Starting phenix.real_space_refine on Fri Jul 19 03:26:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo0_42423/07_2024/8uo0_42423.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo0_42423/07_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_42423/07_2024/8uo0_42423.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo0_42423/07_2024/8uo0_42423.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo0_42423/07_2024/8uo0_42423.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo0_42423/07_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: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 5.51, per 1000 atoms: 0.89 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: 2.64 Conformation dependent library (CDL) restraints added in 1.4 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: 0.71 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: 1.88 Time building geometry restraints manager: 2.83 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 2.440 nonbonded pdb=" O LEU A 272 " pdb=" OG SER A 275 " model vdw 2.274 2.440 nonbonded pdb=" N GLN B 259 " pdb=" OE1 GLN B 259 " model vdw 2.312 2.520 nonbonded pdb=" O VAL R 34 " pdb=" N GLY R 37 " model vdw 2.327 2.520 nonbonded pdb=" O ILE B 37 " pdb=" NZ LYS B 301 " model vdw 2.338 2.520 ... (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 ========== 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: 1.440 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 23.370 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: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.080 ------------------------------------------------------------------------------- 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 : 0.689 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: 0.1660 time to fit residues: 22.8916 Evaluate side-chains 76 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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: 0.7980 chunk 66 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 20.0000 chunk 44 optimal weight: 0.1980 chunk 35 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 51 optimal weight: 0.2980 chunk 79 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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: 0.7715 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6356 Z= 0.187 Angle : 0.488 6.522 8734 Z= 0.270 Chirality : 0.040 0.138 1070 Planarity : 0.003 0.031 1095 Dihedral : 8.905 152.308 972 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.03 % Allowed : 11.09 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.29), residues: 885 helix: 2.43 (0.26), residues: 399 sheet: 0.35 (0.40), residues: 180 loop : -1.06 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.005 0.001 HIS A 357 PHE 0.012 0.001 PHE R 104 TYR 0.026 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: 5 poor density : 81 time to evaluate : 0.699 Fit side-chains REVERT: A 267 GLN cc_start: 0.8106 (tp-100) cc_final: 0.7838 (tp40) REVERT: B 110 ASN cc_start: 0.9290 (m-40) cc_final: 0.8949 (m110) outliers start: 5 outliers final: 4 residues processed: 83 average time/residue: 0.1548 time to fit residues: 18.0317 Evaluate side-chains 79 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 75 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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 275 SER Chi-restraints excluded: chain R residue 67 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 22 optimal weight: 20.0000 chunk 80 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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: 0.7742 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6356 Z= 0.207 Angle : 0.479 6.445 8734 Z= 0.263 Chirality : 0.040 0.129 1070 Planarity : 0.003 0.032 1095 Dihedral : 8.556 148.981 972 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.67 % Allowed : 11.70 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.28), residues: 885 helix: 2.70 (0.26), residues: 393 sheet: 0.22 (0.39), residues: 180 loop : -1.18 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.006 0.001 HIS A 357 PHE 0.011 0.001 PHE B 199 TYR 0.031 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 88 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 75 time to evaluate : 0.673 Fit side-chains REVERT: B 58 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8353 (pt) REVERT: B 110 ASN cc_start: 0.9352 (m-40) cc_final: 0.9000 (m110) REVERT: R 279 MET cc_start: 0.8251 (mmm) cc_final: 0.8049 (mmt) outliers start: 13 outliers final: 12 residues processed: 82 average time/residue: 0.1473 time to fit residues: 16.9627 Evaluate side-chains 86 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 73 time to evaluate : 0.700 ------------------------------------------------------------------------------- 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 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 136 THR Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 196 ASN 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: 1.9990 chunk 8 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 22 optimal weight: 20.0000 chunk 70 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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: 0.7719 moved from start: 0.1686 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= 0.153 Angle : 0.440 6.075 8734 Z= 0.242 Chirality : 0.039 0.126 1070 Planarity : 0.003 0.030 1095 Dihedral : 8.198 147.177 972 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.67 % Allowed : 14.78 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.28), residues: 885 helix: 2.92 (0.26), residues: 393 sheet: 0.40 (0.39), residues: 184 loop : -1.11 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 277 HIS 0.006 0.001 HIS A 357 PHE 0.010 0.001 PHE B 241 TYR 0.028 0.001 TYR R 185 ARG 0.004 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: 13 poor density : 80 time to evaluate : 0.689 Fit side-chains REVERT: A 211 LYS cc_start: 0.8265 (ttmm) cc_final: 0.7792 (mmtt) REVERT: B 110 ASN cc_start: 0.9315 (m-40) cc_final: 0.9023 (m110) REVERT: B 117 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.8061 (tt) outliers start: 13 outliers final: 12 residues processed: 86 average time/residue: 0.1614 time to fit residues: 19.1099 Evaluate side-chains 89 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 76 time to evaluate : 0.713 ------------------------------------------------------------------------------- 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 A residue 350 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 331 SER 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 296 HIS 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: 0.0000 chunk 1 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 35 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 58 optimal weight: 0.0070 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.4604 ------------------------------------------------------------------------------- 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: 0.7679 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6356 Z= 0.118 Angle : 0.412 5.854 8734 Z= 0.225 Chirality : 0.038 0.127 1070 Planarity : 0.002 0.029 1095 Dihedral : 7.712 144.216 972 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.29 % Allowed : 15.40 % 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: 1.66 (0.29), residues: 885 helix: 2.96 (0.26), residues: 398 sheet: 0.26 (0.39), residues: 180 loop : -0.95 (0.32), residues: 307 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 0.008 0.001 PHE B 199 TYR 0.023 0.001 TYR R 185 ARG 0.005 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 101 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 85 time to evaluate : 0.690 Fit side-chains REVERT: A 211 LYS cc_start: 0.8292 (ttmm) cc_final: 0.7854 (mmtt) REVERT: B 110 ASN cc_start: 0.9257 (m-40) cc_final: 0.9031 (m110) REVERT: B 234 PHE cc_start: 0.9094 (OUTLIER) cc_final: 0.8665 (m-80) outliers start: 16 outliers final: 12 residues processed: 92 average time/residue: 0.1575 time to fit residues: 20.5059 Evaluate side-chains 92 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 79 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 158 VAL 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 331 SER Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 136 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 0.0030 chunk 82 optimal weight: 0.7980 overall best weight: 0.7392 ------------------------------------------------------------------------------- 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: 0.7702 moved from start: 0.1976 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= 0.139 Angle : 0.425 5.801 8734 Z= 0.231 Chirality : 0.039 0.136 1070 Planarity : 0.002 0.029 1095 Dihedral : 7.486 141.315 972 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.08 % Allowed : 16.43 % 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: 1.68 (0.29), residues: 885 helix: 3.01 (0.26), residues: 399 sheet: 0.25 (0.39), residues: 180 loop : -1.00 (0.32), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 277 HIS 0.005 0.001 HIS A 357 PHE 0.010 0.001 PHE B 199 TYR 0.010 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 95 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 80 time to evaluate : 0.643 Fit side-chains REVERT: A 211 LYS cc_start: 0.8291 (ttmm) cc_final: 0.7831 (mmtt) REVERT: B 110 ASN cc_start: 0.9278 (m-40) cc_final: 0.9017 (m110) REVERT: R 185 TYR cc_start: 0.6655 (m-80) cc_final: 0.6347 (m-80) REVERT: R 279 MET cc_start: 0.7991 (mmm) cc_final: 0.7777 (mmt) outliers start: 15 outliers final: 15 residues processed: 89 average time/residue: 0.1428 time to fit residues: 17.9899 Evaluate side-chains 92 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 77 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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 154 ASP Chi-restraints excluded: chain B residue 158 VAL 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 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: 0.9980 chunk 62 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 53 optimal weight: 0.0470 chunk 51 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 overall best weight: 1.0084 ------------------------------------------------------------------------------- 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: 0.7729 moved from start: 0.2028 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= 0.165 Angle : 0.436 5.790 8734 Z= 0.238 Chirality : 0.039 0.134 1070 Planarity : 0.003 0.029 1095 Dihedral : 7.312 137.582 972 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 4.11 % Allowed : 15.81 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.29), residues: 885 helix: 3.01 (0.26), residues: 399 sheet: 0.23 (0.39), residues: 180 loop : -1.05 (0.31), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 277 HIS 0.006 0.001 HIS A 357 PHE 0.011 0.001 PHE B 199 TYR 0.009 0.001 TYR R 199 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 101 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 81 time to evaluate : 0.743 Fit side-chains REVERT: A 211 LYS cc_start: 0.8284 (ttmm) cc_final: 0.7850 (mmtt) REVERT: B 58 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8355 (pt) REVERT: B 110 ASN cc_start: 0.9305 (m-40) cc_final: 0.9048 (m110) REVERT: B 234 PHE cc_start: 0.9148 (OUTLIER) cc_final: 0.8654 (m-80) REVERT: R 185 TYR cc_start: 0.6871 (m-80) cc_final: 0.6305 (m-80) REVERT: R 279 MET cc_start: 0.8109 (mmm) cc_final: 0.7856 (mmt) outliers start: 20 outliers final: 16 residues processed: 94 average time/residue: 0.1382 time to fit residues: 18.8868 Evaluate side-chains 97 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 79 time to evaluate : 0.662 ------------------------------------------------------------------------------- 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 154 ASP Chi-restraints excluded: chain B residue 158 VAL 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 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: 2.9990 chunk 25 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 74 optimal weight: 0.7980 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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: 0.7765 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6356 Z= 0.231 Angle : 0.477 5.801 8734 Z= 0.261 Chirality : 0.040 0.144 1070 Planarity : 0.003 0.031 1095 Dihedral : 7.320 134.768 972 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % 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: 1.48 (0.28), residues: 885 helix: 2.93 (0.26), residues: 397 sheet: 0.04 (0.38), residues: 183 loop : -1.13 (0.31), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 277 HIS 0.007 0.001 HIS A 357 PHE 0.012 0.001 PHE B 199 TYR 0.008 0.001 TYR R 141 ARG 0.002 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 97 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 78 time to evaluate : 0.695 Fit side-chains REVERT: A 211 LYS cc_start: 0.8287 (ttmm) cc_final: 0.7830 (mmtt) REVERT: B 58 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8383 (pt) REVERT: B 110 ASN cc_start: 0.9353 (m-40) cc_final: 0.9062 (m110) REVERT: B 234 PHE cc_start: 0.9202 (OUTLIER) cc_final: 0.8609 (m-80) REVERT: R 185 TYR cc_start: 0.7053 (m-80) cc_final: 0.6483 (m-80) outliers start: 19 outliers final: 16 residues processed: 90 average time/residue: 0.1494 time to fit residues: 18.8958 Evaluate side-chains 95 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 77 time to evaluate : 0.713 ------------------------------------------------------------------------------- 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 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 218 VAL Chi-restraints excluded: chain R residue 307 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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: 0.7753 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6356 Z= 0.189 Angle : 0.453 5.708 8734 Z= 0.248 Chirality : 0.040 0.146 1070 Planarity : 0.003 0.031 1095 Dihedral : 7.185 132.146 972 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.70 % Allowed : 17.86 % 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: 1.51 (0.28), residues: 885 helix: 2.94 (0.26), residues: 397 sheet: 0.11 (0.37), residues: 194 loop : -1.17 (0.32), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 277 HIS 0.005 0.001 HIS A 357 PHE 0.011 0.001 PHE B 199 TYR 0.016 0.001 TYR R 174 ARG 0.003 0.000 ARG B 68 *********************** 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 94 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 76 time to evaluate : 0.703 Fit side-chains REVERT: A 211 LYS cc_start: 0.8298 (ttmm) cc_final: 0.7847 (mmtt) REVERT: B 58 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8372 (pt) REVERT: B 110 ASN cc_start: 0.9319 (m-40) cc_final: 0.9056 (m110) REVERT: B 234 PHE cc_start: 0.9188 (OUTLIER) cc_final: 0.8649 (m-80) REVERT: R 185 TYR cc_start: 0.7042 (m-80) cc_final: 0.6555 (m-80) outliers start: 18 outliers final: 16 residues processed: 87 average time/residue: 0.1367 time to fit residues: 17.1800 Evaluate side-chains 94 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 76 time to evaluate : 0.709 ------------------------------------------------------------------------------- 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 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 218 VAL Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 80 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 7 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 172 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6356 Z= 0.210 Angle : 0.465 5.711 8734 Z= 0.256 Chirality : 0.040 0.148 1070 Planarity : 0.003 0.033 1095 Dihedral : 6.980 126.191 972 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.90 % Allowed : 17.86 % Favored : 78.23 % 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: 1.43 (0.28), residues: 885 helix: 2.90 (0.26), residues: 398 sheet: 0.01 (0.37), residues: 194 loop : -1.21 (0.32), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 277 HIS 0.004 0.001 HIS A 357 PHE 0.012 0.001 PHE B 241 TYR 0.015 0.001 TYR R 174 ARG 0.002 0.000 ARG B 68 ********************** 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 97 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 78 time to evaluate : 0.733 Fit side-chains REVERT: A 211 LYS cc_start: 0.8302 (ttmm) cc_final: 0.7839 (mmtt) REVERT: B 58 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8385 (pt) REVERT: B 110 ASN cc_start: 0.9330 (m-40) cc_final: 0.9062 (m110) REVERT: B 234 PHE cc_start: 0.9199 (OUTLIER) cc_final: 0.8671 (m-80) REVERT: R 185 TYR cc_start: 0.6911 (m-80) cc_final: 0.6436 (m-80) outliers start: 19 outliers final: 17 residues processed: 89 average time/residue: 0.1487 time to fit residues: 18.6693 Evaluate side-chains 97 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 78 time to evaluate : 0.670 ------------------------------------------------------------------------------- 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 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 218 VAL Chi-restraints excluded: chain R residue 294 ILE Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 0.9980 chunk 64 optimal weight: 0.0370 chunk 10 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 8.9990 chunk 61 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.126648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.098470 restraints weight = 40612.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.102838 restraints weight = 11866.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.105817 restraints weight = 6101.230| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3454 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3454 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6356 Z= 0.136 Angle : 0.425 5.762 8734 Z= 0.233 Chirality : 0.039 0.149 1070 Planarity : 0.003 0.032 1095 Dihedral : 6.503 119.404 972 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.70 % Allowed : 18.07 % Favored : 78.23 % 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: 1.61 (0.29), residues: 885 helix: 3.04 (0.26), residues: 398 sheet: 0.18 (0.38), residues: 185 loop : -1.15 (0.32), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 277 HIS 0.002 0.001 HIS A 357 PHE 0.009 0.001 PHE B 199 TYR 0.022 0.001 TYR R 174 ARG 0.001 0.000 ARG B 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1539.22 seconds wall clock time: 27 minutes 57.38 seconds (1677.38 seconds total)