Starting phenix.real_space_refine on Wed Feb 14 10:50:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vai_8653/02_2024/5vai_8653.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vai_8653/02_2024/5vai_8653.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vai_8653/02_2024/5vai_8653.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vai_8653/02_2024/5vai_8653.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vai_8653/02_2024/5vai_8653.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vai_8653/02_2024/5vai_8653.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 56 5.16 5 C 5777 2.51 5 N 1582 2.21 5 O 1684 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 176": "NH1" <-> "NH2" Residue "A ARG 389": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "N PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 98": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9099 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2969 Classifications: {'peptide': 387} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 53} Link IDs: {'PTRANS': 13, 'TRANS': 373} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 288 Unresolved non-hydrogen dihedrals: 191 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 5, 'GLU:plan': 3, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 158 Chain: "P" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 231 Classifications: {'peptide': 31} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 30} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 1905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1905 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 2 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 2586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2586 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 438 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 970 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.03, per 1000 atoms: 0.55 Number of scatterers: 9099 At special positions: 0 Unit cell: (168, 101, 102, 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 56 16.00 O 1684 8.00 N 1582 7.00 C 5777 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.95 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.02 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.54 Conformation dependent library (CDL) restraints added in 1.7 seconds 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2210 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 12 sheets defined 43.0% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'R' and resid 31 through 53 Processing helix chain 'R' and resid 123 through 127 Processing helix chain 'R' and resid 137 through 169 removed outlier: 4.122A pdb=" N LEU R 141 " --> pdb=" O PRO R 137 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILE R 146 " --> pdb=" O LEU R 142 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE R 147 " --> pdb=" O SER R 143 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY R 151 " --> pdb=" O ILE R 147 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR R 152 " --> pdb=" O TYR R 148 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU R 154 " --> pdb=" O VAL R 150 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER R 155 " --> pdb=" O GLY R 151 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE R 156 " --> pdb=" O TYR R 152 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER R 157 " --> pdb=" O ALA R 153 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE R 169 " --> pdb=" O ILE R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 211 removed outlier: 3.614A pdb=" N MET R 204 " --> pdb=" O ALA R 200 " (cutoff:3.500A) Processing helix chain 'R' and resid 212 through 223 removed outlier: 4.286A pdb=" N LEU R 217 " --> pdb=" O GLN R 213 " (cutoff:3.500A) Processing helix chain 'R' and resid 224 through 257 Processing helix chain 'R' and resid 261 through 274 removed outlier: 3.544A pdb=" N LEU R 268 " --> pdb=" O ARG R 264 " (cutoff:3.500A) Processing helix chain 'R' and resid 274 through 292 removed outlier: 3.515A pdb=" N LEU R 278 " --> pdb=" O TRP R 274 " (cutoff:3.500A) Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 304 through 338 removed outlier: 3.881A pdb=" N ILE R 308 " --> pdb=" O ASN R 304 " (cutoff:3.500A) Proline residue: R 312 - end of helix removed outlier: 3.973A pdb=" N ASN R 338 " --> pdb=" O LYS R 334 " (cutoff:3.500A) Processing helix chain 'R' and resid 339 through 343 Processing helix chain 'R' and resid 345 through 355 removed outlier: 4.059A pdb=" N LEU R 349 " --> pdb=" O ILE R 345 " (cutoff:3.500A) Processing helix chain 'R' and resid 356 through 361 removed outlier: 3.521A pdb=" N LEU R 360 " --> pdb=" O LEU R 356 " (cutoff:3.500A) Processing helix chain 'R' and resid 364 through 369 Processing helix chain 'R' and resid 379 through 403 removed outlier: 3.911A pdb=" N LYS R 383 " --> pdb=" O LEU R 379 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 421 Processing helix chain 'P' and resid 8 through 34 removed outlier: 4.399A pdb=" N PHE P 12 " --> pdb=" O ALA P 8 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL P 16 " --> pdb=" O PHE P 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 40 removed outlier: 3.778A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 59 removed outlier: 3.814A pdb=" N GLN A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 removed outlier: 3.682A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 removed outlier: 3.653A pdb=" N GLU A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.748A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.023A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.691A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 391 Processing helix chain 'B' and resid 2 through 25 removed outlier: 4.119A pdb=" N GLN B 6 " --> pdb=" O SER B 2 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 8 through 24 removed outlier: 4.508A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 removed outlier: 3.531A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.700A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 65 through 66 Processing sheet with id=AA2, first strand: chain 'R' and resid 79 through 84 Processing sheet with id=AA3, first strand: chain 'A' and resid 210 through 214 removed outlier: 7.163A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR A 360 " --> pdb=" O VAL A 287 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.516A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.859A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.119A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.516A pdb=" N VAL B 158 " --> pdb=" O ARG B 150 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.783A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.493A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.689A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 3 through 6 Processing sheet with id=AB3, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.566A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 473 hydrogen bonds defined for protein. 1341 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: 2.48 Time building geometry restraints manager: 3.84 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: 2987 1.34 - 1.46: 2311 1.46 - 1.59: 3920 1.59 - 1.71: 0 1.71 - 1.83: 75 Bond restraints: 9293 Sorted by residual: bond pdb=" CG1 ILE B 273 " pdb=" CD1 ILE B 273 " ideal model delta sigma weight residual 1.513 1.439 0.074 3.90e-02 6.57e+02 3.63e+00 bond pdb=" CG LEU R 142 " pdb=" CD1 LEU R 142 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.43e+00 bond pdb=" CB TRP R 274 " pdb=" CG TRP R 274 " ideal model delta sigma weight residual 1.498 1.443 0.055 3.10e-02 1.04e+03 3.10e+00 bond pdb=" CB TRP A 281 " pdb=" CG TRP A 281 " ideal model delta sigma weight residual 1.498 1.444 0.054 3.10e-02 1.04e+03 3.03e+00 bond pdb=" CB PHE B 151 " pdb=" CG PHE B 151 " ideal model delta sigma weight residual 1.502 1.462 0.040 2.30e-02 1.89e+03 3.02e+00 ... (remaining 9288 not shown) Histogram of bond angle deviations from ideal: 96.39 - 103.93: 94 103.93 - 111.47: 4106 111.47 - 119.01: 3421 119.01 - 126.55: 4836 126.55 - 134.09: 155 Bond angle restraints: 12612 Sorted by residual: angle pdb=" C LEU R 401 " pdb=" N TYR R 402 " pdb=" CA TYR R 402 " ideal model delta sigma weight residual 122.37 113.37 9.00 1.54e+00 4.22e-01 3.42e+01 angle pdb=" CA LEU R 166 " pdb=" CB LEU R 166 " pdb=" CG LEU R 166 " ideal model delta sigma weight residual 116.30 100.81 15.49 3.50e+00 8.16e-02 1.96e+01 angle pdb=" N ASP R 68 " pdb=" CA ASP R 68 " pdb=" C ASP R 68 " ideal model delta sigma weight residual 113.28 106.56 6.72 1.57e+00 4.06e-01 1.83e+01 angle pdb=" N VAL A 367 " pdb=" CA VAL A 367 " pdb=" C VAL A 367 " ideal model delta sigma weight residual 109.34 100.67 8.67 2.08e+00 2.31e-01 1.74e+01 angle pdb=" N ALA A 366 " pdb=" CA ALA A 366 " pdb=" C ALA A 366 " ideal model delta sigma weight residual 111.69 106.63 5.06 1.23e+00 6.61e-01 1.69e+01 ... (remaining 12607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.04: 5228 16.04 - 32.07: 224 32.07 - 48.11: 36 48.11 - 64.15: 6 64.15 - 80.18: 5 Dihedral angle restraints: 5499 sinusoidal: 2077 harmonic: 3422 Sorted by residual: dihedral pdb=" CA LEU R 167 " pdb=" C LEU R 167 " pdb=" N GLY R 168 " pdb=" CA GLY R 168 " ideal model delta harmonic sigma weight residual -180.00 -156.91 -23.09 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA TYR A 318 " pdb=" C TYR A 318 " pdb=" N THR A 319 " pdb=" CA THR A 319 " ideal model delta harmonic sigma weight residual -180.00 -157.23 -22.77 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA CYS R 296 " pdb=" C CYS R 296 " pdb=" N TRP R 297 " pdb=" CA TRP R 297 " ideal model delta harmonic sigma weight residual 180.00 159.74 20.26 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 5496 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 979 0.051 - 0.101: 353 0.101 - 0.152: 71 0.152 - 0.203: 9 0.203 - 0.253: 4 Chirality restraints: 1416 Sorted by residual: chirality pdb=" CA TRP R 297 " pdb=" N TRP R 297 " pdb=" C TRP R 297 " pdb=" CB TRP R 297 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA PHE R 169 " pdb=" N PHE R 169 " pdb=" C PHE R 169 " pdb=" CB PHE R 169 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA VAL A 367 " pdb=" N VAL A 367 " pdb=" C VAL A 367 " pdb=" CB VAL A 367 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 1413 not shown) Planarity restraints: 1612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG R 176 " -0.017 2.00e-02 2.50e+03 3.47e-02 1.21e+01 pdb=" C ARG R 176 " 0.060 2.00e-02 2.50e+03 pdb=" O ARG R 176 " -0.022 2.00e-02 2.50e+03 pdb=" N ASN R 177 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER R 155 " 0.016 2.00e-02 2.50e+03 3.11e-02 9.64e+00 pdb=" C SER R 155 " -0.054 2.00e-02 2.50e+03 pdb=" O SER R 155 " 0.020 2.00e-02 2.50e+03 pdb=" N PHE R 156 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 156 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.64e+00 pdb=" C PHE R 156 " 0.048 2.00e-02 2.50e+03 pdb=" O PHE R 156 " -0.018 2.00e-02 2.50e+03 pdb=" N SER R 157 " -0.016 2.00e-02 2.50e+03 ... (remaining 1609 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 195 2.62 - 3.19: 9343 3.19 - 3.76: 14482 3.76 - 4.33: 20190 4.33 - 4.90: 31115 Nonbonded interactions: 75325 Sorted by model distance: nonbonded pdb=" OG1 THR A 325 " pdb=" OH TYR A 339 " model vdw 2.049 2.440 nonbonded pdb=" O ASP N 90 " pdb=" OH TYR N 94 " model vdw 2.074 2.440 nonbonded pdb=" OE1 GLN B 176 " pdb=" OG1 THR B 179 " model vdw 2.100 2.440 nonbonded pdb=" OG1 THR R 175 " pdb=" OH TYR R 250 " model vdw 2.113 2.440 nonbonded pdb=" O TYR A 318 " pdb=" NH2 ARG A 336 " model vdw 2.121 2.520 ... (remaining 75320 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 group one per residue 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: 1.070 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: 3.770 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 26.700 Find NCS groups from input model: 0.240 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: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 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 : 0.008 0.091 9293 Z= 0.504 Angle : 1.109 15.490 12612 Z= 0.625 Chirality : 0.054 0.253 1416 Planarity : 0.007 0.055 1612 Dihedral : 9.722 80.183 3271 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 31.73 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.40 % Favored : 95.26 % Rotamer: Outliers : 0.21 % Allowed : 3.84 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.22), residues: 1160 helix: -0.71 (0.22), residues: 407 sheet: -1.16 (0.31), residues: 221 loop : -1.03 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.005 TRP R 120 HIS 0.021 0.004 HIS R 180 PHE 0.034 0.004 PHE A 312 TYR 0.024 0.004 TYR N 32 ARG 0.015 0.001 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 509 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 157 SER cc_start: 0.8754 (m) cc_final: 0.8528 (p) REVERT: R 176 ARG cc_start: 0.7616 (ttm110) cc_final: 0.7285 (ttm-80) REVERT: R 229 VAL cc_start: 0.9257 (t) cc_final: 0.9049 (p) REVERT: R 272 ILE cc_start: 0.8281 (tt) cc_final: 0.7955 (mt) REVERT: R 325 ILE cc_start: 0.8536 (mt) cc_final: 0.8287 (mt) REVERT: R 340 MET cc_start: 0.7809 (tmt) cc_final: 0.7419 (tpt) REVERT: R 351 LYS cc_start: 0.8588 (tptt) cc_final: 0.8079 (tmtt) REVERT: R 387 GLU cc_start: 0.8898 (tm-30) cc_final: 0.8679 (tm-30) REVERT: R 413 PHE cc_start: 0.8138 (t80) cc_final: 0.7907 (t80) REVERT: P 15 ASP cc_start: 0.8876 (t0) cc_final: 0.8600 (t0) REVERT: A 11 ASP cc_start: 0.8495 (t0) cc_final: 0.8014 (t0) REVERT: A 28 LYS cc_start: 0.7186 (mmpt) cc_final: 0.6584 (ptpp) REVERT: A 44 LEU cc_start: 0.8878 (tp) cc_final: 0.8344 (tp) REVERT: A 222 PHE cc_start: 0.7438 (t80) cc_final: 0.7217 (t80) REVERT: A 229 ASP cc_start: 0.8079 (p0) cc_final: 0.7570 (p0) REVERT: A 255 MET cc_start: 0.6727 (ptt) cc_final: 0.6397 (ptm) REVERT: A 283 ARG cc_start: 0.8608 (mtt180) cc_final: 0.7980 (ptp-170) REVERT: A 285 ILE cc_start: 0.9116 (mm) cc_final: 0.8906 (tp) REVERT: A 309 GLU cc_start: 0.9112 (pt0) cc_final: 0.8608 (tp30) REVERT: A 318 TYR cc_start: 0.6146 (t80) cc_final: 0.5830 (t80) REVERT: A 344 GLU cc_start: 0.8953 (mm-30) cc_final: 0.8688 (mm-30) REVERT: A 360 TYR cc_start: 0.8502 (m-10) cc_final: 0.8000 (m-10) REVERT: A 386 MET cc_start: 0.9090 (tmt) cc_final: 0.8635 (tmm) REVERT: B 12 GLU cc_start: 0.8520 (tt0) cc_final: 0.8301 (tm-30) REVERT: B 49 ARG cc_start: 0.7727 (mmt-90) cc_final: 0.7165 (mmt-90) REVERT: B 120 ILE cc_start: 0.8720 (mt) cc_final: 0.8420 (mm) REVERT: B 148 CYS cc_start: 0.8588 (t) cc_final: 0.8010 (t) REVERT: B 160 SER cc_start: 0.8678 (p) cc_final: 0.8255 (t) REVERT: B 210 LEU cc_start: 0.9040 (tp) cc_final: 0.8785 (tp) REVERT: B 228 ASP cc_start: 0.7546 (m-30) cc_final: 0.7339 (m-30) REVERT: B 235 PHE cc_start: 0.7800 (t80) cc_final: 0.7377 (t80) REVERT: B 273 ILE cc_start: 0.9099 (mp) cc_final: 0.8801 (mp) REVERT: N 36 TRP cc_start: 0.6399 (m100) cc_final: 0.5998 (m100) REVERT: N 45 LEU cc_start: 0.8001 (mp) cc_final: 0.7592 (mt) REVERT: N 47 TRP cc_start: 0.8346 (t60) cc_final: 0.7128 (t60) REVERT: N 81 LEU cc_start: 0.9292 (tp) cc_final: 0.8906 (tp) REVERT: N 86 LEU cc_start: 0.8453 (mp) cc_final: 0.8172 (mt) outliers start: 2 outliers final: 0 residues processed: 510 average time/residue: 0.2941 time to fit residues: 196.9544 Evaluate side-chains 341 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 341 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 211 GLN ** R 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 213 GLN R 240 ASN R 302 ASN R 363 HIS A 227 GLN A 267 GLN A 271 ASN ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN N 31 ASN N 77 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 9293 Z= 0.272 Angle : 0.789 10.669 12612 Z= 0.421 Chirality : 0.047 0.222 1416 Planarity : 0.006 0.056 1612 Dihedral : 5.706 27.335 1277 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 22.76 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.62 % Favored : 96.21 % Rotamer: Outliers : 0.21 % Allowed : 5.01 % Favored : 94.78 % 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: -0.73 (0.23), residues: 1160 helix: -0.01 (0.23), residues: 425 sheet: -0.79 (0.32), residues: 222 loop : -0.58 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 281 HIS 0.009 0.002 HIS R 180 PHE 0.031 0.003 PHE R 381 TYR 0.021 0.002 TYR N 32 ARG 0.010 0.001 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 423 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 176 ARG cc_start: 0.7744 (ttm110) cc_final: 0.7124 (ttm-80) REVERT: R 229 VAL cc_start: 0.9237 (t) cc_final: 0.9021 (p) REVERT: R 272 ILE cc_start: 0.8337 (tt) cc_final: 0.8108 (mt) REVERT: R 351 LYS cc_start: 0.8618 (tptt) cc_final: 0.7998 (tmtt) REVERT: A 28 LYS cc_start: 0.6928 (mmpt) cc_final: 0.6523 (ptpp) REVERT: A 32 LYS cc_start: 0.9194 (mttt) cc_final: 0.8935 (mttp) REVERT: A 44 LEU cc_start: 0.8704 (tp) cc_final: 0.8350 (tp) REVERT: A 229 ASP cc_start: 0.8211 (p0) cc_final: 0.7655 (p0) REVERT: A 237 CYS cc_start: 0.8687 (m) cc_final: 0.8208 (m) REVERT: A 271 ASN cc_start: 0.8308 (m110) cc_final: 0.7191 (m110) REVERT: A 273 PHE cc_start: 0.9027 (t80) cc_final: 0.8488 (t80) REVERT: A 283 ARG cc_start: 0.8444 (mtt180) cc_final: 0.8061 (ptp-170) REVERT: A 295 ASP cc_start: 0.8044 (p0) cc_final: 0.7272 (p0) REVERT: A 371 ASN cc_start: 0.8014 (p0) cc_final: 0.7759 (p0) REVERT: A 383 ILE cc_start: 0.9045 (tt) cc_final: 0.8605 (tp) REVERT: A 388 LEU cc_start: 0.9209 (mm) cc_final: 0.8912 (mm) REVERT: B 6 GLN cc_start: 0.7083 (tm-30) cc_final: 0.6741 (tm-30) REVERT: B 13 GLN cc_start: 0.8782 (tt0) cc_final: 0.8223 (pt0) REVERT: B 49 ARG cc_start: 0.7626 (mmt-90) cc_final: 0.7350 (mmt-90) REVERT: B 52 ARG cc_start: 0.7222 (ptp-170) cc_final: 0.6956 (ptp-170) REVERT: B 89 LYS cc_start: 0.9141 (mmmm) cc_final: 0.8874 (mmmm) REVERT: B 120 ILE cc_start: 0.8823 (mt) cc_final: 0.8544 (mm) REVERT: B 173 THR cc_start: 0.9183 (p) cc_final: 0.8871 (t) REVERT: B 210 LEU cc_start: 0.9117 (tp) cc_final: 0.8620 (tp) REVERT: B 220 GLN cc_start: 0.7989 (mp10) cc_final: 0.7530 (mp10) REVERT: B 228 ASP cc_start: 0.7896 (m-30) cc_final: 0.7325 (m-30) REVERT: B 229 ILE cc_start: 0.8406 (mt) cc_final: 0.8195 (mt) REVERT: B 273 ILE cc_start: 0.9079 (mp) cc_final: 0.8840 (mp) REVERT: B 280 LYS cc_start: 0.8358 (tttt) cc_final: 0.7925 (tttm) REVERT: B 308 LEU cc_start: 0.6923 (mt) cc_final: 0.6539 (mt) REVERT: N 32 TYR cc_start: 0.8618 (m-10) cc_final: 0.8384 (m-10) REVERT: N 47 TRP cc_start: 0.8281 (t60) cc_final: 0.6801 (t60) outliers start: 2 outliers final: 0 residues processed: 425 average time/residue: 0.2304 time to fit residues: 129.8810 Evaluate side-chains 348 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 348 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 104 optimal weight: 20.0000 chunk 113 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 83 optimal weight: 7.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 212 HIS R 213 GLN R 240 ASN ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS B 239 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9293 Z= 0.246 Angle : 0.702 9.889 12612 Z= 0.379 Chirality : 0.045 0.167 1416 Planarity : 0.005 0.058 1612 Dihedral : 5.561 27.198 1277 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 21.70 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.79 % Favored : 96.03 % Rotamer: Outliers : 0.21 % Allowed : 4.05 % Favored : 95.74 % 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: -0.68 (0.23), residues: 1160 helix: -0.21 (0.24), residues: 434 sheet: -0.53 (0.34), residues: 219 loop : -0.43 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 169 HIS 0.009 0.002 HIS R 180 PHE 0.023 0.002 PHE R 184 TYR 0.044 0.002 TYR R 269 ARG 0.004 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 401 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 229 VAL cc_start: 0.9284 (t) cc_final: 0.9056 (p) REVERT: R 351 LYS cc_start: 0.8615 (tptt) cc_final: 0.7978 (tmtt) REVERT: A 28 LYS cc_start: 0.6867 (mmpt) cc_final: 0.6596 (ptpp) REVERT: A 32 LYS cc_start: 0.9177 (mttt) cc_final: 0.8970 (mttp) REVERT: A 44 LEU cc_start: 0.8670 (tp) cc_final: 0.8273 (tp) REVERT: A 45 LEU cc_start: 0.9229 (tp) cc_final: 0.8985 (tp) REVERT: A 229 ASP cc_start: 0.8163 (p0) cc_final: 0.7921 (p0) REVERT: A 241 VAL cc_start: 0.9092 (t) cc_final: 0.8736 (p) REVERT: A 255 MET cc_start: 0.6953 (ptm) cc_final: 0.6693 (ptm) REVERT: A 283 ARG cc_start: 0.8295 (mtt180) cc_final: 0.8062 (ptp-170) REVERT: A 291 LEU cc_start: 0.9295 (mt) cc_final: 0.9044 (mt) REVERT: A 295 ASP cc_start: 0.7996 (p0) cc_final: 0.7242 (p0) REVERT: A 299 GLU cc_start: 0.8247 (mp0) cc_final: 0.8036 (mp0) REVERT: A 386 MET cc_start: 0.8600 (tmm) cc_final: 0.7917 (tpp) REVERT: A 388 LEU cc_start: 0.9218 (mm) cc_final: 0.8910 (mm) REVERT: B 49 ARG cc_start: 0.7733 (mmt-90) cc_final: 0.6982 (mmt90) REVERT: B 61 MET cc_start: 0.8971 (ppp) cc_final: 0.8531 (ppp) REVERT: B 66 ASP cc_start: 0.8144 (p0) cc_final: 0.7791 (p0) REVERT: B 89 LYS cc_start: 0.9283 (mmmm) cc_final: 0.8902 (mmmm) REVERT: B 102 THR cc_start: 0.8564 (t) cc_final: 0.8340 (m) REVERT: B 120 ILE cc_start: 0.8854 (mt) cc_final: 0.8592 (mm) REVERT: B 170 ASP cc_start: 0.7233 (t0) cc_final: 0.6953 (t0) REVERT: B 210 LEU cc_start: 0.8932 (tp) cc_final: 0.8546 (tp) REVERT: B 220 GLN cc_start: 0.7901 (mp10) cc_final: 0.7429 (mp10) REVERT: B 293 ASN cc_start: 0.7924 (m-40) cc_final: 0.7686 (m-40) REVERT: N 27 PHE cc_start: 0.8176 (p90) cc_final: 0.7854 (p90) REVERT: N 28 THR cc_start: 0.9129 (m) cc_final: 0.8838 (t) REVERT: N 32 TYR cc_start: 0.8569 (m-10) cc_final: 0.8322 (m-10) REVERT: N 68 PHE cc_start: 0.8787 (m-80) cc_final: 0.8426 (m-80) outliers start: 2 outliers final: 1 residues processed: 403 average time/residue: 0.2368 time to fit residues: 126.2980 Evaluate side-chains 329 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 328 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 chunk 111 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 92 optimal weight: 7.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 240 ASN R 263 GLN R 302 ASN ** R 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS A 267 GLN ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 225 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.4921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9293 Z= 0.247 Angle : 0.700 10.084 12612 Z= 0.375 Chirality : 0.046 0.379 1416 Planarity : 0.005 0.056 1612 Dihedral : 5.494 26.184 1277 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 22.03 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.22 % Favored : 95.60 % Rotamer: Outliers : 0.32 % Allowed : 3.94 % Favored : 95.74 % 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: -0.58 (0.24), residues: 1160 helix: 0.02 (0.24), residues: 424 sheet: -0.55 (0.33), residues: 216 loop : -0.50 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 169 HIS 0.005 0.001 HIS B 62 PHE 0.032 0.002 PHE R 184 TYR 0.024 0.002 TYR A 391 ARG 0.005 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 385 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 181 LEU cc_start: 0.8930 (mt) cc_final: 0.8507 (mt) REVERT: R 205 TYR cc_start: 0.7765 (t80) cc_final: 0.7516 (t80) REVERT: R 229 VAL cc_start: 0.9284 (t) cc_final: 0.9068 (p) REVERT: R 351 LYS cc_start: 0.8626 (tptt) cc_final: 0.7997 (tmtt) REVERT: A 28 LYS cc_start: 0.6816 (mmpt) cc_final: 0.6449 (ptpp) REVERT: A 32 LYS cc_start: 0.9141 (mttt) cc_final: 0.8912 (mttp) REVERT: A 229 ASP cc_start: 0.8243 (p0) cc_final: 0.7860 (p0) REVERT: A 279 ASN cc_start: 0.8921 (t0) cc_final: 0.8719 (t0) REVERT: A 283 ARG cc_start: 0.8242 (mtt180) cc_final: 0.8004 (ptp-170) REVERT: A 383 ILE cc_start: 0.8837 (tp) cc_final: 0.8513 (tp) REVERT: A 386 MET cc_start: 0.8632 (tmm) cc_final: 0.7933 (tpp) REVERT: A 388 LEU cc_start: 0.9214 (mm) cc_final: 0.8892 (mm) REVERT: B 6 GLN cc_start: 0.7054 (tm-30) cc_final: 0.6717 (tm-30) REVERT: B 49 ARG cc_start: 0.7723 (mmt-90) cc_final: 0.7260 (mmt90) REVERT: B 61 MET cc_start: 0.8980 (ppp) cc_final: 0.8668 (ppp) REVERT: B 102 THR cc_start: 0.8506 (t) cc_final: 0.8251 (m) REVERT: B 120 ILE cc_start: 0.8959 (mt) cc_final: 0.8714 (mm) REVERT: B 170 ASP cc_start: 0.7228 (t0) cc_final: 0.6998 (t0) REVERT: B 210 LEU cc_start: 0.8888 (tp) cc_final: 0.8482 (tp) REVERT: B 220 GLN cc_start: 0.7891 (mp10) cc_final: 0.7387 (mp10) REVERT: B 235 PHE cc_start: 0.7379 (t80) cc_final: 0.7162 (t80) REVERT: B 246 ASP cc_start: 0.8571 (m-30) cc_final: 0.8072 (m-30) REVERT: B 249 THR cc_start: 0.8902 (p) cc_final: 0.8421 (p) REVERT: B 293 ASN cc_start: 0.8065 (m-40) cc_final: 0.7807 (m-40) REVERT: B 297 TRP cc_start: 0.8094 (m100) cc_final: 0.7515 (m100) REVERT: B 325 MET cc_start: 0.8111 (tpp) cc_final: 0.7587 (tmm) REVERT: N 27 PHE cc_start: 0.8246 (p90) cc_final: 0.7948 (p90) REVERT: N 34 MET cc_start: 0.9075 (ttm) cc_final: 0.8849 (ttm) REVERT: N 46 GLU cc_start: 0.7869 (pm20) cc_final: 0.7630 (pm20) REVERT: N 81 LEU cc_start: 0.8888 (tp) cc_final: 0.8680 (tp) outliers start: 3 outliers final: 1 residues processed: 387 average time/residue: 0.2301 time to fit residues: 118.1125 Evaluate side-chains 325 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 324 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 82 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 56 optimal weight: 0.2980 chunk 99 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 180 HIS R 213 GLN R 240 ASN R 263 GLN ** R 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 23 ASN ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.5281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9293 Z= 0.233 Angle : 0.693 9.034 12612 Z= 0.367 Chirality : 0.046 0.374 1416 Planarity : 0.004 0.043 1612 Dihedral : 5.365 25.855 1277 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 20.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.48 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % 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: -0.51 (0.24), residues: 1160 helix: -0.01 (0.24), residues: 434 sheet: -0.61 (0.33), residues: 212 loop : -0.32 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 169 HIS 0.009 0.002 HIS A 357 PHE 0.039 0.002 PHE N 68 TYR 0.020 0.002 TYR A 391 ARG 0.006 0.001 ARG N 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 391 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 181 LEU cc_start: 0.8689 (mt) cc_final: 0.8296 (mt) REVERT: R 205 TYR cc_start: 0.7698 (t80) cc_final: 0.7486 (t80) REVERT: R 351 LYS cc_start: 0.8631 (tptt) cc_final: 0.7971 (tmtt) REVERT: A 28 LYS cc_start: 0.6746 (mmpt) cc_final: 0.6318 (ptpp) REVERT: A 32 LYS cc_start: 0.9063 (mttt) cc_final: 0.8702 (mttp) REVERT: A 44 LEU cc_start: 0.8676 (tp) cc_final: 0.8335 (tp) REVERT: A 229 ASP cc_start: 0.8239 (p0) cc_final: 0.7783 (p0) REVERT: A 279 ASN cc_start: 0.8901 (t0) cc_final: 0.8679 (t0) REVERT: A 283 ARG cc_start: 0.8198 (mtt180) cc_final: 0.7666 (ptp-170) REVERT: A 318 TYR cc_start: 0.5196 (t80) cc_final: 0.4981 (t80) REVERT: A 343 ASP cc_start: 0.8255 (m-30) cc_final: 0.7423 (m-30) REVERT: A 386 MET cc_start: 0.8146 (tmm) cc_final: 0.7937 (tmm) REVERT: A 388 LEU cc_start: 0.9283 (mm) cc_final: 0.9056 (mm) REVERT: B 6 GLN cc_start: 0.7104 (tm-30) cc_final: 0.6796 (tm-30) REVERT: B 49 ARG cc_start: 0.7898 (mmt-90) cc_final: 0.7583 (mmt90) REVERT: B 61 MET cc_start: 0.8964 (ppp) cc_final: 0.8237 (ppp) REVERT: B 66 ASP cc_start: 0.8155 (p0) cc_final: 0.7883 (p0) REVERT: B 89 LYS cc_start: 0.9434 (mmmm) cc_final: 0.9034 (mmmm) REVERT: B 120 ILE cc_start: 0.8587 (mt) cc_final: 0.8372 (mm) REVERT: B 153 ASP cc_start: 0.8306 (p0) cc_final: 0.7190 (p0) REVERT: B 170 ASP cc_start: 0.7278 (t0) cc_final: 0.7063 (t0) REVERT: B 204 CYS cc_start: 0.8126 (m) cc_final: 0.7840 (m) REVERT: B 220 GLN cc_start: 0.7837 (mp10) cc_final: 0.7414 (mp10) REVERT: B 235 PHE cc_start: 0.7427 (t80) cc_final: 0.7128 (t80) REVERT: B 246 ASP cc_start: 0.8602 (m-30) cc_final: 0.8120 (m-30) REVERT: B 273 ILE cc_start: 0.9285 (mp) cc_final: 0.8937 (mp) REVERT: G 24 ASN cc_start: 0.6921 (p0) cc_final: 0.6464 (t0) REVERT: N 47 TRP cc_start: 0.8089 (t60) cc_final: 0.6878 (t60) REVERT: N 81 LEU cc_start: 0.8828 (tp) cc_final: 0.8483 (tt) outliers start: 0 outliers final: 0 residues processed: 391 average time/residue: 0.2432 time to fit residues: 126.8483 Evaluate side-chains 325 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 325 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 0.2980 chunk 21 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 27 optimal weight: 0.0670 chunk 111 optimal weight: 0.0970 chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 0.4980 chunk 36 optimal weight: 3.9990 chunk 58 optimal weight: 0.4980 chunk 107 optimal weight: 0.0970 overall best weight: 0.2114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 240 ASN R 263 GLN R 302 ASN ** P 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.5662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9293 Z= 0.191 Angle : 0.679 8.978 12612 Z= 0.357 Chirality : 0.046 0.322 1416 Planarity : 0.004 0.040 1612 Dihedral : 5.200 24.306 1277 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.88 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % 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: -0.40 (0.24), residues: 1160 helix: 0.16 (0.24), residues: 436 sheet: -0.50 (0.33), residues: 215 loop : -0.37 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 169 HIS 0.010 0.002 HIS R 180 PHE 0.036 0.002 PHE R 184 TYR 0.015 0.002 TYR N 32 ARG 0.004 0.000 ARG N 118 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 401 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 181 LEU cc_start: 0.8788 (mt) cc_final: 0.8576 (mt) REVERT: R 205 TYR cc_start: 0.7724 (t80) cc_final: 0.7512 (t80) REVERT: R 351 LYS cc_start: 0.8628 (tptt) cc_final: 0.7956 (tmtt) REVERT: R 411 MET cc_start: 0.7790 (mmp) cc_final: 0.7572 (mmp) REVERT: A 28 LYS cc_start: 0.6848 (mmpt) cc_final: 0.6511 (mtmt) REVERT: A 44 LEU cc_start: 0.8598 (tp) cc_final: 0.8056 (tp) REVERT: A 229 ASP cc_start: 0.8228 (p0) cc_final: 0.7965 (p0) REVERT: A 274 LYS cc_start: 0.8612 (tttt) cc_final: 0.8272 (tttt) REVERT: A 279 ASN cc_start: 0.8898 (t0) cc_final: 0.8667 (t0) REVERT: A 374 ARG cc_start: 0.7930 (ttt180) cc_final: 0.7479 (ttm170) REVERT: A 386 MET cc_start: 0.8334 (tmm) cc_final: 0.7893 (tmm) REVERT: A 388 LEU cc_start: 0.9369 (mm) cc_final: 0.9130 (mm) REVERT: B 6 GLN cc_start: 0.7188 (tm-30) cc_final: 0.6862 (tm-30) REVERT: B 49 ARG cc_start: 0.7922 (mmt-90) cc_final: 0.7539 (mmt90) REVERT: B 61 MET cc_start: 0.8637 (ppp) cc_final: 0.8131 (ppp) REVERT: B 66 ASP cc_start: 0.8171 (p0) cc_final: 0.7855 (p0) REVERT: B 89 LYS cc_start: 0.9366 (mmmm) cc_final: 0.9059 (mmmm) REVERT: B 153 ASP cc_start: 0.7538 (p0) cc_final: 0.7238 (p0) REVERT: B 170 ASP cc_start: 0.7125 (t0) cc_final: 0.6899 (t0) REVERT: B 180 PHE cc_start: 0.7961 (m-80) cc_final: 0.7620 (m-10) REVERT: B 204 CYS cc_start: 0.7955 (m) cc_final: 0.7727 (m) REVERT: B 210 LEU cc_start: 0.8682 (tp) cc_final: 0.8436 (tp) REVERT: B 246 ASP cc_start: 0.8539 (m-30) cc_final: 0.8121 (m-30) REVERT: B 297 TRP cc_start: 0.7976 (m100) cc_final: 0.7566 (m100) REVERT: B 313 ASN cc_start: 0.6983 (t0) cc_final: 0.6625 (m110) REVERT: B 317 CYS cc_start: 0.6897 (t) cc_final: 0.6693 (t) REVERT: B 325 MET cc_start: 0.7903 (tpp) cc_final: 0.7314 (tmm) REVERT: G 24 ASN cc_start: 0.6852 (p0) cc_final: 0.6296 (t0) REVERT: N 81 LEU cc_start: 0.8796 (tp) cc_final: 0.8516 (tt) REVERT: N 111 THR cc_start: 0.7270 (m) cc_final: 0.6601 (p) REVERT: N 117 TYR cc_start: 0.6717 (m-80) cc_final: 0.6340 (m-80) REVERT: N 124 VAL cc_start: 0.8259 (t) cc_final: 0.7842 (m) outliers start: 0 outliers final: 0 residues processed: 401 average time/residue: 0.2283 time to fit residues: 121.4609 Evaluate side-chains 321 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 321 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 69 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 240 ASN R 263 GLN A 23 ASN ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.5800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9293 Z= 0.328 Angle : 0.755 13.794 12612 Z= 0.400 Chirality : 0.047 0.220 1416 Planarity : 0.006 0.082 1612 Dihedral : 5.438 25.391 1277 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 26.07 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.57 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % 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: -0.74 (0.24), residues: 1160 helix: -0.08 (0.24), residues: 446 sheet: -0.64 (0.33), residues: 217 loop : -0.64 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP A 281 HIS 0.012 0.002 HIS A 357 PHE 0.045 0.003 PHE B 235 TYR 0.031 0.002 TYR G 40 ARG 0.007 0.001 ARG N 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 384 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 181 LEU cc_start: 0.8851 (mt) cc_final: 0.8554 (mt) REVERT: R 351 LYS cc_start: 0.8738 (tptt) cc_final: 0.8526 (tptm) REVERT: A 28 LYS cc_start: 0.7090 (mmpt) cc_final: 0.6834 (mtmt) REVERT: A 31 GLN cc_start: 0.8838 (mm-40) cc_final: 0.8594 (tp40) REVERT: A 222 PHE cc_start: 0.7378 (t80) cc_final: 0.6552 (t80) REVERT: A 229 ASP cc_start: 0.8354 (p0) cc_final: 0.7833 (p0) REVERT: A 279 ASN cc_start: 0.9040 (t0) cc_final: 0.8799 (t0) REVERT: A 295 ASP cc_start: 0.8065 (p0) cc_final: 0.7467 (p0) REVERT: A 343 ASP cc_start: 0.8347 (m-30) cc_final: 0.8134 (m-30) REVERT: A 386 MET cc_start: 0.8435 (tmm) cc_final: 0.8159 (tmm) REVERT: A 388 LEU cc_start: 0.9297 (mm) cc_final: 0.9062 (mm) REVERT: B 6 GLN cc_start: 0.7043 (tm-30) cc_final: 0.6725 (tm-30) REVERT: B 49 ARG cc_start: 0.8175 (mmt-90) cc_final: 0.7696 (mmt90) REVERT: B 66 ASP cc_start: 0.8269 (p0) cc_final: 0.7969 (p0) REVERT: B 71 VAL cc_start: 0.9279 (m) cc_final: 0.9002 (p) REVERT: B 120 ILE cc_start: 0.8868 (mt) cc_final: 0.8617 (mm) REVERT: B 153 ASP cc_start: 0.7478 (p0) cc_final: 0.7182 (p0) REVERT: B 180 PHE cc_start: 0.8130 (m-80) cc_final: 0.7921 (m-10) REVERT: B 220 GLN cc_start: 0.7709 (mp10) cc_final: 0.7455 (mp10) REVERT: B 229 ILE cc_start: 0.8308 (mt) cc_final: 0.8069 (mt) REVERT: B 246 ASP cc_start: 0.8521 (m-30) cc_final: 0.8169 (m-30) REVERT: B 249 THR cc_start: 0.8745 (p) cc_final: 0.8029 (p) REVERT: B 273 ILE cc_start: 0.9201 (mp) cc_final: 0.8856 (mp) REVERT: B 290 ASP cc_start: 0.8990 (m-30) cc_final: 0.8781 (m-30) REVERT: B 313 ASN cc_start: 0.7471 (t0) cc_final: 0.7016 (m-40) REVERT: N 27 PHE cc_start: 0.8073 (p90) cc_final: 0.7856 (p90) REVERT: N 31 ASN cc_start: 0.8602 (m110) cc_final: 0.8283 (m110) REVERT: N 47 TRP cc_start: 0.8289 (t60) cc_final: 0.6931 (t60) REVERT: N 81 LEU cc_start: 0.8626 (tp) cc_final: 0.8363 (tp) REVERT: N 124 VAL cc_start: 0.8376 (t) cc_final: 0.8058 (m) outliers start: 0 outliers final: 0 residues processed: 384 average time/residue: 0.2289 time to fit residues: 117.1411 Evaluate side-chains 306 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 306 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 87 optimal weight: 0.1980 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 182 ASN R 213 GLN ** R 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 263 GLN ** R 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.6197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9293 Z= 0.223 Angle : 0.701 9.054 12612 Z= 0.374 Chirality : 0.047 0.275 1416 Planarity : 0.004 0.050 1612 Dihedral : 5.280 25.256 1277 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 21.98 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.74 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % 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: -0.59 (0.24), residues: 1160 helix: 0.06 (0.24), residues: 440 sheet: -0.67 (0.33), residues: 217 loop : -0.50 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 281 HIS 0.013 0.002 HIS R 180 PHE 0.035 0.002 PHE R 184 TYR 0.020 0.002 TYR R 250 ARG 0.008 0.001 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 381 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 181 LEU cc_start: 0.8844 (mt) cc_final: 0.8627 (mt) REVERT: R 351 LYS cc_start: 0.8740 (tptt) cc_final: 0.8505 (tptm) REVERT: A 23 ASN cc_start: 0.8679 (t0) cc_final: 0.8308 (t0) REVERT: A 27 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8438 (mt-10) REVERT: A 28 LYS cc_start: 0.6998 (mmpt) cc_final: 0.6690 (mtmm) REVERT: A 44 LEU cc_start: 0.8605 (tp) cc_final: 0.8275 (tp) REVERT: A 229 ASP cc_start: 0.8184 (p0) cc_final: 0.7913 (p0) REVERT: A 279 ASN cc_start: 0.9027 (t0) cc_final: 0.8799 (t0) REVERT: A 295 ASP cc_start: 0.8007 (p0) cc_final: 0.7431 (p0) REVERT: A 386 MET cc_start: 0.8357 (tmm) cc_final: 0.8085 (tmm) REVERT: A 388 LEU cc_start: 0.9343 (mm) cc_final: 0.9123 (mm) REVERT: B 6 GLN cc_start: 0.7256 (tm-30) cc_final: 0.6853 (tm-30) REVERT: B 49 ARG cc_start: 0.8136 (mmt-90) cc_final: 0.7665 (mmt90) REVERT: B 61 MET cc_start: 0.8979 (ppp) cc_final: 0.8524 (ppp) REVERT: B 66 ASP cc_start: 0.8297 (p0) cc_final: 0.7964 (p0) REVERT: B 89 LYS cc_start: 0.9314 (mmmm) cc_final: 0.9018 (mmmm) REVERT: B 101 MET cc_start: 0.8025 (mmm) cc_final: 0.7563 (mtt) REVERT: B 120 ILE cc_start: 0.8838 (mt) cc_final: 0.8604 (mm) REVERT: B 139 LEU cc_start: 0.8798 (mt) cc_final: 0.8356 (mp) REVERT: B 145 TYR cc_start: 0.8066 (p90) cc_final: 0.7856 (p90) REVERT: B 220 GLN cc_start: 0.7610 (mp10) cc_final: 0.7324 (mp10) REVERT: B 246 ASP cc_start: 0.8525 (m-30) cc_final: 0.8124 (m-30) REVERT: B 251 ARG cc_start: 0.6969 (mtt180) cc_final: 0.5819 (mtt90) REVERT: B 273 ILE cc_start: 0.9202 (mp) cc_final: 0.8913 (mp) REVERT: B 297 TRP cc_start: 0.8290 (m100) cc_final: 0.7772 (m100) REVERT: B 337 LYS cc_start: 0.8255 (tppt) cc_final: 0.7847 (tppp) REVERT: N 19 ARG cc_start: 0.6924 (tpm170) cc_final: 0.6673 (tpm170) REVERT: N 27 PHE cc_start: 0.7992 (p90) cc_final: 0.7716 (p90) REVERT: N 81 LEU cc_start: 0.8452 (tp) cc_final: 0.7598 (tt) REVERT: N 82 GLN cc_start: 0.6809 (mm110) cc_final: 0.6021 (mm110) REVERT: N 124 VAL cc_start: 0.8350 (t) cc_final: 0.7879 (m) outliers start: 0 outliers final: 0 residues processed: 381 average time/residue: 0.2319 time to fit residues: 118.3039 Evaluate side-chains 319 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 319 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 8.9990 chunk 106 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 81 optimal weight: 0.5980 chunk 31 optimal weight: 5.9990 chunk 93 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 180 HIS R 182 ASN ** R 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 240 ASN R 302 ASN ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 ASN G 18 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.6397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9293 Z= 0.246 Angle : 0.703 9.726 12612 Z= 0.377 Chirality : 0.047 0.233 1416 Planarity : 0.004 0.041 1612 Dihedral : 5.240 24.119 1277 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 21.75 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.91 % Favored : 94.91 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.24), residues: 1160 helix: 0.15 (0.25), residues: 435 sheet: -0.68 (0.33), residues: 219 loop : -0.52 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 281 HIS 0.009 0.002 HIS B 54 PHE 0.035 0.002 PHE R 184 TYR 0.020 0.002 TYR A 391 ARG 0.007 0.001 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 363 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 181 LEU cc_start: 0.8764 (mt) cc_final: 0.8484 (mt) REVERT: R 340 MET cc_start: 0.7774 (tpt) cc_final: 0.7413 (tpt) REVERT: R 351 LYS cc_start: 0.8692 (tptt) cc_final: 0.8469 (tptm) REVERT: R 402 TYR cc_start: 0.7509 (p90) cc_final: 0.7203 (p90) REVERT: R 407 ASN cc_start: 0.7248 (p0) cc_final: 0.7029 (p0) REVERT: P 27 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8441 (mm-30) REVERT: A 28 LYS cc_start: 0.7037 (mmpt) cc_final: 0.6734 (mtmm) REVERT: A 229 ASP cc_start: 0.8225 (p0) cc_final: 0.7959 (p0) REVERT: A 279 ASN cc_start: 0.9037 (t0) cc_final: 0.8802 (t0) REVERT: A 295 ASP cc_start: 0.7959 (p0) cc_final: 0.7428 (p0) REVERT: A 383 ILE cc_start: 0.8926 (tp) cc_final: 0.8535 (tp) REVERT: A 386 MET cc_start: 0.8290 (tmm) cc_final: 0.7978 (tmm) REVERT: A 388 LEU cc_start: 0.9355 (mm) cc_final: 0.9139 (mm) REVERT: B 6 GLN cc_start: 0.7224 (tm-30) cc_final: 0.6832 (tm-30) REVERT: B 49 ARG cc_start: 0.8201 (mmt-90) cc_final: 0.7768 (mmt90) REVERT: B 61 MET cc_start: 0.8959 (ppp) cc_final: 0.8512 (ppp) REVERT: B 66 ASP cc_start: 0.8280 (p0) cc_final: 0.7955 (p0) REVERT: B 89 LYS cc_start: 0.9309 (mmmm) cc_final: 0.9079 (mmmm) REVERT: B 101 MET cc_start: 0.7901 (mmm) cc_final: 0.7601 (mtt) REVERT: B 120 ILE cc_start: 0.8868 (mt) cc_final: 0.8620 (mm) REVERT: B 210 LEU cc_start: 0.8806 (tp) cc_final: 0.8454 (tp) REVERT: B 220 GLN cc_start: 0.7608 (mp10) cc_final: 0.7187 (mp10) REVERT: B 249 THR cc_start: 0.8739 (p) cc_final: 0.8382 (p) REVERT: B 297 TRP cc_start: 0.8187 (m100) cc_final: 0.7719 (m100) REVERT: B 313 ASN cc_start: 0.7613 (m110) cc_final: 0.7153 (m-40) REVERT: B 337 LYS cc_start: 0.8260 (tppt) cc_final: 0.7889 (tppp) REVERT: N 27 PHE cc_start: 0.7959 (p90) cc_final: 0.7676 (p90) REVERT: N 46 GLU cc_start: 0.7661 (pm20) cc_final: 0.7458 (pm20) REVERT: N 47 TRP cc_start: 0.8330 (t60) cc_final: 0.6751 (t60) REVERT: N 81 LEU cc_start: 0.8524 (tp) cc_final: 0.7727 (tt) REVERT: N 124 VAL cc_start: 0.8370 (t) cc_final: 0.7923 (m) outliers start: 0 outliers final: 0 residues processed: 363 average time/residue: 0.2326 time to fit residues: 111.5515 Evaluate side-chains 315 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 114 optimal weight: 0.0770 chunk 105 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 213 GLN ** R 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 302 ASN ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN N 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.6566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9293 Z= 0.235 Angle : 0.711 8.736 12612 Z= 0.380 Chirality : 0.046 0.209 1416 Planarity : 0.005 0.069 1612 Dihedral : 5.145 24.076 1277 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 22.31 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.34 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.24), residues: 1160 helix: 0.28 (0.25), residues: 429 sheet: -0.72 (0.32), residues: 223 loop : -0.60 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 281 HIS 0.008 0.002 HIS B 54 PHE 0.036 0.003 PHE R 184 TYR 0.029 0.002 TYR R 269 ARG 0.009 0.001 ARG N 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 364 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 181 LEU cc_start: 0.8778 (mt) cc_final: 0.8490 (mt) REVERT: R 340 MET cc_start: 0.7742 (tpt) cc_final: 0.7320 (tpt) REVERT: R 351 LYS cc_start: 0.8670 (tptt) cc_final: 0.8438 (tptm) REVERT: R 402 TYR cc_start: 0.7505 (p90) cc_final: 0.7288 (p90) REVERT: R 407 ASN cc_start: 0.7269 (p0) cc_final: 0.6958 (p0) REVERT: P 27 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8436 (mm-30) REVERT: A 28 LYS cc_start: 0.7136 (mmpt) cc_final: 0.6832 (mtmm) REVERT: A 229 ASP cc_start: 0.8338 (p0) cc_final: 0.8017 (p0) REVERT: A 246 PHE cc_start: 0.7635 (t80) cc_final: 0.7280 (t80) REVERT: A 279 ASN cc_start: 0.8976 (t0) cc_final: 0.8711 (t0) REVERT: A 295 ASP cc_start: 0.7840 (p0) cc_final: 0.7199 (p0) REVERT: A 318 TYR cc_start: 0.5302 (t80) cc_final: 0.4968 (t80) REVERT: A 381 ASP cc_start: 0.8911 (m-30) cc_final: 0.8661 (m-30) REVERT: A 386 MET cc_start: 0.8337 (tmm) cc_final: 0.8018 (tmm) REVERT: A 388 LEU cc_start: 0.9371 (mm) cc_final: 0.9151 (mm) REVERT: B 6 GLN cc_start: 0.7163 (tm-30) cc_final: 0.6762 (tm-30) REVERT: B 61 MET cc_start: 0.8952 (ppp) cc_final: 0.8497 (ppp) REVERT: B 66 ASP cc_start: 0.8291 (p0) cc_final: 0.7938 (p0) REVERT: B 89 LYS cc_start: 0.9368 (mmmm) cc_final: 0.9152 (mmmm) REVERT: B 120 ILE cc_start: 0.8906 (mt) cc_final: 0.8644 (mm) REVERT: B 210 LEU cc_start: 0.8779 (tp) cc_final: 0.8423 (tp) REVERT: B 220 GLN cc_start: 0.7582 (mp10) cc_final: 0.7183 (mp10) REVERT: B 251 ARG cc_start: 0.6869 (mtt180) cc_final: 0.5698 (mtt90) REVERT: B 273 ILE cc_start: 0.9151 (mp) cc_final: 0.8765 (mp) REVERT: N 27 PHE cc_start: 0.7863 (p90) cc_final: 0.7590 (p90) REVERT: N 110 VAL cc_start: 0.8574 (t) cc_final: 0.8206 (t) REVERT: N 124 VAL cc_start: 0.8386 (t) cc_final: 0.7949 (m) outliers start: 0 outliers final: 0 residues processed: 364 average time/residue: 0.2085 time to fit residues: 102.7263 Evaluate side-chains 310 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 310 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 80 optimal weight: 7.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 ASN G 18 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.135419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.117740 restraints weight = 28353.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.121267 restraints weight = 16650.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.123658 restraints weight = 10970.450| |-----------------------------------------------------------------------------| r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.6750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9293 Z= 0.230 Angle : 0.705 8.451 12612 Z= 0.376 Chirality : 0.046 0.200 1416 Planarity : 0.005 0.063 1612 Dihedral : 5.150 23.528 1277 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 22.37 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.43 % Favored : 94.40 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: -0.51 (0.24), residues: 1160 helix: 0.38 (0.25), residues: 429 sheet: -0.86 (0.33), residues: 223 loop : -0.57 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 281 HIS 0.008 0.002 HIS R 180 PHE 0.033 0.002 PHE R 184 TYR 0.034 0.002 TYR G 40 ARG 0.011 0.001 ARG N 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2834.07 seconds wall clock time: 51 minutes 34.75 seconds (3094.75 seconds total)