Starting phenix.real_space_refine on Sat Aug 3 00:07:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo0_42423/08_2024/8uo0_42423.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo0_42423/08_2024/8uo0_42423.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo0_42423/08_2024/8uo0_42423.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo0_42423/08_2024/8uo0_42423.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo0_42423/08_2024/8uo0_42423.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo0_42423/08_2024/8uo0_42423.cif" } resolution = 3.5 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= 0.019 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 3 5.49 5 S 30 5.16 5 C 4018 2.51 5 N 1076 2.21 5 O 1095 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 122": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 6222 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1595 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 229, 1583 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 4 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 336 Unresolved non-hydrogen angles: 411 Unresolved non-hydrogen dihedrals: 272 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 13, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 17, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 219 Conformer: "B" Number of residues, atoms: 229, 1583 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 4 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 336 Unresolved non-hydrogen angles: 411 Unresolved non-hydrogen dihedrals: 272 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 13, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 17, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 219 bond proxies already assigned to first conformer: 1597 Chain: "B" Number of atoms: 2290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2290 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PTRANS': 5, 'TRANS': 327} Chain breaks: 1 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 337 Unresolved non-hydrogen dihedrals: 203 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 8, 'GLU:plan': 6, 'ARG:plan': 10, 'ASN:plan1': 6, 'ASP:plan': 24} Unresolved non-hydrogen planarities: 196 Chain: "G" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 327 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 48 Chain: "R" Number of atoms: 1963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 1963 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 7, 'TRANS': 277} Chain breaks: 1 Unresolved non-hydrogen bonds: 344 Unresolved non-hydrogen angles: 431 Unresolved non-hydrogen dihedrals: 279 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 192 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR A 360 " occ=0.17 ... (22 atoms not shown) pdb=" OH BTYR A 360 " occ=0.83 Time building chain proxies: 5.43, per 1000 atoms: 0.87 Number of scatterers: 6222 At special positions: 0 Unit cell: (82.4315, 134.493, 98.0501, 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 30 16.00 P 3 15.00 O 1095 8.00 N 1076 7.00 C 4018 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.57 Conformation dependent library (CDL) restraints added in 1.6 seconds 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1712 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 8 sheets defined 47.8% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 12 through 40 removed outlier: 3.764A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 64 removed outlier: 3.679A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLN A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET A 60 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N HIS A 64 " --> pdb=" O MET A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 239 removed outlier: 3.789A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 293 through 302 removed outlier: 3.682A pdb=" N ALA A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 333 through 352 removed outlier: 3.525A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYR A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 5 through 26 removed outlier: 3.634A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.654A pdb=" N THR B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 9 through 23 removed outlier: 3.807A pdb=" N LYS G 20 " --> pdb=" O VAL G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.881A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 61 removed outlier: 3.590A pdb=" N MET R 36 " --> pdb=" O TRP R 32 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY R 37 " --> pdb=" O VAL R 33 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE R 47 " --> pdb=" O ILE R 43 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL R 48 " --> pdb=" O VAL R 44 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 97 removed outlier: 4.126A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER R 74 " --> pdb=" O TYR R 70 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 102 through 137 Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 171 removed outlier: 3.693A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix removed outlier: 3.846A pdb=" N MET R 171 " --> pdb=" O LEU R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 187 Processing helix chain 'R' and resid 196 through 208 Processing helix chain 'R' and resid 208 through 238 Processing helix chain 'R' and resid 269 through 299 removed outlier: 3.607A pdb=" N ILE R 278 " --> pdb=" O THR R 274 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.817A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 317 removed outlier: 3.633A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 327 Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 329 through 339 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 3.674A pdb=" N THR A 210 " --> pdb=" O MET A 221 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 9.143A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL A 287 " --> pdb=" O ATYR A 360 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 49 removed outlier: 6.907A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.236A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.936A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.986A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 4.048A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.812A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.811A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 351 hydrogen bonds defined for protein. 1026 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.90 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1058 1.32 - 1.45: 1741 1.45 - 1.57: 3513 1.57 - 1.69: 5 1.69 - 1.81: 39 Bond restraints: 6356 Sorted by residual: bond pdb=" C ALA A 18 " pdb=" O ALA A 18 " ideal model delta sigma weight residual 1.237 1.278 -0.041 1.17e-02 7.31e+03 1.25e+01 bond pdb=" N SER A 352 " pdb=" CA SER A 352 " ideal model delta sigma weight residual 1.454 1.496 -0.043 1.23e-02 6.61e+03 1.22e+01 bond pdb=" N VAL A 301 " pdb=" CA VAL A 301 " ideal model delta sigma weight residual 1.460 1.502 -0.042 1.21e-02 6.83e+03 1.21e+01 bond pdb=" C LYS A 58 " pdb=" O LYS A 58 " ideal model delta sigma weight residual 1.236 1.272 -0.035 1.15e-02 7.56e+03 9.46e+00 bond pdb=" CA SER A 275 " pdb=" CB SER A 275 " ideal model delta sigma weight residual 1.530 1.483 0.047 1.56e-02 4.11e+03 9.00e+00 ... (remaining 6351 not shown) Histogram of bond angle deviations from ideal: 99.61 - 106.54: 139 106.54 - 113.47: 3535 113.47 - 120.40: 2475 120.40 - 127.34: 2511 127.34 - 134.27: 74 Bond angle restraints: 8734 Sorted by residual: angle pdb=" N PRO A 332 " pdb=" CA PRO A 332 " pdb=" C PRO A 332 " ideal model delta sigma weight residual 113.53 100.73 12.80 1.39e+00 5.18e-01 8.48e+01 angle pdb=" N ASN A 23 " pdb=" CA ASN A 23 " pdb=" C ASN A 23 " ideal model delta sigma weight residual 111.28 103.13 8.15 1.09e+00 8.42e-01 5.59e+01 angle pdb=" N LEU A 270 " pdb=" CA LEU A 270 " pdb=" C LEU A 270 " ideal model delta sigma weight residual 111.28 104.14 7.14 1.09e+00 8.42e-01 4.29e+01 angle pdb=" N GLN A 267 " pdb=" CA GLN A 267 " pdb=" C GLN A 267 " ideal model delta sigma weight residual 111.28 104.35 6.93 1.09e+00 8.42e-01 4.04e+01 angle pdb=" N PRO A 328 " pdb=" CA PRO A 328 " pdb=" C PRO A 328 " ideal model delta sigma weight residual 111.26 101.71 9.55 1.63e+00 3.76e-01 3.43e+01 ... (remaining 8729 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.25: 3545 33.25 - 66.49: 70 66.49 - 99.74: 0 99.74 - 132.98: 1 132.98 - 166.23: 2 Dihedral angle restraints: 3618 sinusoidal: 985 harmonic: 2633 Sorted by residual: dihedral pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " pdb=" O3A GTP A 401 " ideal model delta sinusoidal sigma weight residual 69.27 -96.96 166.23 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" C8 GTP A 401 " pdb=" C1' GTP A 401 " pdb=" N9 GTP A 401 " pdb=" O4' GTP A 401 " ideal model delta sinusoidal sigma weight residual 104.59 -48.14 152.74 1 2.00e+01 2.50e-03 4.53e+01 dihedral pdb=" O3B GTP A 401 " pdb=" O3A GTP A 401 " pdb=" PB GTP A 401 " pdb=" PA GTP A 401 " ideal model delta sinusoidal sigma weight residual -68.92 -172.61 103.69 1 2.00e+01 2.50e-03 2.97e+01 ... (remaining 3615 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 759 0.047 - 0.094: 188 0.094 - 0.141: 82 0.141 - 0.189: 35 0.189 - 0.236: 6 Chirality restraints: 1070 Sorted by residual: chirality pdb=" CA GLU A 230 " pdb=" N GLU A 230 " pdb=" C GLU A 230 " pdb=" CB GLU A 230 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA ARG A 20 " pdb=" N ARG A 20 " pdb=" C ARG A 20 " pdb=" CB ARG A 20 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA ILE G 9 " pdb=" N ILE G 9 " pdb=" C ILE G 9 " pdb=" CB ILE G 9 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 1067 not shown) Planarity restraints: 1095 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 333 " -0.233 9.50e-02 1.11e+02 1.05e-01 6.71e+00 pdb=" NE ARG A 333 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 333 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 333 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 333 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 28 " -0.012 2.00e-02 2.50e+03 2.49e-02 6.21e+00 pdb=" C LYS A 28 " 0.043 2.00e-02 2.50e+03 pdb=" O LYS A 28 " -0.016 2.00e-02 2.50e+03 pdb=" N GLN A 29 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 29 " -0.012 2.00e-02 2.50e+03 2.45e-02 6.01e+00 pdb=" C GLN A 29 " 0.042 2.00e-02 2.50e+03 pdb=" O GLN A 29 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU A 30 " -0.015 2.00e-02 2.50e+03 ... (remaining 1092 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1580 2.79 - 3.32: 5825 3.32 - 3.85: 9667 3.85 - 4.37: 10099 4.37 - 4.90: 18574 Nonbonded interactions: 45745 Sorted by model distance: nonbonded pdb=" OD2 ASP B 83 " pdb=" OG1 THR B 86 " model vdw 2.268 3.040 nonbonded pdb=" O LEU A 272 " pdb=" OG SER A 275 " model vdw 2.274 3.040 nonbonded pdb=" N GLN B 259 " pdb=" OE1 GLN B 259 " model vdw 2.312 3.120 nonbonded pdb=" O VAL R 34 " pdb=" N GLY R 37 " model vdw 2.327 3.120 nonbonded pdb=" O ILE B 37 " pdb=" NZ LYS B 301 " model vdw 2.338 3.120 ... (remaining 45740 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.17 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: 1.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 23.400 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 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 : 0.006 0.054 6356 Z= 0.394 Angle : 0.928 13.344 8734 Z= 0.634 Chirality : 0.057 0.236 1070 Planarity : 0.005 0.105 1095 Dihedral : 13.945 166.231 1903 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.21 % Allowed : 0.62 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.29), residues: 885 helix: 2.48 (0.27), residues: 373 sheet: 0.36 (0.39), residues: 184 loop : -0.93 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 332 HIS 0.009 0.001 HIS R 296 PHE 0.011 0.001 PHE R 104 TYR 0.034 0.002 TYR R 185 ARG 0.004 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 0.843 Fit side-chains REVERT: A 267 GLN cc_start: 0.8654 (tp-100) cc_final: 0.8269 (tp40) REVERT: B 110 ASN cc_start: 0.9283 (m-40) cc_final: 0.8919 (m110) REVERT: R 161 SER cc_start: 0.8939 (t) cc_final: 0.8470 (p) outliers start: 1 outliers final: 0 residues processed: 102 average time/residue: 0.2249 time to fit residues: 31.2152 Evaluate side-chains 76 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 20.0000 chunk 44 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6356 Z= 0.243 Angle : 0.523 6.518 8734 Z= 0.288 Chirality : 0.041 0.137 1070 Planarity : 0.003 0.033 1095 Dihedral : 9.012 154.366 972 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.46 % Allowed : 10.27 % Favored : 87.27 % 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: 1.09 (0.28), residues: 885 helix: 2.34 (0.26), residues: 399 sheet: 0.18 (0.40), residues: 175 loop : -1.12 (0.31), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.006 0.001 HIS A 357 PHE 0.012 0.001 PHE R 104 TYR 0.024 0.001 TYR R 185 ARG 0.003 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 74 time to evaluate : 0.781 Fit side-chains REVERT: A 267 GLN cc_start: 0.8110 (tp-100) cc_final: 0.7850 (tp40) REVERT: B 110 ASN cc_start: 0.9301 (m-40) cc_final: 0.9051 (m110) outliers start: 12 outliers final: 11 residues processed: 80 average time/residue: 0.2070 time to fit residues: 23.2761 Evaluate side-chains 82 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 71 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 307 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 chunk 22 optimal weight: 20.0000 chunk 80 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 79 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6356 Z= 0.149 Angle : 0.444 6.359 8734 Z= 0.246 Chirality : 0.039 0.134 1070 Planarity : 0.003 0.030 1095 Dihedral : 8.477 148.917 972 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.82 % Allowed : 13.96 % Favored : 85.22 % 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 (0.29), residues: 885 helix: 2.83 (0.26), residues: 392 sheet: 0.20 (0.40), residues: 174 loop : -1.11 (0.32), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.004 0.001 HIS A 357 PHE 0.009 0.001 PHE B 199 TYR 0.024 0.001 TYR R 185 ARG 0.004 0.000 ARG A 231 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 81 time to evaluate : 0.720 Fit side-chains REVERT: B 110 ASN cc_start: 0.9246 (m-40) cc_final: 0.9037 (m110) outliers start: 4 outliers final: 4 residues processed: 81 average time/residue: 0.1606 time to fit residues: 17.9038 Evaluate side-chains 78 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 74 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 307 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 1.9990 chunk 60 optimal weight: 20.0000 chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 38 optimal weight: 0.3980 chunk 53 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 76 optimal weight: 0.4980 chunk 22 optimal weight: 20.0000 chunk 70 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 69 ASN ** R 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6356 Z= 0.194 Angle : 0.472 6.432 8734 Z= 0.258 Chirality : 0.040 0.133 1070 Planarity : 0.003 0.031 1095 Dihedral : 8.256 147.058 972 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.70 % Allowed : 14.17 % Favored : 82.14 % 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 (0.29), residues: 885 helix: 2.93 (0.26), residues: 391 sheet: 0.00 (0.38), residues: 183 loop : -1.13 (0.32), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.006 0.001 HIS A 357 PHE 0.011 0.001 PHE B 199 TYR 0.026 0.001 TYR R 185 ARG 0.003 0.000 ARG A 231 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 75 time to evaluate : 0.720 Fit side-chains REVERT: A 211 LYS cc_start: 0.8269 (ttmm) cc_final: 0.7787 (mmtt) REVERT: B 58 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8389 (pt) REVERT: B 110 ASN cc_start: 0.9301 (m-40) cc_final: 0.9049 (m110) REVERT: B 117 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8079 (tt) outliers start: 18 outliers final: 14 residues processed: 85 average time/residue: 0.1521 time to fit residues: 18.2083 Evaluate side-chains 89 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 73 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 69 ASN Chi-restraints excluded: chain R residue 104 PHE Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 171 MET Chi-restraints excluded: chain R residue 307 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 43 optimal weight: 0.5980 chunk 76 optimal weight: 0.0970 chunk 21 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 HIS ** R 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6356 Z= 0.135 Angle : 0.439 6.042 8734 Z= 0.241 Chirality : 0.039 0.132 1070 Planarity : 0.003 0.029 1095 Dihedral : 7.989 145.698 972 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.67 % Allowed : 16.02 % Favored : 81.31 % 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: 1.62 (0.29), residues: 885 helix: 3.07 (0.26), residues: 391 sheet: 0.18 (0.38), residues: 186 loop : -1.06 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 277 HIS 0.008 0.001 HIS A 357 PHE 0.009 0.001 PHE B 241 TYR 0.025 0.001 TYR R 185 ARG 0.004 0.000 ARG A 231 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 80 time to evaluate : 0.735 Fit side-chains REVERT: A 211 LYS cc_start: 0.8298 (ttmm) cc_final: 0.7833 (mmtt) REVERT: B 58 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8366 (pt) REVERT: B 110 ASN cc_start: 0.9270 (m-40) cc_final: 0.9038 (m110) REVERT: B 117 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.8018 (tt) outliers start: 13 outliers final: 10 residues processed: 87 average time/residue: 0.1648 time to fit residues: 20.0459 Evaluate side-chains 89 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 77 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 104 PHE Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 171 MET Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 7 optimal weight: 0.4980 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 0.0870 chunk 82 optimal weight: 1.9990 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** R 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6356 Z= 0.159 Angle : 0.447 5.916 8734 Z= 0.244 Chirality : 0.040 0.145 1070 Planarity : 0.003 0.029 1095 Dihedral : 7.710 143.206 972 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.31 % Allowed : 15.20 % Favored : 80.49 % 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: 1.64 (0.29), residues: 885 helix: 3.00 (0.26), residues: 397 sheet: 0.13 (0.37), residues: 192 loop : -0.98 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 277 HIS 0.007 0.001 HIS A 357 PHE 0.011 0.001 PHE B 199 TYR 0.026 0.001 TYR R 185 ARG 0.004 0.000 ARG A 231 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 78 time to evaluate : 0.729 Fit side-chains REVERT: A 211 LYS cc_start: 0.8322 (ttmm) cc_final: 0.7746 (mmtt) REVERT: B 58 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8412 (pt) REVERT: B 110 ASN cc_start: 0.9302 (m-40) cc_final: 0.9049 (m110) REVERT: B 234 PHE cc_start: 0.9192 (OUTLIER) cc_final: 0.8690 (m-80) outliers start: 21 outliers final: 16 residues processed: 91 average time/residue: 0.1447 time to fit residues: 18.5352 Evaluate side-chains 94 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 76 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 332 TRP Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 104 PHE Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 171 MET Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 307 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 71 optimal weight: 0.1980 chunk 47 optimal weight: 7.9990 chunk 84 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6356 Z= 0.148 Angle : 0.437 5.833 8734 Z= 0.238 Chirality : 0.039 0.153 1070 Planarity : 0.003 0.029 1095 Dihedral : 7.458 140.419 972 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 4.31 % Allowed : 16.22 % Favored : 79.47 % 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: 1.68 (0.29), residues: 885 helix: 3.06 (0.26), residues: 397 sheet: 0.12 (0.37), residues: 192 loop : -0.96 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 277 HIS 0.006 0.001 HIS A 357 PHE 0.010 0.001 PHE B 199 TYR 0.027 0.001 TYR R 185 ARG 0.001 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 76 time to evaluate : 0.743 Fit side-chains REVERT: A 211 LYS cc_start: 0.8295 (ttmm) cc_final: 0.7804 (mmtt) REVERT: B 58 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8419 (pt) REVERT: B 110 ASN cc_start: 0.9288 (m-40) cc_final: 0.9047 (m110) REVERT: B 234 PHE cc_start: 0.9181 (OUTLIER) cc_final: 0.8676 (m-80) outliers start: 21 outliers final: 18 residues processed: 87 average time/residue: 0.1508 time to fit residues: 18.4752 Evaluate side-chains 96 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 76 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 332 TRP Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 104 PHE Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 171 MET Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 307 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 0.6980 chunk 25 optimal weight: 10.0000 chunk 16 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 7 optimal weight: 0.0010 chunk 66 optimal weight: 8.9990 chunk 77 optimal weight: 0.8980 chunk 81 optimal weight: 8.9990 chunk 74 optimal weight: 0.2980 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6356 Z= 0.116 Angle : 0.419 5.692 8734 Z= 0.229 Chirality : 0.039 0.156 1070 Planarity : 0.002 0.028 1095 Dihedral : 7.094 136.141 972 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.49 % Allowed : 17.25 % Favored : 79.26 % 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: 1.80 (0.29), residues: 885 helix: 3.05 (0.26), residues: 398 sheet: 0.33 (0.37), residues: 188 loop : -0.87 (0.34), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 277 HIS 0.004 0.001 HIS A 357 PHE 0.008 0.001 PHE B 199 TYR 0.030 0.001 TYR R 185 ARG 0.001 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 86 time to evaluate : 0.641 Fit side-chains REVERT: A 211 LYS cc_start: 0.8312 (ttmm) cc_final: 0.7666 (mmtt) REVERT: B 58 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8408 (pt) REVERT: B 234 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.8676 (m-80) REVERT: R 185 TYR cc_start: 0.7032 (m-80) cc_final: 0.6613 (m-80) outliers start: 17 outliers final: 14 residues processed: 95 average time/residue: 0.1434 time to fit residues: 19.1816 Evaluate side-chains 97 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 81 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 104 PHE Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 34 optimal weight: 0.4980 chunk 62 optimal weight: 0.8980 chunk 24 optimal weight: 0.3980 chunk 71 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 51 ASN ** R 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6356 Z= 0.124 Angle : 0.431 6.223 8734 Z= 0.233 Chirality : 0.039 0.159 1070 Planarity : 0.002 0.028 1095 Dihedral : 6.950 132.943 972 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.90 % Allowed : 17.45 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.29), residues: 885 helix: 3.07 (0.26), residues: 399 sheet: 0.36 (0.37), residues: 187 loop : -0.89 (0.34), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 277 HIS 0.004 0.001 HIS A 357 PHE 0.009 0.001 PHE B 199 TYR 0.020 0.001 TYR R 185 ARG 0.001 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 79 time to evaluate : 0.656 Fit side-chains REVERT: A 211 LYS cc_start: 0.8338 (ttmm) cc_final: 0.7739 (mmtt) REVERT: B 58 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8421 (pt) REVERT: B 234 PHE cc_start: 0.9150 (OUTLIER) cc_final: 0.8657 (m-80) REVERT: R 185 TYR cc_start: 0.7048 (m-80) cc_final: 0.6594 (m-80) outliers start: 19 outliers final: 16 residues processed: 90 average time/residue: 0.1354 time to fit residues: 17.6775 Evaluate side-chains 95 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 77 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 332 TRP Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 104 PHE Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 307 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 53 optimal weight: 0.1980 chunk 42 optimal weight: 0.1980 chunk 55 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6356 Z= 0.129 Angle : 0.431 5.855 8734 Z= 0.233 Chirality : 0.039 0.165 1070 Planarity : 0.002 0.028 1095 Dihedral : 6.823 127.615 972 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.90 % Allowed : 17.25 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.29), residues: 885 helix: 3.12 (0.26), residues: 398 sheet: 0.27 (0.37), residues: 188 loop : -0.84 (0.34), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 277 HIS 0.003 0.001 HIS A 357 PHE 0.009 0.001 PHE B 199 TYR 0.019 0.001 TYR R 185 ARG 0.001 0.000 ARG A 389 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 77 time to evaluate : 0.750 Fit side-chains REVERT: A 211 LYS cc_start: 0.8310 (ttmm) cc_final: 0.7731 (mmtt) REVERT: B 58 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8422 (pt) REVERT: B 234 PHE cc_start: 0.9160 (OUTLIER) cc_final: 0.8670 (m-80) REVERT: R 185 TYR cc_start: 0.7162 (m-80) cc_final: 0.6901 (m-80) outliers start: 19 outliers final: 17 residues processed: 89 average time/residue: 0.1368 time to fit residues: 17.4957 Evaluate side-chains 96 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 77 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 332 TRP Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 104 PHE Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 307 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.128124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.099848 restraints weight = 40235.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.104218 restraints weight = 11851.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.107210 restraints weight = 6120.155| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3474 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3474 r_free = 0.3474 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3474 r_free = 0.3474 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3474 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6356 Z= 0.139 Angle : 0.435 5.755 8734 Z= 0.235 Chirality : 0.040 0.167 1070 Planarity : 0.003 0.029 1095 Dihedral : 6.478 120.821 972 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 4.31 % Allowed : 17.25 % Favored : 78.44 % 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: 1.82 (0.29), residues: 885 helix: 3.14 (0.26), residues: 398 sheet: 0.26 (0.37), residues: 188 loop : -0.91 (0.33), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 277 HIS 0.002 0.001 HIS A 357 PHE 0.009 0.001 PHE B 241 TYR 0.018 0.001 TYR R 185 ARG 0.002 0.000 ARG A 389 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1561.75 seconds wall clock time: 28 minutes 31.94 seconds (1711.94 seconds total)