Starting phenix.real_space_refine on Tue May 7 10:59:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ww2_37881/05_2024/8ww2_37881.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ww2_37881/05_2024/8ww2_37881.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ww2_37881/05_2024/8ww2_37881.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ww2_37881/05_2024/8ww2_37881.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ww2_37881/05_2024/8ww2_37881.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ww2_37881/05_2024/8ww2_37881.pdb" } resolution = 2.79 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= -0.002 sd= 0.164 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 55 5.16 5 C 4950 2.51 5 N 1331 2.21 5 O 1456 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 32": "OE1" <-> "OE2" Residue "A GLU 314": "OE1" <-> "OE2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "G GLU 22": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 7792 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1808 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 57 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "B" Number of atoms: 2565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2565 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "G" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 406 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "N" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 965 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 1973 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 11, 'TRANS': 256} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 2, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "R" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 75 Unusual residues: {'OLA': 1, 'PLM': 1, 'Y01': 1} Classifications: {'undetermined': 3, 'water': 2} Link IDs: {None: 4} Time building chain proxies: 4.86, per 1000 atoms: 0.62 Number of scatterers: 7792 At special positions: 0 Unit cell: (78.1, 101.2, 134.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 55 16.00 O 1456 8.00 N 1331 7.00 C 4950 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 177 " - pdb=" SG CYS R 184 " 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: 2.72 Conformation dependent library (CDL) restraints added in 1.5 seconds 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1902 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 10 sheets defined 39.9% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 18 through 37 removed outlier: 3.658A pdb=" N LYS A 24 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG A 28 " --> pdb=" O LYS A 24 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN A 29 " --> pdb=" O MET A 25 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS A 36 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 37 " --> pdb=" O ASP A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 61 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.662A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 removed outlier: 3.777A pdb=" N GLU A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 301 removed outlier: 3.797A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 312 removed outlier: 3.641A pdb=" N ASP A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 removed outlier: 3.747A pdb=" N TYR A 318 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.509A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.555A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.985A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.627A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.592A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.514A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.548A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 67 removed outlier: 3.811A pdb=" N VAL R 45 " --> pdb=" O LYS R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 92 Processing helix chain 'R' and resid 106 through 140 Processing helix chain 'R' and resid 141 through 144 removed outlier: 3.816A pdb=" N TYR R 144 " --> pdb=" O ALA R 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 141 through 144' Processing helix chain 'R' and resid 146 through 167 removed outlier: 3.883A pdb=" N VAL R 150 " --> pdb=" O SER R 146 " (cutoff:3.500A) Processing helix chain 'R' and resid 192 through 230 removed outlier: 4.156A pdb=" N GLN R 230 " --> pdb=" O GLN R 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 243 through 270 removed outlier: 4.020A pdb=" N PHE R 256 " --> pdb=" O VAL R 252 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ALA R 257 " --> pdb=" O LEU R 253 " (cutoff:3.500A) Proline residue: R 262 - end of helix removed outlier: 3.684A pdb=" N LEU R 268 " --> pdb=" O THR R 264 " (cutoff:3.500A) Processing helix chain 'R' and resid 275 through 283 removed outlier: 4.257A pdb=" N THR R 279 " --> pdb=" O PRO R 275 " (cutoff:3.500A) Processing helix chain 'R' and resid 284 through 298 removed outlier: 4.381A pdb=" N SER R 290 " --> pdb=" O ALA R 286 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET R 291 " --> pdb=" O THR R 287 " (cutoff:3.500A) Proline residue: R 294 - end of helix Processing helix chain 'R' and resid 301 through 313 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.341A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.958A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.729A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.870A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.081A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.865A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN B 125 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.727A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.037A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.878A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.869A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.032A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 368 hydrogen bonds defined for protein. 1059 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: 2.04 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2365 1.34 - 1.46: 1302 1.46 - 1.58: 4196 1.58 - 1.70: 0 1.70 - 1.82: 77 Bond restraints: 7940 Sorted by residual: bond pdb=" N VAL R 94 " pdb=" CA VAL R 94 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.35e-02 5.49e+03 7.32e+00 bond pdb=" N LEU R 95 " pdb=" CA LEU R 95 " ideal model delta sigma weight residual 1.458 1.488 -0.031 1.22e-02 6.72e+03 6.26e+00 bond pdb=" N LEU R 93 " pdb=" CA LEU R 93 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.33e-02 5.65e+03 6.05e+00 bond pdb=" N HIS R 96 " pdb=" CA HIS R 96 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.42e-02 4.96e+03 5.87e+00 bond pdb=" N THR R 279 " pdb=" CA THR R 279 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.28e-02 6.10e+03 5.60e+00 ... (remaining 7935 not shown) Histogram of bond angle deviations from ideal: 100.10 - 106.89: 179 106.89 - 113.68: 4401 113.68 - 120.46: 3115 120.46 - 127.25: 3023 127.25 - 134.04: 75 Bond angle restraints: 10793 Sorted by residual: angle pdb=" N VAL R 100 " pdb=" CA VAL R 100 " pdb=" C VAL R 100 " ideal model delta sigma weight residual 113.10 108.68 4.42 9.70e-01 1.06e+00 2.07e+01 angle pdb=" N ILE R 103 " pdb=" CA ILE R 103 " pdb=" C ILE R 103 " ideal model delta sigma weight residual 113.71 110.13 3.58 9.50e-01 1.11e+00 1.42e+01 angle pdb=" N VAL R 94 " pdb=" CA VAL R 94 " pdb=" C VAL R 94 " ideal model delta sigma weight residual 112.29 108.87 3.42 9.40e-01 1.13e+00 1.32e+01 angle pdb=" C ILE B 58 " pdb=" N TYR B 59 " pdb=" CA TYR B 59 " ideal model delta sigma weight residual 121.98 116.53 5.45 1.53e+00 4.27e-01 1.27e+01 angle pdb=" N PHE R 97 " pdb=" CA PHE R 97 " pdb=" C PHE R 97 " ideal model delta sigma weight residual 113.55 109.28 4.27 1.26e+00 6.30e-01 1.15e+01 ... (remaining 10788 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.43: 4266 16.43 - 32.86: 385 32.86 - 49.29: 71 49.29 - 65.72: 20 65.72 - 82.15: 14 Dihedral angle restraints: 4756 sinusoidal: 1808 harmonic: 2948 Sorted by residual: dihedral pdb=" CB CYS R 177 " pdb=" SG CYS R 177 " pdb=" SG CYS R 184 " pdb=" CB CYS R 184 " ideal model delta sinusoidal sigma weight residual -86.00 -153.70 67.70 1 1.00e+01 1.00e-02 5.96e+01 dihedral pdb=" CA LYS B 127 " pdb=" C LYS B 127 " pdb=" N THR B 128 " pdb=" CA THR B 128 " ideal model delta harmonic sigma weight residual 180.00 160.85 19.15 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA LEU B 139 " pdb=" C LEU B 139 " pdb=" N ALA B 140 " pdb=" CA ALA B 140 " ideal model delta harmonic sigma weight residual 180.00 -161.16 -18.84 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 4753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1011 0.057 - 0.115: 212 0.115 - 0.172: 31 0.172 - 0.229: 1 0.229 - 0.287: 2 Chirality restraints: 1257 Sorted by residual: chirality pdb=" CBG Y01 R 602 " pdb=" CAQ Y01 R 602 " pdb=" CBD Y01 R 602 " pdb=" CBI Y01 R 602 " both_signs ideal model delta sigma weight residual False -2.33 -2.62 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CBF Y01 R 602 " pdb=" CAS Y01 R 602 " pdb=" CBD Y01 R 602 " pdb=" CBH Y01 R 602 " both_signs ideal model delta sigma weight residual False -2.45 -2.68 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CBE Y01 R 602 " pdb=" CAP Y01 R 602 " pdb=" CBB Y01 R 602 " pdb=" CBI Y01 R 602 " both_signs ideal model delta sigma weight residual False 2.57 2.77 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 1254 not shown) Planarity restraints: 1375 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 OLA R 601 " -0.039 2.00e-02 2.50e+03 3.01e-02 9.09e+00 pdb=" C11 OLA R 601 " 0.017 2.00e-02 2.50e+03 pdb=" C8 OLA R 601 " -0.017 2.00e-02 2.50e+03 pdb=" C9 OLA R 601 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN G 59 " -0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO G 60 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO G 60 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO G 60 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO B 236 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.027 5.00e-02 4.00e+02 ... (remaining 1372 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 9 2.43 - 3.05: 4501 3.05 - 3.66: 10444 3.66 - 4.28: 15904 4.28 - 4.90: 27810 Nonbonded interactions: 58668 Sorted by model distance: nonbonded pdb=" O LEU R 95 " pdb=" CD1 LEU R 112 " model vdw 1.809 3.460 nonbonded pdb=" O THR B 86 " pdb=" OG1 THR B 87 " model vdw 2.236 2.440 nonbonded pdb=" OD1 ASN A 239 " pdb=" NZ LYS B 57 " model vdw 2.287 2.520 nonbonded pdb=" NE2 GLN G 18 " pdb=" OE2 GLU G 22 " model vdw 2.301 2.520 nonbonded pdb=" O ASP B 195 " pdb=" OG1 THR B 196 " model vdw 2.332 2.440 ... (remaining 58663 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.970 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 23.790 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 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 : 0.004 0.045 7940 Z= 0.261 Angle : 0.714 8.383 10793 Z= 0.409 Chirality : 0.048 0.287 1257 Planarity : 0.005 0.051 1375 Dihedral : 13.756 82.154 2845 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.26), residues: 1004 helix: 1.59 (0.28), residues: 360 sheet: 0.52 (0.35), residues: 232 loop : -1.66 (0.27), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 82 HIS 0.012 0.002 HIS A 357 PHE 0.022 0.002 PHE N 108 TYR 0.020 0.002 TYR B 59 ARG 0.005 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.912 Fit side-chains REVERT: B 134 ARG cc_start: 0.6840 (ptp-110) cc_final: 0.6584 (pmt170) REVERT: R 118 MET cc_start: 0.6560 (ttp) cc_final: 0.6211 (ttm) outliers start: 0 outliers final: 1 residues processed: 105 average time/residue: 1.4608 time to fit residues: 161.7905 Evaluate side-chains 94 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 292 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 96 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7940 Z= 0.329 Angle : 0.690 11.202 10793 Z= 0.366 Chirality : 0.047 0.158 1257 Planarity : 0.006 0.070 1375 Dihedral : 7.115 59.169 1201 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.35 % Allowed : 7.80 % Favored : 89.85 % 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: 0.22 (0.26), residues: 1004 helix: 1.72 (0.28), residues: 357 sheet: 0.66 (0.35), residues: 224 loop : -1.60 (0.27), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 82 HIS 0.013 0.002 HIS A 357 PHE 0.024 0.002 PHE N 108 TYR 0.015 0.002 TYR R 213 ARG 0.004 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 106 time to evaluate : 0.857 Fit side-chains REVERT: B 134 ARG cc_start: 0.6949 (ptp-110) cc_final: 0.6581 (pmt170) REVERT: B 197 ARG cc_start: 0.7089 (mmp80) cc_final: 0.6731 (mmp80) REVERT: B 214 ARG cc_start: 0.7581 (mmt180) cc_final: 0.7297 (mpt-90) REVERT: R 283 LEU cc_start: 0.7800 (tp) cc_final: 0.7482 (tm) outliers start: 19 outliers final: 11 residues processed: 113 average time/residue: 1.3436 time to fit residues: 160.2047 Evaluate side-chains 113 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 102 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain R residue 269 LEU Chi-restraints excluded: chain R residue 277 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 24 optimal weight: 0.1980 chunk 90 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN N 120 GLN R 140 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7940 Z= 0.162 Angle : 0.511 6.858 10793 Z= 0.279 Chirality : 0.042 0.140 1257 Planarity : 0.004 0.051 1375 Dihedral : 6.595 59.310 1199 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.86 % Allowed : 10.77 % Favored : 87.38 % 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: 0.66 (0.27), residues: 1004 helix: 2.11 (0.28), residues: 362 sheet: 0.77 (0.35), residues: 234 loop : -1.38 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.015 0.001 PHE N 108 TYR 0.009 0.001 TYR R 213 ARG 0.005 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 97 time to evaluate : 1.318 Fit side-chains REVERT: A 28 ARG cc_start: 0.7675 (ptp-110) cc_final: 0.6923 (mtm-85) REVERT: B 59 TYR cc_start: 0.8545 (OUTLIER) cc_final: 0.8259 (t80) REVERT: B 134 ARG cc_start: 0.6911 (ptp-110) cc_final: 0.6567 (pmt170) REVERT: N 35 ASN cc_start: 0.8520 (OUTLIER) cc_final: 0.7942 (p0) REVERT: R 118 MET cc_start: 0.6435 (ttp) cc_final: 0.5988 (ttm) REVERT: R 283 LEU cc_start: 0.7702 (tp) cc_final: 0.7407 (tm) outliers start: 15 outliers final: 7 residues processed: 102 average time/residue: 1.5148 time to fit residues: 162.8185 Evaluate side-chains 102 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 93 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 292 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 6.9990 chunk 67 optimal weight: 0.0980 chunk 46 optimal weight: 0.9980 chunk 9 optimal weight: 0.0270 chunk 42 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN R 140 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7940 Z= 0.167 Angle : 0.503 6.287 10793 Z= 0.274 Chirality : 0.042 0.136 1257 Planarity : 0.004 0.051 1375 Dihedral : 6.447 58.060 1199 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.86 % Allowed : 12.50 % Favored : 85.64 % 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: 0.82 (0.27), residues: 1004 helix: 2.31 (0.28), residues: 360 sheet: 0.83 (0.36), residues: 225 loop : -1.27 (0.27), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.017 0.001 PHE N 108 TYR 0.010 0.001 TYR R 139 ARG 0.006 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 0.802 Fit side-chains REVERT: A 28 ARG cc_start: 0.7453 (ptp-110) cc_final: 0.6859 (mtm-85) REVERT: B 59 TYR cc_start: 0.8585 (OUTLIER) cc_final: 0.8252 (t80) REVERT: B 134 ARG cc_start: 0.6935 (ptp-110) cc_final: 0.6565 (pmt170) REVERT: B 217 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.8046 (ppp) REVERT: R 118 MET cc_start: 0.6478 (ttp) cc_final: 0.6029 (ttm) REVERT: R 283 LEU cc_start: 0.7700 (tp) cc_final: 0.7369 (tm) outliers start: 15 outliers final: 11 residues processed: 105 average time/residue: 1.4156 time to fit residues: 156.3957 Evaluate side-chains 109 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 96 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 269 LEU Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 292 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 71 optimal weight: 0.2980 chunk 39 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 48 optimal weight: 0.0070 chunk 85 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN R 140 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7940 Z= 0.136 Angle : 0.461 4.981 10793 Z= 0.252 Chirality : 0.041 0.137 1257 Planarity : 0.004 0.052 1375 Dihedral : 6.111 55.662 1199 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.98 % Allowed : 13.61 % Favored : 84.41 % 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: 1.08 (0.27), residues: 1004 helix: 2.46 (0.28), residues: 362 sheet: 0.90 (0.36), residues: 233 loop : -1.06 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.012 0.001 PHE N 108 TYR 0.008 0.001 TYR R 213 ARG 0.006 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 105 time to evaluate : 0.744 Fit side-chains REVERT: A 28 ARG cc_start: 0.7503 (ptp-110) cc_final: 0.6898 (mtm-85) REVERT: B 59 TYR cc_start: 0.8571 (OUTLIER) cc_final: 0.8235 (t80) REVERT: B 175 GLN cc_start: 0.7377 (OUTLIER) cc_final: 0.6748 (mp10) REVERT: B 186 ASP cc_start: 0.7645 (m-30) cc_final: 0.7272 (m-30) REVERT: B 217 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.8049 (ppp) REVERT: N 35 ASN cc_start: 0.8524 (OUTLIER) cc_final: 0.8020 (p0) REVERT: N 80 TYR cc_start: 0.8008 (m-80) cc_final: 0.7680 (m-80) REVERT: R 118 MET cc_start: 0.6393 (ttp) cc_final: 0.5931 (ttm) outliers start: 16 outliers final: 9 residues processed: 111 average time/residue: 1.3567 time to fit residues: 159.1351 Evaluate side-chains 112 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 99 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 292 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 0.7980 chunk 86 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 56 optimal weight: 0.2980 chunk 23 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 79 optimal weight: 0.0970 chunk 44 optimal weight: 0.1980 chunk 7 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN R 140 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7940 Z= 0.129 Angle : 0.448 4.980 10793 Z= 0.245 Chirality : 0.040 0.140 1257 Planarity : 0.004 0.053 1375 Dihedral : 5.863 56.285 1199 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.86 % Allowed : 14.85 % Favored : 83.29 % 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: 1.23 (0.27), residues: 1004 helix: 2.64 (0.28), residues: 360 sheet: 0.91 (0.36), residues: 231 loop : -0.95 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.013 0.001 PHE A 212 TYR 0.009 0.001 TYR R 213 ARG 0.005 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 93 time to evaluate : 0.828 Fit side-chains REVERT: A 28 ARG cc_start: 0.7579 (ptp-110) cc_final: 0.6954 (mtm-85) REVERT: B 59 TYR cc_start: 0.8555 (OUTLIER) cc_final: 0.8215 (t80) REVERT: B 186 ASP cc_start: 0.7611 (m-30) cc_final: 0.7170 (m-30) REVERT: B 217 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.8127 (ppp) REVERT: N 35 ASN cc_start: 0.8505 (OUTLIER) cc_final: 0.7964 (p0) REVERT: N 80 TYR cc_start: 0.7996 (m-80) cc_final: 0.7661 (m-80) REVERT: R 118 MET cc_start: 0.6334 (ttp) cc_final: 0.5869 (ttm) outliers start: 15 outliers final: 8 residues processed: 101 average time/residue: 1.3430 time to fit residues: 143.2311 Evaluate side-chains 102 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 91 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 292 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 0.1980 chunk 10 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 59 optimal weight: 0.3980 chunk 58 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN R 140 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7940 Z= 0.143 Angle : 0.461 5.472 10793 Z= 0.251 Chirality : 0.041 0.139 1257 Planarity : 0.004 0.052 1375 Dihedral : 5.811 56.640 1199 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.49 % Allowed : 15.97 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.27), residues: 1004 helix: 2.59 (0.28), residues: 366 sheet: 0.92 (0.35), residues: 234 loop : -0.87 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.015 0.001 PHE N 108 TYR 0.010 0.001 TYR R 139 ARG 0.005 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 0.831 Fit side-chains REVERT: A 28 ARG cc_start: 0.7635 (ptp-110) cc_final: 0.6901 (mtm-85) REVERT: B 59 TYR cc_start: 0.8585 (OUTLIER) cc_final: 0.8262 (t80) REVERT: B 186 ASP cc_start: 0.7615 (m-30) cc_final: 0.7181 (m-30) REVERT: B 217 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.8119 (ppp) REVERT: N 80 TYR cc_start: 0.8031 (m-80) cc_final: 0.7695 (m-80) REVERT: R 118 MET cc_start: 0.6347 (ttp) cc_final: 0.5887 (ttm) outliers start: 12 outliers final: 9 residues processed: 98 average time/residue: 1.3877 time to fit residues: 143.3243 Evaluate side-chains 103 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 292 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 8.9990 chunk 28 optimal weight: 0.0870 chunk 18 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN R 140 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7940 Z= 0.211 Angle : 0.533 7.629 10793 Z= 0.289 Chirality : 0.043 0.141 1257 Planarity : 0.004 0.052 1375 Dihedral : 6.073 58.850 1199 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.10 % Allowed : 15.97 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.27), residues: 1004 helix: 2.45 (0.28), residues: 366 sheet: 0.81 (0.35), residues: 239 loop : -0.92 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.007 0.001 HIS A 357 PHE 0.022 0.002 PHE N 108 TYR 0.014 0.001 TYR R 213 ARG 0.008 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 102 time to evaluate : 0.996 Fit side-chains REVERT: A 28 ARG cc_start: 0.7644 (ptp-110) cc_final: 0.6936 (mtm-85) REVERT: A 314 GLU cc_start: 0.7200 (mp0) cc_final: 0.6947 (mp0) REVERT: B 59 TYR cc_start: 0.8667 (OUTLIER) cc_final: 0.8364 (t80) REVERT: B 165 THR cc_start: 0.8937 (m) cc_final: 0.8452 (t) REVERT: B 186 ASP cc_start: 0.7724 (m-30) cc_final: 0.7317 (m-30) REVERT: B 217 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.8129 (ppp) REVERT: R 118 MET cc_start: 0.6475 (ttp) cc_final: 0.6013 (ttm) REVERT: R 249 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7680 (mp) outliers start: 17 outliers final: 12 residues processed: 112 average time/residue: 1.5639 time to fit residues: 186.2884 Evaluate side-chains 115 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 100 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 277 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 0.2980 chunk 91 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 80 optimal weight: 7.9990 chunk 84 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 94 optimal weight: 0.5980 chunk 57 optimal weight: 9.9990 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 29 ASN R 140 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7940 Z= 0.148 Angle : 0.474 5.688 10793 Z= 0.259 Chirality : 0.041 0.141 1257 Planarity : 0.004 0.052 1375 Dihedral : 5.874 58.506 1199 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.49 % Allowed : 16.83 % Favored : 81.68 % 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: 1.26 (0.27), residues: 1004 helix: 2.57 (0.28), residues: 366 sheet: 0.90 (0.35), residues: 234 loop : -0.89 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.015 0.001 PHE N 108 TYR 0.010 0.001 TYR R 139 ARG 0.004 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 100 time to evaluate : 0.961 Fit side-chains REVERT: A 28 ARG cc_start: 0.7540 (ptp-110) cc_final: 0.6886 (mtm-85) REVERT: B 59 TYR cc_start: 0.8567 (OUTLIER) cc_final: 0.8263 (t80) REVERT: B 186 ASP cc_start: 0.7574 (m-30) cc_final: 0.7075 (m-30) REVERT: N 80 TYR cc_start: 0.8087 (m-80) cc_final: 0.7719 (m-80) REVERT: R 118 MET cc_start: 0.6394 (ttp) cc_final: 0.5942 (ttm) outliers start: 12 outliers final: 7 residues processed: 105 average time/residue: 1.3207 time to fit residues: 146.7232 Evaluate side-chains 108 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 100 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain R residue 277 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 0.0970 chunk 65 optimal weight: 0.0170 chunk 98 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 8 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN B 32 GLN R 140 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7940 Z= 0.144 Angle : 0.467 5.409 10793 Z= 0.255 Chirality : 0.041 0.140 1257 Planarity : 0.004 0.052 1375 Dihedral : 5.797 59.757 1199 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.36 % Allowed : 17.08 % Favored : 81.56 % 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: 1.32 (0.27), residues: 1004 helix: 2.62 (0.28), residues: 366 sheet: 0.96 (0.35), residues: 229 loop : -0.85 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.015 0.001 PHE N 108 TYR 0.012 0.001 TYR R 266 ARG 0.008 0.000 ARG B 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 1.074 Fit side-chains REVERT: A 28 ARG cc_start: 0.7545 (ptp-110) cc_final: 0.6901 (mtm-85) REVERT: B 59 TYR cc_start: 0.8549 (OUTLIER) cc_final: 0.8238 (t80) REVERT: B 188 MET cc_start: 0.8731 (mmt) cc_final: 0.8517 (mmm) REVERT: N 35 ASN cc_start: 0.8551 (OUTLIER) cc_final: 0.8122 (p0) REVERT: N 80 TYR cc_start: 0.8046 (m-80) cc_final: 0.7675 (m-80) REVERT: R 118 MET cc_start: 0.6321 (ttp) cc_final: 0.5869 (ttm) REVERT: R 266 TYR cc_start: 0.7692 (t80) cc_final: 0.7467 (t80) outliers start: 11 outliers final: 8 residues processed: 102 average time/residue: 1.3713 time to fit residues: 147.4065 Evaluate side-chains 107 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 277 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 69 optimal weight: 0.0070 chunk 4 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN B 32 GLN R 140 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.172553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.128581 restraints weight = 7686.917| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.00 r_work: 0.3177 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7940 Z= 0.181 Angle : 0.507 6.701 10793 Z= 0.275 Chirality : 0.042 0.139 1257 Planarity : 0.004 0.051 1375 Dihedral : 5.905 58.862 1199 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.36 % Allowed : 17.08 % Favored : 81.56 % 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: 1.21 (0.27), residues: 1004 helix: 2.55 (0.27), residues: 366 sheet: 0.98 (0.36), residues: 224 loop : -0.97 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.019 0.002 PHE N 108 TYR 0.013 0.001 TYR R 266 ARG 0.009 0.000 ARG B 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3207.03 seconds wall clock time: 58 minutes 1.84 seconds (3481.84 seconds total)