 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 141 time to evaluate : 0.933 Fit side-chains revert: symmetry clash REVERT: A 122 ASP cc_start: 0.6126 (m-30) cc_final: 0.5814 (t0) REVERT: A 180 TYR cc_start: 0.7245 (m-80) cc_final: 0.6623 (m-10) REVERT: A 302 TYR cc_start: 0.8119 (m-80) cc_final: 0.7876 (m-80) REVERT: B 24 ARG cc_start: 0.7500 (ttp-110) cc_final: 0.7070 (ttp-110) REVERT: C 154 ASP cc_start: 0.7648 (m-30) cc_final: 0.7276 (m-30) REVERT: C 325 MET cc_start: 0.7274 (tpp) cc_final: 0.6881 (mmt) REVERT: E 19 LYS cc_start: 0.8501 (tttp) cc_final: 0.8044 (tppp) REVERT: E 234 GLU cc_start: 0.7477 (pt0) cc_final: 0.7229 (pt0) outliers start: 45 outliers final: 28 residues processed: 171 average time/residue: 1.0337 time to fit residues: 189.3265 Evaluate side-chains 167 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 139 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 215 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 50 optimal weight: 30.0000 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN E 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8567 Z= 0.201 Angle : 0.599 12.362 11660 Z= 0.310 Chirality : 0.043 0.175 1376 Planarity : 0.004 0.053 1489 Dihedral : 5.400 54.702 1219 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 4.71 % Allowed : 22.94 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -2.26 (0.24), residues: 1120 helix: -1.41 (0.26), residues: 367 sheet: -1.27 (0.30), residues: 266 loop : -1.54 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 99 HIS 0.004 0.001 HIS C 91 PHE 0.026 0.002 PHE B 189 TYR 0.012 0.001 TYR C 59 ARG 0.006 0.000 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 154 time to evaluate : 1.058 Fit side-chains REVERT: A 122 ASP cc_start: 0.6230 (m-30) cc_final: 0.5669 (t0) REVERT: A 180 TYR cc_start: 0.7065 (m-80) cc_final: 0.6406 (m-10) REVERT: A 218 LEU cc_start: 0.7315 (mm) cc_final: 0.7028 (tp) REVERT: B 9 ASP cc_start: 0.7871 (m-30) cc_final: 0.7389 (m-30) REVERT: B 21 ARG cc_start: 0.7633 (ptp90) cc_final: 0.7251 (mtm110) REVERT: B 24 ARG cc_start: 0.7640 (ttp-110) cc_final: 0.7251 (ttp-110) REVERT: B 274 PHE cc_start: 0.5935 (OUTLIER) cc_final: 0.5361 (p90) REVERT: B 308 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7710 (mp0) REVERT: C 325 MET cc_start: 0.7330 (tpp) cc_final: 0.6909 (mmt) REVERT: E 19 LYS cc_start: 0.8457 (tttp) cc_final: 0.8048 (tppp) REVERT: E 214 LEU cc_start: 0.5570 (OUTLIER) cc_final: 0.4699 (tp) outliers start: 40 outliers final: 25 residues processed: 183 average time/residue: 0.9873 time to fit residues: 194.1787 Evaluate side-chains 171 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 143 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 215 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.0870 chunk 61 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 67 optimal weight: 0.0070 chunk 65 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8567 Z= 0.207 Angle : 0.604 12.219 11660 Z= 0.311 Chirality : 0.044 0.186 1376 Planarity : 0.004 0.052 1489 Dihedral : 5.294 56.524 1219 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 4.12 % Allowed : 24.59 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.96 (0.25), residues: 1120 helix: -1.12 (0.27), residues: 362 sheet: -1.11 (0.30), residues: 271 loop : -1.38 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.003 0.001 HIS C 91 PHE 0.025 0.002 PHE C 241 TYR 0.013 0.002 TYR E 103 ARG 0.005 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 149 time to evaluate : 0.983 Fit side-chains REVERT: A 122 ASP cc_start: 0.6171 (m-30) cc_final: 0.5680 (t0) REVERT: A 180 TYR cc_start: 0.7090 (m-80) cc_final: 0.6440 (m-10) REVERT: A 218 LEU cc_start: 0.7318 (mm) cc_final: 0.7024 (tp) REVERT: B 21 ARG cc_start: 0.7582 (ptp90) cc_final: 0.7238 (mtm110) REVERT: B 24 ARG cc_start: 0.7629 (ttp-110) cc_final: 0.7233 (ttp-110) REVERT: B 274 PHE cc_start: 0.5908 (OUTLIER) cc_final: 0.5357 (p90) REVERT: C 325 MET cc_start: 0.7332 (tpp) cc_final: 0.6908 (mmt) REVERT: E 19 LYS cc_start: 0.8428 (tttp) cc_final: 0.8004 (tppp) REVERT: E 214 LEU cc_start: 0.5622 (OUTLIER) cc_final: 0.4842 (tp) REVERT: E 220 GLU cc_start: 0.7632 (mp0) cc_final: 0.7107 (mp0) outliers start: 35 outliers final: 23 residues processed: 176 average time/residue: 0.9794 time to fit residues: 185.4125 Evaluate side-chains 171 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 146 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 214 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 20 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 84 optimal weight: 0.0980 chunk 98 optimal weight: 7.9990 chunk 103 optimal weight: 20.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8567 Z= 0.167 Angle : 0.585 12.177 11660 Z= 0.300 Chirality : 0.043 0.170 1376 Planarity : 0.004 0.050 1489 Dihedral : 5.133 59.749 1219 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 4.00 % Allowed : 24.59 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.73 (0.25), residues: 1120 helix: -0.88 (0.28), residues: 360 sheet: -0.98 (0.30), residues: 270 loop : -1.30 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 82 HIS 0.003 0.001 HIS C 91 PHE 0.030 0.001 PHE C 241 TYR 0.011 0.001 TYR E 190 ARG 0.004 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 147 time to evaluate : 0.888 Fit side-chains REVERT: A 180 TYR cc_start: 0.7034 (m-80) cc_final: 0.6375 (m-10) REVERT: A 218 LEU cc_start: 0.7249 (mm) cc_final: 0.7001 (tp) REVERT: B 21 ARG cc_start: 0.7513 (OUTLIER) cc_final: 0.7240 (mtm110) REVERT: B 24 ARG cc_start: 0.7567 (ttp-110) cc_final: 0.7160 (ttp-110) REVERT: C 325 MET cc_start: 0.7305 (tpp) cc_final: 0.7005 (mmt) REVERT: E 19 LYS cc_start: 0.8291 (tttp) cc_final: 0.8059 (tppp) REVERT: E 43 LYS cc_start: 0.7799 (OUTLIER) cc_final: 0.7188 (tppp) REVERT: E 214 LEU cc_start: 0.5689 (OUTLIER) cc_final: 0.4903 (tp) outliers start: 34 outliers final: 17 residues processed: 171 average time/residue: 1.1331 time to fit residues: 207.5323 Evaluate side-chains 159 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 139 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 214 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.0570 chunk 100 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 60 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 78 optimal weight: 0.0070 chunk 30 optimal weight: 0.0870 chunk 90 optimal weight: 20.0000 chunk 95 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 106 optimal weight: 0.6980 overall best weight: 1.1696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 ASN A 308 ASN E 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8567 Z= 0.228 Angle : 0.646 11.688 11660 Z= 0.332 Chirality : 0.044 0.162 1376 Planarity : 0.004 0.051 1489 Dihedral : 5.231 58.318 1219 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.41 % Allowed : 26.00 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.74 (0.25), residues: 1120 helix: -0.84 (0.28), residues: 360 sheet: -1.02 (0.31), residues: 271 loop : -1.32 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 47 HIS 0.004 0.001 HIS E 35 PHE 0.029 0.002 PHE C 241 TYR 0.026 0.002 TYR A 205 ARG 0.007 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 138 time to evaluate : 0.841 Fit side-chains REVERT: A 205 TYR cc_start: 0.6111 (t80) cc_final: 0.5898 (t80) REVERT: A 218 LEU cc_start: 0.7336 (mm) cc_final: 0.7063 (tp) REVERT: B 21 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.7257 (mtm110) REVERT: B 24 ARG cc_start: 0.7590 (ttp-110) cc_final: 0.7176 (ttp-110) REVERT: C 325 MET cc_start: 0.7321 (tpp) cc_final: 0.7012 (mmt) REVERT: E 19 LYS cc_start: 0.8335 (tttp) cc_final: 0.8016 (tppp) REVERT: E 43 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7152 (tppp) REVERT: E 189 ILE cc_start: 0.7982 (OUTLIER) cc_final: 0.7623 (mp) REVERT: E 214 LEU cc_start: 0.5587 (OUTLIER) cc_final: 0.4761 (tp) REVERT: E 220 GLU cc_start: 0.7624 (mp0) cc_final: 0.7002 (mp0) outliers start: 29 outliers final: 22 residues processed: 161 average time/residue: 1.0939 time to fit residues: 188.0486 Evaluate side-chains 164 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 138 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 215 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 54 optimal weight: 0.0070 chunk 70 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8567 Z= 0.174 Angle : 0.612 11.523 11660 Z= 0.314 Chirality : 0.043 0.160 1376 Planarity : 0.004 0.058 1489 Dihedral : 5.050 52.855 1219 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.94 % Allowed : 27.18 % Favored : 69.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.60 (0.25), residues: 1120 helix: -0.66 (0.28), residues: 361 sheet: -0.94 (0.31), residues: 270 loop : -1.31 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 47 HIS 0.003 0.001 HIS C 91 PHE 0.027 0.001 PHE C 241 TYR 0.025 0.001 TYR A 205 ARG 0.015 0.001 ARG C 304 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 141 time to evaluate : 1.300 Fit side-chains REVERT: A 218 LEU cc_start: 0.7228 (mm) cc_final: 0.6960 (tp) REVERT: B 21 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.7210 (mtm110) REVERT: B 24 ARG cc_start: 0.7542 (ttp-110) cc_final: 0.7134 (ttp-110) REVERT: C 325 MET cc_start: 0.7316 (tpp) cc_final: 0.7016 (mmt) REVERT: E 19 LYS cc_start: 0.8296 (tttp) cc_final: 0.8007 (tppp) REVERT: E 189 ILE cc_start: 0.8041 (OUTLIER) cc_final: 0.7681 (mp) REVERT: E 214 LEU cc_start: 0.5659 (OUTLIER) cc_final: 0.4812 (tp) REVERT: E 220 GLU cc_start: 0.7478 (mp0) cc_final: 0.6861 (mp0) outliers start: 25 outliers final: 22 residues processed: 163 average time/residue: 1.1065 time to fit residues: 193.3122 Evaluate side-chains 164 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 139 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 214 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 5.9990 chunk 81 optimal weight: 0.2980 chunk 13 optimal weight: 0.0770 chunk 24 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 16 optimal weight: 0.3980 chunk 78 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.208710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.153598 restraints weight = 9869.623| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.57 r_work: 0.3571 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8567 Z= 0.182 Angle : 0.604 11.513 11660 Z= 0.313 Chirality : 0.043 0.156 1376 Planarity : 0.004 0.049 1489 Dihedral : 4.973 45.777 1219 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.18 % Allowed : 26.35 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.53 (0.25), residues: 1120 helix: -0.52 (0.28), residues: 361 sheet: -0.86 (0.31), residues: 269 loop : -1.37 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 47 HIS 0.003 0.001 HIS C 91 PHE 0.034 0.002 PHE B 189 TYR 0.014 0.001 TYR E 228 ARG 0.009 0.000 ARG C 304 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3648.19 seconds wall clock time: 64 minutes 15.65 seconds (3855.65 seconds total)