Starting phenix.real_space_refine on Sat Jul 20 09:39:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0j_28758/07_2024/8f0j_28758.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0j_28758/07_2024/8f0j_28758.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0j_28758/07_2024/8f0j_28758.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0j_28758/07_2024/8f0j_28758.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0j_28758/07_2024/8f0j_28758.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0j_28758/07_2024/8f0j_28758.cif" } resolution = 2.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 67 5.16 5 C 6237 2.51 5 N 1605 2.21 5 O 1765 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "P ARG 11": "NH1" <-> "NH2" Residue "R GLU 106": "OE1" <-> "OE2" Residue "R GLU 123": "OE1" <-> "OE2" Residue "R ARG 126": "NH1" <-> "NH2" Residue "R GLU 140": "OE1" <-> "OE2" Residue "R GLU 204": "OE1" <-> "OE2" Residue "R ARG 258": "NH1" <-> "NH2" Residue "R ARG 321": "NH1" <-> "NH2" Residue "R GLU 329": "OE1" <-> "OE2" Residue "R GLU 332": "OE1" <-> "OE2" Residue "R ARG 362": "NH1" <-> "NH2" Residue "R GLU 397": "OE1" <-> "OE2" Residue "R ARG 404": "NH1" <-> "NH2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "A ARG 42": "NH1" <-> "NH2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "N GLU 6": "OE1" <-> "OE2" Residue "N GLU 89": "OE1" <-> "OE2" Residue "N ARG 98": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 9678 Number of models: 1 Model: "" Number of chains: 12 Chain: "P" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 277 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 3058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 3058 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 16, 'TRANS': 354} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 1844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1844 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "P" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'D6M': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D6M:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 444 Unusual residues: {'NAG': 2, 'P42': 1, 'PLM': 8, 'PTY': 3, 'Y01': 2} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "R" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 6.88, per 1000 atoms: 0.71 Number of scatterers: 9678 At special positions: 0 Unit cell: (109.85, 100.1, 143.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 67 16.00 P 4 15.00 O 1765 8.00 N 1605 7.00 C 6237 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS P 2 " - pdb=" SG CYS P 7 " distance=2.03 Simple disulfide: pdb=" SG CYS R 55 " - pdb=" SG CYS R 81 " distance=2.03 Simple disulfide: pdb=" SG CYS R 72 " - pdb=" SG CYS R 112 " distance=2.03 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 219 " - pdb=" SG CYS R 289 " distance=2.03 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=2, symmetry=0 Links applied NAG-ASN " NAG R 501 " - " ASN R 73 " " NAG R 502 " - " ASN R 130 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.96 Conformation dependent library (CDL) restraints added in 1.7 seconds 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2178 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 13 sheets defined 43.1% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'P' and resid 4 through 6 No H-bonds generated for 'chain 'P' and resid 4 through 6' Processing helix chain 'P' and resid 7 through 19 removed outlier: 3.727A pdb=" N HIS P 18 " --> pdb=" O ASN P 14 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 62 removed outlier: 3.643A pdb=" N GLN R 60 " --> pdb=" O TYR R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 135 removed outlier: 3.911A pdb=" N ASN R 135 " --> pdb=" O THR R 132 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 173 Processing helix chain 'R' and resid 174 through 177 Processing helix chain 'R' and resid 178 through 205 Processing helix chain 'R' and resid 208 through 215 Processing helix chain 'R' and resid 216 through 249 removed outlier: 3.748A pdb=" N LYS R 220 " --> pdb=" O PRO R 216 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 267 Processing helix chain 'R' and resid 270 through 284 Processing helix chain 'R' and resid 287 through 291 Processing helix chain 'R' and resid 295 through 297 No H-bonds generated for 'chain 'R' and resid 295 through 297' Processing helix chain 'R' and resid 298 through 330 Proline residue: R 304 - end of helix Processing helix chain 'R' and resid 333 through 353 Proline residue: R 350 - end of helix Processing helix chain 'R' and resid 354 through 359 Processing helix chain 'R' and resid 365 through 382 removed outlier: 3.572A pdb=" N SER R 378 " --> pdb=" O TYR R 374 " (cutoff:3.500A) Processing helix chain 'R' and resid 382 through 392 Processing helix chain 'R' and resid 395 through 408 Processing helix chain 'A' and resid 12 through 40 removed outlier: 3.571A pdb=" N GLN A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.504A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 280 through 283 removed outlier: 3.792A pdb=" N ARG A 283 " --> pdb=" O LYS A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.505A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.345A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.957A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 391 removed outlier: 4.474A pdb=" N ARG A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.528A pdb=" N LEU B 14 " --> pdb=" O GLU B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.688A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.509A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'R' and resid 71 through 72 Processing sheet with id=AA2, first strand: chain 'R' and resid 75 through 76 Processing sheet with id=AA3, first strand: chain 'R' and resid 89 through 94 Processing sheet with id=AA4, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.396A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.605A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.592A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.780A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.559A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.266A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.534A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.764A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.798A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 475 hydrogen bonds defined for protein. 1335 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: 3.46 Time building geometry restraints manager: 4.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1507 1.31 - 1.43: 2698 1.43 - 1.56: 5551 1.56 - 1.69: 9 1.69 - 1.81: 96 Bond restraints: 9861 Sorted by residual: bond pdb=" C LYS P 21 " pdb=" O LYS P 21 " ideal model delta sigma weight residual 1.242 1.182 0.059 1.00e-02 1.00e+04 3.54e+01 bond pdb=" C02 D6M P 101 " pdb=" N03 D6M P 101 " ideal model delta sigma weight residual 1.339 1.452 -0.113 2.00e-02 2.50e+03 3.18e+01 bond pdb=" N VAL R 250 " pdb=" CA VAL R 250 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.15e-02 7.56e+03 1.21e+01 bond pdb=" C07 D6M P 101 " pdb=" O08 D6M P 101 " ideal model delta sigma weight residual 1.247 1.185 0.062 2.00e-02 2.50e+03 9.68e+00 bond pdb=" N ILE R 248 " pdb=" CA ILE R 248 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.21e-02 6.83e+03 8.89e+00 ... (remaining 9856 not shown) Histogram of bond angle deviations from ideal: 98.77 - 105.82: 184 105.82 - 112.86: 5149 112.86 - 119.91: 3386 119.91 - 126.96: 4433 126.96 - 134.00: 125 Bond angle restraints: 13277 Sorted by residual: angle pdb=" N ILE R 248 " pdb=" CA ILE R 248 " pdb=" C ILE R 248 " ideal model delta sigma weight residual 110.72 115.31 -4.59 1.01e+00 9.80e-01 2.06e+01 angle pdb=" N VAL R 293 " pdb=" CA VAL R 293 " pdb=" C VAL R 293 " ideal model delta sigma weight residual 112.17 107.88 4.29 9.50e-01 1.11e+00 2.04e+01 angle pdb=" N SER P 19 " pdb=" CA SER P 19 " pdb=" C SER P 19 " ideal model delta sigma weight residual 110.53 104.74 5.79 1.32e+00 5.74e-01 1.93e+01 angle pdb=" N ILE R 319 " pdb=" CA ILE R 319 " pdb=" C ILE R 319 " ideal model delta sigma weight residual 111.58 106.98 4.60 1.06e+00 8.90e-01 1.89e+01 angle pdb=" CA GLY P 33 " pdb=" C GLY P 33 " pdb=" O GLY P 33 " ideal model delta sigma weight residual 122.28 118.30 3.98 1.00e+00 1.00e+00 1.58e+01 ... (remaining 13272 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.13: 5696 24.13 - 48.26: 293 48.26 - 72.39: 58 72.39 - 96.52: 19 96.52 - 120.65: 5 Dihedral angle restraints: 6071 sinusoidal: 2696 harmonic: 3375 Sorted by residual: dihedral pdb=" C THR R 254 " pdb=" N THR R 254 " pdb=" CA THR R 254 " pdb=" CB THR R 254 " ideal model delta harmonic sigma weight residual -122.00 -136.85 14.85 0 2.50e+00 1.60e-01 3.53e+01 dihedral pdb=" N THR R 254 " pdb=" C THR R 254 " pdb=" CA THR R 254 " pdb=" CB THR R 254 " ideal model delta harmonic sigma weight residual 123.40 134.35 -10.95 0 2.50e+00 1.60e-01 1.92e+01 dihedral pdb=" CAM P42 R 509 " pdb=" CAN P42 R 509 " pdb=" CAO P42 R 509 " pdb=" CAP P42 R 509 " ideal model delta sinusoidal sigma weight residual 179.85 -59.50 -120.65 1 3.00e+01 1.11e-03 1.61e+01 ... (remaining 6068 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1352 0.095 - 0.190: 81 0.190 - 0.284: 4 0.284 - 0.379: 1 0.379 - 0.474: 2 Chirality restraints: 1440 Sorted by residual: chirality pdb=" CA THR R 254 " pdb=" N THR R 254 " pdb=" C THR R 254 " pdb=" CB THR R 254 " both_signs ideal model delta sigma weight residual False 2.53 2.05 0.47 2.00e-01 2.50e+01 5.62e+00 chirality pdb=" C6 PTY R 504 " pdb=" C1 PTY R 504 " pdb=" C5 PTY R 504 " pdb=" O7 PTY R 504 " both_signs ideal model delta sigma weight residual False 2.49 2.04 0.45 2.00e-01 2.50e+01 5.05e+00 chirality pdb=" C6 PTY R 508 " pdb=" C1 PTY R 508 " pdb=" C5 PTY R 508 " pdb=" O7 PTY R 508 " both_signs ideal model delta sigma weight residual False 2.49 2.18 0.31 2.00e-01 2.50e+01 2.40e+00 ... (remaining 1437 not shown) Planarity restraints: 1648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL P 17 " 0.008 2.00e-02 2.50e+03 1.52e-02 2.32e+00 pdb=" C VAL P 17 " -0.026 2.00e-02 2.50e+03 pdb=" O VAL P 17 " 0.010 2.00e-02 2.50e+03 pdb=" N HIS P 18 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY R 303 " -0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO R 304 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO R 304 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO R 304 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR R 254 " -0.006 2.00e-02 2.50e+03 1.23e-02 1.52e+00 pdb=" C THR R 254 " 0.021 2.00e-02 2.50e+03 pdb=" O THR R 254 " -0.008 2.00e-02 2.50e+03 pdb=" N GLU R 255 " -0.007 2.00e-02 2.50e+03 ... (remaining 1645 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1829 2.78 - 3.31: 9039 3.31 - 3.84: 16058 3.84 - 4.37: 20380 4.37 - 4.90: 33984 Nonbonded interactions: 81290 Sorted by model distance: nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.246 2.440 nonbonded pdb=" OE1 GLU A 330 " pdb=" OG1 THR A 335 " model vdw 2.317 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.319 2.440 nonbonded pdb=" NH2 ARG A 228 " pdb=" OD1 ASP B 186 " model vdw 2.352 2.520 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.376 2.440 ... (remaining 81285 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 31.880 Find NCS groups from input model: 0.120 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:12.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 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 : 0.005 0.113 9861 Z= 0.291 Angle : 0.613 10.024 13277 Z= 0.373 Chirality : 0.048 0.474 1440 Planarity : 0.003 0.038 1646 Dihedral : 15.417 120.653 3872 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.40 % Allowed : 5.36 % Favored : 94.23 % Cbeta Deviations : 0.09 % 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: -1.49 (0.22), residues: 1141 helix: -1.49 (0.19), residues: 439 sheet: -0.12 (0.32), residues: 231 loop : -0.70 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.004 0.001 HIS R 302 PHE 0.010 0.001 PHE R 235 TYR 0.013 0.001 TYR P 37 ARG 0.004 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 167 time to evaluate : 1.409 Fit side-chains revert: symmetry clash REVERT: R 59 MET cc_start: 0.2331 (mtm) cc_final: 0.1359 (ttt) REVERT: R 295 THR cc_start: 0.6162 (t) cc_final: 0.5960 (t) REVERT: R 306 MET cc_start: 0.7539 (mmm) cc_final: 0.7337 (mmm) REVERT: A 60 MET cc_start: 0.3732 (mtm) cc_final: 0.3141 (mmt) REVERT: N 87 LYS cc_start: 0.7713 (mttt) cc_final: 0.7451 (mttm) outliers start: 4 outliers final: 3 residues processed: 171 average time/residue: 1.3997 time to fit residues: 254.1440 Evaluate side-chains 141 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 138 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain G residue 52 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 47 optimal weight: 0.7980 chunk 28 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 10 GLN P 18 HIS R 60 GLN ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 144 ASN R 226 HIS R 257 GLN R 288 ASN A 218 ASN B 13 GLN B 16 ASN B 340 ASN G 11 GLN G 24 ASN N 13 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9861 Z= 0.241 Angle : 0.644 7.549 13277 Z= 0.343 Chirality : 0.045 0.160 1440 Planarity : 0.005 0.054 1646 Dihedral : 12.990 100.201 1763 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.33 % Allowed : 10.02 % Favored : 87.65 % 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: 0.47 (0.24), residues: 1141 helix: 1.04 (0.23), residues: 442 sheet: 0.20 (0.32), residues: 235 loop : -0.20 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 234 HIS 0.006 0.002 HIS P 18 PHE 0.023 0.002 PHE R 235 TYR 0.014 0.002 TYR R 391 ARG 0.006 0.001 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 145 time to evaluate : 0.973 Fit side-chains REVERT: R 59 MET cc_start: 0.2397 (mtm) cc_final: 0.1059 (ptm) REVERT: R 143 LYS cc_start: 0.5227 (ttpt) cc_final: 0.4850 (tttt) REVERT: R 346 MET cc_start: 0.6990 (OUTLIER) cc_final: 0.6625 (mmm) REVERT: R 367 MET cc_start: 0.4980 (tpp) cc_final: 0.4657 (tpp) REVERT: R 386 PHE cc_start: 0.7192 (m-80) cc_final: 0.6974 (m-80) REVERT: A 19 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.7048 (tt0) REVERT: A 38 ARG cc_start: 0.7350 (OUTLIER) cc_final: 0.7075 (mpt-90) outliers start: 23 outliers final: 10 residues processed: 156 average time/residue: 1.4575 time to fit residues: 241.2123 Evaluate side-chains 149 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 136 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 MET Chi-restraints excluded: chain R residue 133 MET Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain R residue 346 MET Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 17 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 8.9990 chunk 31 optimal weight: 0.7980 chunk 84 optimal weight: 7.9990 chunk 69 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 34 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 100 optimal weight: 0.0980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9861 Z= 0.149 Angle : 0.514 6.579 13277 Z= 0.276 Chirality : 0.041 0.153 1440 Planarity : 0.004 0.036 1646 Dihedral : 12.065 89.877 1763 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.23 % Allowed : 10.93 % Favored : 86.84 % 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: 1.18 (0.25), residues: 1141 helix: 1.93 (0.24), residues: 443 sheet: 0.41 (0.33), residues: 234 loop : -0.07 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 234 HIS 0.005 0.001 HIS B 266 PHE 0.018 0.001 PHE R 235 TYR 0.013 0.001 TYR R 149 ARG 0.004 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 131 time to evaluate : 1.100 Fit side-chains REVERT: R 59 MET cc_start: 0.2433 (mtm) cc_final: 0.1095 (ptm) REVERT: R 346 MET cc_start: 0.6958 (mmp) cc_final: 0.6526 (mmm) outliers start: 22 outliers final: 10 residues processed: 140 average time/residue: 1.4364 time to fit residues: 213.8249 Evaluate side-chains 137 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 127 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 MET Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 17 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 96 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 90 optimal weight: 9.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 144 ASN B 13 GLN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9861 Z= 0.136 Angle : 0.493 6.054 13277 Z= 0.265 Chirality : 0.040 0.147 1440 Planarity : 0.004 0.038 1646 Dihedral : 11.722 89.549 1760 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.72 % Allowed : 12.15 % Favored : 86.13 % 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 (0.25), residues: 1141 helix: 2.33 (0.24), residues: 443 sheet: 0.50 (0.33), residues: 234 loop : 0.04 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 234 HIS 0.005 0.001 HIS B 266 PHE 0.016 0.001 PHE R 235 TYR 0.013 0.001 TYR R 149 ARG 0.006 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 132 time to evaluate : 0.940 Fit side-chains REVERT: R 59 MET cc_start: 0.2466 (mtm) cc_final: 0.1177 (ptm) REVERT: R 208 ASN cc_start: 0.5112 (t0) cc_final: 0.4815 (m110) REVERT: R 346 MET cc_start: 0.6961 (mmp) cc_final: 0.6506 (mmm) outliers start: 17 outliers final: 11 residues processed: 140 average time/residue: 1.3692 time to fit residues: 204.1145 Evaluate side-chains 144 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 133 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 MET Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 230 MET Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain R residue 335 SER Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 52 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 80 optimal weight: 8.9990 chunk 44 optimal weight: 0.6980 chunk 92 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 55 optimal weight: 0.0370 chunk 97 optimal weight: 8.9990 chunk 27 optimal weight: 8.9990 chunk 36 optimal weight: 8.9990 overall best weight: 2.3262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 144 ASN B 13 GLN ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9861 Z= 0.203 Angle : 0.567 6.551 13277 Z= 0.303 Chirality : 0.042 0.150 1440 Planarity : 0.004 0.039 1646 Dihedral : 12.267 89.825 1760 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.02 % Allowed : 12.55 % Favored : 85.43 % 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: 1.46 (0.25), residues: 1141 helix: 2.24 (0.24), residues: 443 sheet: 0.50 (0.33), residues: 235 loop : 0.03 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 234 HIS 0.004 0.001 HIS B 266 PHE 0.022 0.002 PHE R 235 TYR 0.012 0.002 TYR A 358 ARG 0.005 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 137 time to evaluate : 1.132 Fit side-chains REVERT: R 59 MET cc_start: 0.2597 (mtm) cc_final: 0.1219 (ptm) REVERT: R 102 PHE cc_start: 0.5457 (OUTLIER) cc_final: 0.4213 (m-10) REVERT: R 208 ASN cc_start: 0.5232 (t0) cc_final: 0.4760 (m110) outliers start: 20 outliers final: 13 residues processed: 147 average time/residue: 1.3612 time to fit residues: 213.8028 Evaluate side-chains 148 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 134 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 MET Chi-restraints excluded: chain R residue 49 MET Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain R residue 335 SER Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 17 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 144 ASN B 13 GLN ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9861 Z= 0.187 Angle : 0.558 6.271 13277 Z= 0.298 Chirality : 0.042 0.149 1440 Planarity : 0.004 0.039 1646 Dihedral : 12.426 89.556 1760 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.33 % Allowed : 12.85 % Favored : 84.82 % 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: 1.42 (0.25), residues: 1141 helix: 2.21 (0.24), residues: 443 sheet: 0.44 (0.33), residues: 240 loop : 0.03 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 234 HIS 0.005 0.001 HIS B 266 PHE 0.021 0.002 PHE R 235 TYR 0.012 0.002 TYR B 59 ARG 0.006 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 140 time to evaluate : 1.084 Fit side-chains REVERT: R 59 MET cc_start: 0.2674 (mtm) cc_final: 0.1242 (ptm) REVERT: R 102 PHE cc_start: 0.5562 (OUTLIER) cc_final: 0.4237 (m-10) REVERT: R 256 LYS cc_start: 0.2936 (OUTLIER) cc_final: 0.2471 (ptpt) outliers start: 23 outliers final: 14 residues processed: 150 average time/residue: 1.4261 time to fit residues: 227.5729 Evaluate side-chains 151 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 135 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 MET Chi-restraints excluded: chain R residue 49 MET Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 256 LYS Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 17 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 79 optimal weight: 0.0980 chunk 91 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 144 ASN B 13 GLN N 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9861 Z= 0.203 Angle : 0.585 6.427 13277 Z= 0.311 Chirality : 0.043 0.147 1440 Planarity : 0.004 0.039 1646 Dihedral : 12.537 89.687 1760 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.43 % Allowed : 13.26 % Favored : 84.31 % 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: 1.37 (0.25), residues: 1141 helix: 2.14 (0.24), residues: 443 sheet: 0.43 (0.33), residues: 240 loop : 0.03 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 234 HIS 0.005 0.001 HIS A 41 PHE 0.023 0.002 PHE R 235 TYR 0.013 0.002 TYR B 59 ARG 0.006 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 133 time to evaluate : 0.938 Fit side-chains REVERT: R 59 MET cc_start: 0.2629 (mtm) cc_final: 0.1186 (ptm) REVERT: R 102 PHE cc_start: 0.5576 (OUTLIER) cc_final: 0.4235 (m-10) REVERT: R 204 GLU cc_start: 0.5103 (OUTLIER) cc_final: 0.4837 (mm-30) REVERT: R 256 LYS cc_start: 0.2886 (OUTLIER) cc_final: 0.2395 (ptpt) REVERT: R 346 MET cc_start: 0.7185 (mmp) cc_final: 0.6608 (mmm) outliers start: 24 outliers final: 15 residues processed: 144 average time/residue: 1.3861 time to fit residues: 212.2578 Evaluate side-chains 150 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 132 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 MET Chi-restraints excluded: chain R residue 49 MET Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 204 GLU Chi-restraints excluded: chain R residue 256 LYS Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 17 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 144 ASN R 277 HIS B 13 GLN N 13 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9861 Z= 0.300 Angle : 0.701 8.859 13277 Z= 0.367 Chirality : 0.047 0.235 1440 Planarity : 0.005 0.045 1646 Dihedral : 13.664 87.426 1760 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.43 % Allowed : 13.46 % Favored : 84.11 % 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: 0.95 (0.24), residues: 1141 helix: 1.64 (0.23), residues: 443 sheet: 0.40 (0.33), residues: 240 loop : -0.15 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 234 HIS 0.008 0.002 HIS A 41 PHE 0.030 0.003 PHE R 235 TYR 0.018 0.003 TYR B 59 ARG 0.008 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 138 time to evaluate : 0.935 Fit side-chains REVERT: R 59 MET cc_start: 0.2661 (mtm) cc_final: 0.1242 (ptm) REVERT: R 102 PHE cc_start: 0.5449 (OUTLIER) cc_final: 0.4166 (m-10) REVERT: R 204 GLU cc_start: 0.5183 (OUTLIER) cc_final: 0.4858 (mm-30) REVERT: R 256 LYS cc_start: 0.2912 (OUTLIER) cc_final: 0.2502 (ptpt) outliers start: 24 outliers final: 14 residues processed: 151 average time/residue: 1.4039 time to fit residues: 225.6211 Evaluate side-chains 152 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 135 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 MET Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 204 GLU Chi-restraints excluded: chain R residue 256 LYS Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain R residue 335 SER Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 17 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 144 ASN A 213 GLN B 13 GLN N 13 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9861 Z= 0.188 Angle : 0.574 6.534 13277 Z= 0.306 Chirality : 0.042 0.146 1440 Planarity : 0.004 0.039 1646 Dihedral : 13.131 89.129 1760 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.92 % Allowed : 14.17 % Favored : 83.91 % 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: 1.28 (0.25), residues: 1141 helix: 2.07 (0.24), residues: 443 sheet: 0.53 (0.34), residues: 235 loop : -0.11 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 234 HIS 0.004 0.001 HIS A 41 PHE 0.020 0.002 PHE R 235 TYR 0.015 0.002 TYR R 191 ARG 0.005 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 134 time to evaluate : 1.109 Fit side-chains REVERT: R 59 MET cc_start: 0.2669 (mtm) cc_final: 0.1230 (ptm) REVERT: R 102 PHE cc_start: 0.5383 (OUTLIER) cc_final: 0.4164 (m-10) REVERT: R 204 GLU cc_start: 0.5033 (OUTLIER) cc_final: 0.4778 (mm-30) REVERT: R 256 LYS cc_start: 0.2944 (OUTLIER) cc_final: 0.2440 (ptpt) outliers start: 19 outliers final: 12 residues processed: 145 average time/residue: 1.4303 time to fit residues: 220.4192 Evaluate side-chains 148 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 133 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 MET Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 105 SER Chi-restraints excluded: chain R residue 204 GLU Chi-restraints excluded: chain R residue 256 LYS Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 17 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 68 optimal weight: 0.0050 chunk 54 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 208 ASN B 13 GLN N 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9861 Z= 0.171 Angle : 0.552 6.240 13277 Z= 0.295 Chirality : 0.042 0.146 1440 Planarity : 0.004 0.038 1646 Dihedral : 12.643 89.084 1760 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.82 % Allowed : 14.27 % Favored : 83.91 % 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: 1.47 (0.25), residues: 1141 helix: 2.25 (0.24), residues: 443 sheet: 0.55 (0.34), residues: 235 loop : 0.00 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 234 HIS 0.004 0.001 HIS A 41 PHE 0.019 0.002 PHE R 235 TYR 0.018 0.002 TYR R 191 ARG 0.008 0.001 ARG A 347 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 131 time to evaluate : 1.074 Fit side-chains REVERT: R 59 MET cc_start: 0.2627 (mtm) cc_final: 0.1198 (ptm) REVERT: R 102 PHE cc_start: 0.5351 (OUTLIER) cc_final: 0.4166 (m-10) REVERT: R 196 MET cc_start: 0.7060 (mtp) cc_final: 0.6856 (mtp) REVERT: R 256 LYS cc_start: 0.2913 (OUTLIER) cc_final: 0.2359 (ptpt) REVERT: R 346 MET cc_start: 0.7191 (mmp) cc_final: 0.6601 (mmm) outliers start: 18 outliers final: 14 residues processed: 140 average time/residue: 1.4821 time to fit residues: 220.8775 Evaluate side-chains 146 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 130 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 MET Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 105 SER Chi-restraints excluded: chain R residue 256 LYS Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 17 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 5 optimal weight: 20.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 208 ASN B 13 GLN N 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.206090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.178553 restraints weight = 7391.032| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 0.62 r_work: 0.3815 rms_B_bonded: 1.18 restraints_weight: 0.5000 r_work: 0.3749 rms_B_bonded: 1.92 restraints_weight: 0.2500 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9861 Z= 0.183 Angle : 0.570 6.855 13277 Z= 0.304 Chirality : 0.042 0.146 1440 Planarity : 0.004 0.057 1646 Dihedral : 12.621 89.075 1760 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.62 % Allowed : 14.37 % Favored : 84.01 % 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: 1.46 (0.25), residues: 1141 helix: 2.22 (0.24), residues: 443 sheet: 0.67 (0.34), residues: 230 loop : -0.05 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 234 HIS 0.004 0.001 HIS A 41 PHE 0.020 0.002 PHE R 235 TYR 0.016 0.002 TYR R 191 ARG 0.015 0.001 ARG A 347 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4385.53 seconds wall clock time: 77 minutes 46.46 seconds (4666.46 seconds total)